
#######################################################
#                                                     #
#                        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   68 (   68),  selected   61 , name T0348TS393_5
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS393_5.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:    20        43 - 62          4.88    22.41
  LCS_AVERAGE:     27.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        39 - 47          1.91    28.08
  LCS_AVERAGE:      9.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        42 - 47          0.98    28.19
  LCS_AVERAGE:      6.23

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     D       2     D       2      3    3   13     3    3    3    3    3    4    5    6    7    7    8   12   13   14   14   17   19   22   28   30 
LCS_GDT     A       3     A       3      3    3   15     3    3    3    3    5    5    7    8   10   11   13   13   13   15   16   18   26   26   28   30 
LCS_GDT     K       4     K       4      3    3   15     3    3    3    3    3    5    7    8   10   11   13   13   14   17   22   23   26   26   28   31 
LCS_GDT     F       5     F       5      3    3   15     1    3    3    3    5    5    7    8   10   11   14   17   18   20   22   24   26   26   28   31 
LCS_GDT     L       6     L       6      3    3   15     0    3    3    3    4    5    6    8   10   10   13   14   18   20   22   23   26   26   28   31 
LCS_GDT     E       7     E       7      3    5   15     3    3    3    3    5    6    7    9   12   13   14   17   18   20   22   24   26   26   28   31 
LCS_GDT     I       8     I       8      4    6   15     3    4    5    5    8   11   12   13   14   16   19   21   23   24   24   25   26   27   28   31 
LCS_GDT     L       9     L       9      4    7   15     3    4    5    6    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     V      10     V      10      4    7   15     3    4    5    6    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     C      11     C      11      4    7   15     3    4    5    6    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     P      12     P      12      3    7   15     3    3    4    5    8   10   11   13   13   15   19   22   23   24   25   26   26   27   28   29 
LCS_GDT     L      13     L      13      3    7   15     3    4    5    6    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     C      14     C      14      3    7   15     3    3    4    6    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     K      15     K      15      3    7   15     3    3    4    5    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     G      16     G      16      4    6   15     2    3    4    5    6    9   11   13   13   14   18   22   23   24   25   26   26   27   28   31 
LCS_GDT     P      17     P      17      4    6   15     3    3    4    5    6    7   11   13   13   13   16   18   23   24   25   26   26   27   28   31 
LCS_GDT     L      18     L      18      4    6   15     3    3    4    5    6    8   11   13   13   13   16   18   20   24   25   26   26   27   28   31 
LCS_GDT     V      19     V      19      4    6   15     3    4    4    5    5    8   10   10   13   13   15   17   18   20   22   25   26   27   28   31 
LCS_GDT     F      20     F      20      4    6   15     3    4    4    5    5    7    9   10   12   13   15   17   18   19   21   23   26   26   28   31 
LCS_GDT     D      21     D      21      4    5   15     3    4    4    4    6    6    9   10   12   13   14   17   19   20   21   23   26   26   28   31 
LCS_GDT     K      22     K      22      4    6   15     3    4    4    4    6    8    9   10   12   13   14   17   19   20   21   23   26   26   28   31 
LCS_GDT     S      23     S      23      4    6   15     3    4    4    5    6    8    9   10   12   13   14   17   19   20   22   23   26   26   28   31 
LCS_GDT     K      24     K      24      4    6   15     3    4    4    5    6    8    9   10   12   13   14   17   19   20   22   24   26   26   28   31 
LCS_GDT     D      25     D      25      4    6   15     3    4    4    5    6    8    9   10   12   13   14   17   19   20   22   24   26   26   28   31 
LCS_GDT     E      26     E      26      4    6   16     3    4    4    5    6    8    9   10   12   13   14   17   19   21   22   25   26   27   28   31 
LCS_GDT     L      27     L      27      4    6   16     3    4    4    5    6    8    9   12   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     I      28     I      28      4    6   16     3    4    4    4    6    8    9   12   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     C      29     C      29      3    5   16     3    3    4    5    6    8   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     K      30     K      30      3    4   16     3    3    4    4    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     G      31     G      31      3    4   16     3    3    4    4    6    7   10   10   12   15   19   22   23   24   25   26   26   27   28   29 
LCS_GDT     D      32     D      32      3    5   16     3    3    3    4    6    6    8   10   11   13   15   17   19   24   25   26   26   27   28   29 
LCS_GDT     R      33     R      33      4    5   16     4    4    4    4    6    7    8   10   11   13   17   22   23   24   25   26   26   27   28   29 
LCS_GDT     L      34     L      34      4    5   16     4    4    4    4    6    8   10   10   11   13   18   22   23   24   25   26   26   27   28   29 
LCS_GDT     A      35     A      35      4    5   16     4    4    4    5    6    8   10   10   13   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     F      36     F      36      4    5   16     4    4    4    5    6    7    9   13   13   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     P      37     P      37      4    5   16     3    4    4    5    7    8   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     I      38     I      38      4    5   17     3    4    4    5    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     K      39     K      39      4    9   17     3    4    4    5    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     D      40     D      40      3    9   17     3    5    7    7    8   11   12   13   14   16   19   22   23   24   25   26   26   27   28   31 
LCS_GDT     G      41     G      41      4    9   17     3    4    5    7    8    9   11   13   13   15   18   22   23   24   25   26   26   27   28   31 
LCS_GDT     I      42     I      42      6    9   18     3    5    7    7    7    8    8    9   11   12   16   19   23   24   25   26   26   27   28   31 
LCS_GDT     P      43     P      43      6    9   20     3    5    7    7    7    8    8    9   11   13   14   17   17   18   19   20   23   23   25   27 
LCS_GDT     M      44     M      44      6    9   20     3    5    7    7    7    8    8    9   11   13   15   17   17   18   19   20   23   24   25   27 
LCS_GDT     M      45     M      45      6    9   20     3    5    7    7    7    8    8   11   13   15   16   17   17   18   19   20   21   22   24   27 
LCS_GDT     L      46     L      46      6    9   20     3    5    7    7    7    8    8    9   11   15   16   17   17   18   19   20   23   23   24   27 
LCS_GDT     E      47     E      47      6    9   20     4    4    7    7    7    8   10   11   13   15   16   17   17   18   19   20   23   23   24   27 
LCS_GDT     S      48     S      48      4    6   20     4    4    5    5    6    6    8    9   11   12   14   16   17   18   19   20   23   23   24   27 
LCS_GDT     E      49     E      49      4    6   20     4    4    5    5    6    7    8   11   13   15   16   17   17   18   19   20   23   23   24   27 
LCS_GDT     A      50     A      50      4    6   20     4    4    5    5    6    8   10   11   13   15   16   17   17   18   19   20   23   23   24   27 
LCS_GDT     R      51     R      51      4    6   20     4    4    5    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     E      52     E      52      4    6   20     4    4    5    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     L      53     L      53      4    6   20     4    4    5    5    6    8    9   11   12   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     A      54     A      54      4    6   20     1    3    5    5    6    8    9   11   13   15   16   16   18   19   20   21   22   23   24   27 
LCS_GDT     P      55     P      55      4    6   20     3    3    4    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     E      56     E      56      4    5   20     3    3    4    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     E      57     E      57      3    4   20     3    3    4    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     E      58     E      58      3    4   20     3    3    3    4    4    4    7   10   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     V      59     V      59      3    4   20     3    3    4    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     K      60     K      60      3    4   20     3    3    3    5    6    8   10   11   13   15   16   17   18   19   20   21   23   23   24   27 
LCS_GDT     L      61     L      61      3    4   20     3    3    3    5    5    8   10   11   13   15   16   17   17   19   20   21   22   23   24   27 
LCS_GDT     E      62     E      62      0    4   20     0    0    3    3    4    4    7    8   11   14   15   16   17   18   19   21   22   23   24   26 
LCS_AVERAGE  LCS_A:  14.57  (   6.23    9.62   27.84 )

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      5      7      7      8     11     12     13     14     16     19     22     23     24     25     26     26     27     28     31 
GDT PERCENT_CA   6.56   8.20  11.48  11.48  13.11  18.03  19.67  21.31  22.95  26.23  31.15  36.07  37.70  39.34  40.98  42.62  42.62  44.26  45.90  50.82
GDT RMS_LOCAL    0.38   0.63   0.96   0.96   1.65   2.23   2.36   2.56   2.72   3.27   8.15   4.29   4.38   4.53   4.83   4.99   4.99   5.41   5.51   7.06
GDT RMS_ALL_CA  28.00  27.98  28.26  28.26  24.60  24.14  24.11  23.91  23.96  23.41  23.34  22.58  22.99  22.87  22.13  21.94  21.94  21.90  21.95  22.84

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         26.243
LGA    A       3      A       3         24.778
LGA    K       4      K       4         18.291
LGA    F       5      F       5         12.838
LGA    L       6      L       6         13.141
LGA    E       7      E       7         10.315
LGA    I       8      I       8          3.535
LGA    L       9      L       9          2.216
LGA    V      10      V      10          2.082
LGA    C      11      C      11          2.199
LGA    P      12      P      12          5.247
LGA    L      13      L      13          1.679
LGA    C      14      C      14          2.474
LGA    K      15      K      15          0.760
LGA    G      16      G      16          7.604
LGA    P      17      P      17         11.122
LGA    L      18      L      18         10.733
LGA    V      19      V      19         13.441
LGA    F      20      F      20         15.488
LGA    D      21      D      21         19.478
LGA    K      22      K      22         21.887
LGA    S      23      S      23         20.037
LGA    K      24      K      24         14.175
LGA    D      25      D      25         11.687
LGA    E      26      E      26          8.596
LGA    L      27      L      27          4.694
LGA    I      28      I      28          5.055
LGA    C      29      C      29          3.357
LGA    K      30      K      30          3.069
LGA    G      31      G      31          5.905
LGA    D      32      D      32          9.771
LGA    R      33      R      33          7.390
LGA    L      34      L      34          7.961
LGA    A      35      A      35          5.371
LGA    F      36      F      36          5.544
LGA    P      37      P      37          3.262
LGA    I      38      I      38          2.560
LGA    K      39      K      39          3.817
LGA    D      40      D      40          2.892
LGA    G      41      G      41          6.473
LGA    I      42      I      42          7.350
LGA    P      43      P      43         13.078
LGA    M      44      M      44         15.875
LGA    M      45      M      45         21.121
LGA    L      46      L      46         23.991
LGA    E      47      E      47         30.303
LGA    S      48      S      48         32.305
LGA    E      49      E      49         32.293
LGA    A      50      A      50         33.884
LGA    R      51      R      51         36.089
LGA    E      52      E      52         36.836
LGA    L      53      L      53         37.522
LGA    A      54      A      54         41.882
LGA    P      55      P      55         45.615
LGA    E      56      E      56         48.446
LGA    E      57      E      57         45.063
LGA    E      58      E      58         47.939
LGA    V      59      V      59         47.682
LGA    K      60      K      60         47.173
LGA    L      61      L      61         43.824
LGA    E      62      E      62         46.771

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     13    2.56    20.902    18.669     0.490

LGA_LOCAL      RMSD =  2.555  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.549  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 14.207  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.742451 * X  +   0.601968 * Y  +  -0.293938 * Z  +   8.412901
  Y_new =  -0.341533 * X  +   0.717610 * Y  +   0.606952 * Z  +  37.104057
  Z_new =   0.576299 * X  +  -0.350243 * Y  +   0.738383 * Z  +  50.388317 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.442908    2.698684  [ DEG:   -25.3768    154.6232 ]
  Theta =  -0.614193   -2.527400  [ DEG:   -35.1907   -144.8093 ]
  Phi   =  -0.431145    2.710448  [ DEG:   -24.7028    155.2972 ]
 
# 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: T0348TS393_5                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS393_5.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   68   61   4.0   13   2.56  18.669    14.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS393_5
PFRMAT TS
TARGET T0348
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      18.353  33.316  47.360  1.00 25.00           C
ATOM      2  CA  ASP     2      17.948  33.310  51.149  1.00 25.00           C
ATOM      3  CA  ALA     3      18.058  34.294  54.818  1.00 25.00           C
ATOM      4  CA  LYS     4      15.935  37.360  55.686  1.00 25.00           C
ATOM      5  CA  PHE     5      13.100  36.056  53.465  1.00 25.00           C
ATOM      6  CA  LEU     6      13.298  32.637  55.179  1.00 25.00           C
ATOM      7  CA  GLU     7      13.153  34.323  58.615  1.00 25.00           C
ATOM      8  CA  ILE     8      10.095  36.352  57.517  1.00 25.00           C
ATOM      9  CA  LEU     9       8.390  33.156  56.273  1.00 25.00           C
ATOM     10  CA  VAL    10       8.033  31.113  59.406  1.00 25.00           C
ATOM     11  CA  CYS    11       5.681  28.173  59.504  1.00 25.00           C
ATOM     12  CA  PRO    12       5.005  24.880  61.288  1.00 25.00           C
ATOM     13  CA  LEU    13       4.583  26.819  64.534  1.00 25.00           C
ATOM     14  CA  CYS    14       7.930  28.496  64.226  1.00 25.00           C
ATOM     15  CA  LYS    15       7.209  32.181  65.059  1.00 25.00           C
ATOM     16  CA  GLY    16       4.057  33.764  66.551  1.00 25.00           C
ATOM     17  CA  PRO    17       2.285  31.262  64.227  1.00 25.00           C
ATOM     18  CA  LEU    18       3.279  32.764  60.909  1.00 25.00           C
ATOM     19  CA  VAL    19       3.452  32.522  57.061  1.00 25.00           C
ATOM     20  CA  PHE    20       1.380  29.297  56.952  1.00 25.00           C
ATOM     21  CA  ASP    21       0.333  28.284  60.405  1.00 25.00           C
ATOM     22  CA  LYS    22       0.136  24.610  59.283  1.00 25.00           C
ATOM     23  CA  SER    23       1.480  22.114  56.708  1.00 25.00           C
ATOM     24  CA  LYS    24       3.134  24.971  54.766  1.00 25.00           C
ATOM     25  CA  ASP    25       6.157  22.668  54.867  1.00 25.00           C
ATOM     26  CA  GLU    26       8.370  24.156  57.582  1.00 25.00           C
ATOM     27  CA  LEU    27      10.640  27.125  57.835  1.00 25.00           C
ATOM     28  CA  ILE    28      13.699  28.020  59.960  1.00 25.00           C
ATOM     29  CA  CYS    29      12.346  25.896  62.845  1.00 25.00           C
ATOM     30  CA  LYS    30      11.117  22.410  62.029  1.00 25.00           C
ATOM     31  CA  GLY    31      13.435  22.806  59.005  1.00 25.00           C
ATOM     32  CA  ASP    32      15.004  24.706  56.083  1.00 25.00           C
ATOM     33  CA  ARG    33      12.197  23.095  53.976  1.00 25.00           C
ATOM     34  CA  LEU    34      11.480  26.613  52.698  1.00 25.00           C
ATOM     35  CA  ALA    35       8.004  27.897  53.569  1.00 25.00           C
ATOM     36  CA  PHE    36       6.488  30.964  51.956  1.00 25.00           C
ATOM     37  CA  PRO    37       7.308  29.288  48.625  1.00 25.00           C
ATOM     38  CA  ILE    38       9.722  30.609  46.020  1.00 25.00           C
ATOM     39  CA  LYS    39       8.871  27.628  43.785  1.00 25.00           C
ATOM     40  CA  ASP    40       5.701  29.504  42.659  1.00 25.00           C
ATOM     41  CA  GLY    41       2.873  32.000  41.945  1.00 25.00           C
ATOM     42  CA  ILE    42       5.083  33.855  39.450  1.00 25.00           C
ATOM     43  CA  PRO    43       8.069  35.020  37.329  1.00 25.00           C
ATOM     44  CA  MET    44      10.985  37.116  38.580  1.00 25.00           C
ATOM     45  CA  MET    45       9.381  39.829  36.436  1.00 25.00           C
ATOM     46  CA  LEU    46      11.353  42.105  38.712  1.00 25.00           C
ATOM     47  CA  GLU    47      14.626  42.635  36.930  1.00 25.00           C
ATOM     48  CA  SER    48      12.749  43.614  33.786  1.00 25.00           C
ATOM     49  CA  GLU    49      14.701  46.832  33.565  1.00 25.00           C
ATOM     50  CA  ALA    50      18.285  46.436  34.897  1.00 25.00           C
ATOM     51  CA  ARG    51      20.266  47.970  37.805  1.00 25.00           C
ATOM     52  CA  GLU    52      19.308  48.437  41.457  1.00 25.00           C
ATOM     53  CA  LEU    53      17.996  51.253  43.701  1.00 25.00           C
ATOM     54  CA  ALA    54      16.959  53.731  46.403  1.00 25.00           C
ATOM     55  CA  PRO    55      14.676  55.335  43.858  1.00 25.00           C
ATOM     56  CA  GLU    56      15.527  58.466  41.780  1.00 25.00           C
ATOM     57  CA  GLU    57      11.866  58.182  40.812  1.00 25.00           C
ATOM     58  CA  GLU    58       9.044  60.472  41.946  1.00 25.00           C
ATOM     59  CA  VAL    59       6.317  58.005  43.101  1.00 25.00           C
ATOM     60  CA  LYS    60       3.730  58.809  40.420  1.00 25.00           C
ATOM     61  CA  LEU    61       1.414  55.887  41.082  1.00 25.00           C
ATOM     62  CA  GLU    62      -1.329  54.445  43.264  1.00 25.00           C
ATOM     63  CA  HIS    63      -2.423  52.553  40.165  1.00 25.00           C
ATOM     64  CA  HIS    64      -4.903  50.995  42.556  1.00 25.00           C
ATOM     65  CA  HIS    65      -4.466  48.723  45.587  1.00 25.00           C
ATOM     66  CA  HIS    66      -2.506  49.978  48.561  1.00 25.00           C
ATOM     67  CA  HIS    67      -3.930  48.224  51.681  1.00 25.00           C
ATOM     68  CA  HIS    68      -0.278  47.218  52.403  1.00 25.00           C
TER
END
