
#######################################################
#                                                     #
#                        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 T0348TS599_4
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS599_4.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:    23        14 - 36          4.94    17.09
  LCS_AVERAGE:     33.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        11 - 27          1.72    16.28
  LCS_AVERAGE:     18.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        13 - 24          0.93    16.20
  LCS_AVERAGE:     13.11

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    9     3    3    3    3    3    3    5    6    6    6    7    7    8   14   16   22   26   29   32   34 
LCS_GDT     A       3     A       3      3    3   11     3    3    3    3    3    4    5    7    9    9   17   17   18   19   21   25   28   29   33   34 
LCS_GDT     K       4     K       4      3    3   11     3    3    4    4    4    6    8   10   12   13   15   22   24   27   27   29   31   33   35   39 
LCS_GDT     F       5     F       5      3    3   14     3    3    4    4    7    9   10   12   14   19   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     L       6     L       6      3    3   14     3    3    4    4    8    9   10   12   14   19   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     E       7     E       7      3    3   16     3    3    5    5    7    9   11   15   17   20   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     I       8     I       8      3    4   21     3    3    8   12   14   15   16   17   19   20   22   25   27   29   29   31   31   33   35   39 
LCS_GDT     L       9     L       9      3    8   21     3    4    8   12   14   15   16   17   19   20   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     V      10     V      10      5   16   21     3    4    9   12   14   15   16   17   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     C      11     C      11      7   17   21     4    7   13   16   17   18   18   19   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     P      12     P      12     11   17   21     4    7   13   16   17   18   18   19   19   20   21   24   25   26   28   30   32   34   36   39 
LCS_GDT     L      13     L      13     12   17   21     6   10   13   16   17   18   18   19   19   20   20   24   25   26   28   30   32   34   35   37 
LCS_GDT     C      14     C      14     12   17   23     6   10   13   16   17   18   18   19   19   20   21   24   25   26   28   30   32   34   36   39 
LCS_GDT     K      15     K      15     12   17   23     6   10   13   16   17   18   18   19   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     G      16     G      16     12   17   23     6   10   13   16   17   18   18   19   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     P      17     P      17     12   17   23     6   10   13   16   17   18   18   19   19   21   21   24   27   29   29   31   32   34   36   39 
LCS_GDT     L      18     L      18     12   17   23     3    6   12   16   17   18   18   19   19   21   21   24   27   29   30   31   32   34   36   39 
LCS_GDT     V      19     V      19     12   17   23     4    8   11   16   17   18   18   19   19   21   21   24   25   26   28   30   32   34   36   38 
LCS_GDT     F      20     F      20     12   17   23     5   10   13   16   17   18   18   19   19   21   21   24   25   26   28   30   32   34   36   38 
LCS_GDT     D      21     D      21     12   17   23     5   10   13   16   17   18   18   19   19   21   21   24   25   26   28   30   32   34   36   38 
LCS_GDT     K      22     K      22     12   17   23     6   10   13   16   17   18   18   19   19   21   21   24   25   26   28   30   32   34   35   37 
LCS_GDT     S      23     S      23     12   17   23     5   10   13   16   17   18   18   19   19   21   21   24   25   26   28   30   32   34   36   38 
LCS_GDT     K      24     K      24     12   17   23     5   10   13   16   17   18   18   19   19   21   21   24   25   28   30   31   32   34   36   39 
LCS_GDT     D      25     D      25      9   17   23     5    8   12   16   17   18   18   19   19   21   21   24   25   26   30   31   32   34   36   38 
LCS_GDT     E      26     E      26      9   17   23     4    8   11   14   17   18   18   19   19   21   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     L      27     L      27      9   17   23     3    7    8   10   11   13   18   19   19   21   21   24   27   29   30   31   32   34   36   39 
LCS_GDT     I      28     I      28      8   12   23     6    7    8   10   11   13   15   16   19   21   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     C      29     C      29      8   12   23     6    6    8   11   14   15   16   17   19   21   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     K      30     K      30      7   12   23     6    6    8   12   14   15   16   17   19   21   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     G      31     G      31      9   12   23     6    8    9   12   14   15   16   17   19   21   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     D      32     D      32      9   12   23     6    8    9   12   14   15   16   17   19   21   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     R      33     R      33      9   12   23     6    8    9   12   14   15   16   17   19   21   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     L      34     L      34      9   12   23     4    8    9   12   14   15   16   17   19   21   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     A      35     A      35      9   12   23     5    8    9   12   14   15   16   17   19   21   23   26   27   29   30   31   32   33   36   39 
LCS_GDT     F      36     F      36      9   12   23     5    8   11   14   16   18   18   19   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     P      37     P      37      9   12   22     5    8   13   16   17   18   18   19   19   20   23   26   27   29   30   31   32   34   35   39 
LCS_GDT     I      38     I      38      9   12   22     5    8    9   12   14   15   16   17   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     K      39     K      39      9   12   22     5    7    9   12   14   15   16   17   19   20   23   26   27   29   30   31   32   34   35   39 
LCS_GDT     D      40     D      40      4    5   22     3    4    4    4    4    4    8   10   13   19   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     G      41     G      41      4    5   22     3    4    5    5    5    6    7   11   14   19   21   26   27   29   30   31   32   34   36   39 
LCS_GDT     I      42     I      42      3    5   22     3    4    9    9   12   15   16   17   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     P      43     P      43      3    5   22     3    4    5    5    8    9   15   17   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     M      44     M      44      4    5   22     3    4    4    5    6    8   14   16   19   20   23   26   27   29   30   31   32   34   36   39 
LCS_GDT     M      45     M      45      4    5   22     3    4    5    5    6    8   13   14   17   19   21   24   25   27   30   31   32   34   36   39 
LCS_GDT     L      46     L      46      4    5   21     3    4    5    5    6    7   13   14   16   19   21   24   25   26   28   30   32   34   35   37 
LCS_GDT     E      47     E      47      4    5   19     4    4    5    5    6    8   11   13   16   19   20   21   25   26   28   30   32   34   35   35 
LCS_GDT     S      48     S      48      4    5   19     4    4    4    5    6    7   11   13   16   19   20   21   25   26   28   30   32   33   35   35 
LCS_GDT     E      49     E      49      4    5   19     4    4    4    5    5    6    8   12   16   19   20   20   22   24   25   28   30   32   34   35 
LCS_GDT     A      50     A      50      4    5   19     4    4    5    5    5    8   11   13   16   19   20   22   23   25   25   28   30   32   33   35 
LCS_GDT     R      51     R      51      3   12   19     3    4    4    5    5    8   11   16   17   19   20   22   23   25   25   28   28   31   31   33 
LCS_GDT     E      52     E      52     11   12   19     7    9   11   11   11   11   11   13   16   19   20   20   22   24   24   25   26   28   29   30 
LCS_GDT     L      53     L      53     11   12   19     7    9   11   11   11   11   11   13   16   19   20   20   22   24   24   25   27   28   30   31 
LCS_GDT     A      54     A      54     11   12   19     7    9   11   11   11   11   11   13   16   19   20   22   24   24   24   25   27   29   31   32 
LCS_GDT     P      55     P      55     11   12   19     7    9   11   11   11   11   11   14   18   19   20   22   24   24   24   26   28   30   31   32 
LCS_GDT     E      56     E      56     11   12   19     7    9   11   11   11   11   11   13   16   19   20   20   22   24   26   26   28   30   34   36 
LCS_GDT     E      57     E      57     11   12   19     7    9   11   11   11   11   11   13   16   19   20   20   22   24   24   25   28   30   34   36 
LCS_GDT     E      58     E      58     11   12   19     7    9   11   11   11   11   11   13   15   19   20   20   22   24   26   26   28   30   34   36 
LCS_GDT     V      59     V      59     11   12   19     4    9   11   11   11   11   14   16   19   21   21   22   22   24   26   26   29   32   35   39 
LCS_GDT     K      60     K      60     11   12   19     4    9   11   11   11   11   11   13   15   19   20   20   22   24   25   27   29   32   35   39 
LCS_GDT     L      61     L      61     11   12   19     4    5   11   11   11   11   11   12   14   15   19   20   22   24   26   26   29   32   35   39 
LCS_GDT     E      62     E      62     11   12   19     4    9   11   11   11   13   15   16   19   21   21   22   23   24   26   27   28   31   35   39 
LCS_AVERAGE  LCS_A:  21.67  (  13.11   18.22   33.67 )

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      7     10     13     16     17     18     18     19     19     21     23     26     27     29     30     31     32     34     36     39 
GDT PERCENT_CA  11.48  16.39  21.31  26.23  27.87  29.51  29.51  31.15  31.15  34.43  37.70  42.62  44.26  47.54  49.18  50.82  52.46  55.74  59.02  63.93
GDT RMS_LOCAL    0.35   0.70   0.99   1.20   1.37   1.57   1.57   1.83   1.83   3.23   3.74   4.24   4.14   4.58   5.20   4.82   5.63   5.83   6.66   7.05
GDT RMS_ALL_CA  19.93  16.17  16.19  16.24  16.25  16.26  16.26  16.31  16.31  18.56  13.70  13.94  14.07  14.10  14.26  14.08  16.28  16.38  14.80  12.91

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         41.183
LGA    A       3      A       3         37.453
LGA    K       4      K       4         35.898
LGA    F       5      F       5         30.433
LGA    L       6      L       6         24.937
LGA    E       7      E       7         21.169
LGA    I       8      I       8         19.023
LGA    L       9      L       9         13.208
LGA    V      10      V      10          7.250
LGA    C      11      C      11          3.002
LGA    P      12      P      12          2.263
LGA    L      13      L      13          1.124
LGA    C      14      C      14          0.998
LGA    K      15      K      15          0.989
LGA    G      16      G      16          1.122
LGA    P      17      P      17          0.934
LGA    L      18      L      18          1.249
LGA    V      19      V      19          1.648
LGA    F      20      F      20          1.214
LGA    D      21      D      21          1.142
LGA    K      22      K      22          1.348
LGA    S      23      S      23          1.946
LGA    K      24      K      24          1.244
LGA    D      25      D      25          1.712
LGA    E      26      E      26          1.907
LGA    L      27      L      27          3.977
LGA    I      28      I      28          5.951
LGA    C      29      C      29          8.499
LGA    K      30      K      30         13.780
LGA    G      31      G      31         16.789
LGA    D      32      D      32         18.559
LGA    R      33      R      33         18.831
LGA    L      34      L      34         13.686
LGA    A      35      A      35          9.131
LGA    F      36      F      36          2.497
LGA    P      37      P      37          2.813
LGA    I      38      I      38          9.512
LGA    K      39      K      39         13.541
LGA    D      40      D      40         17.081
LGA    G      41      G      41         16.565
LGA    I      42      I      42         18.528
LGA    P      43      P      43         17.685
LGA    M      44      M      44         16.363
LGA    M      45      M      45         14.861
LGA    L      46      L      46         17.265
LGA    E      47      E      47         15.594
LGA    S      48      S      48         18.088
LGA    E      49      E      49         17.463
LGA    A      50      A      50         11.091
LGA    R      51      R      51          8.610
LGA    E      52      E      52          8.829
LGA    L      53      L      53         11.779
LGA    A      54      A      54         14.061
LGA    P      55      P      55         17.572
LGA    E      56      E      56         22.586
LGA    E      57      E      57         20.868
LGA    E      58      E      58         18.119
LGA    V      59      V      59         24.206
LGA    K      60      K      60         26.987
LGA    L      61      L      61         22.697
LGA    E      62      E      62         23.770

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     19    1.83    31.148    28.261     0.983

LGA_LOCAL      RMSD =  1.833  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.366  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 12.174  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.519621 * X  +   0.853946 * Y  +  -0.027765 * Z  +   7.207562
  Y_new =  -0.450082 * X  +  -0.301205 * Y  +  -0.840655 * Z  +  23.330961
  Z_new =  -0.726237 * X  +  -0.424325 * Y  +   0.540858 * Z  +  57.409740 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.665243    2.476350  [ DEG:   -38.1156    141.8844 ]
  Theta =   0.812832    2.328760  [ DEG:    46.5719    133.4281 ]
  Phi   =  -2.427783    0.713809  [ DEG:  -139.1017     40.8983 ]
 
# 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: T0348TS599_4                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS599_4.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   19   1.83  28.261    12.17
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS599_4
PFRMAT TS                                                                       
TARGET T0348                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       7.019  17.866  64.855  1.00  0.00              
ATOM      2  CA  ASP     2       8.979  17.427  68.549  1.00  0.00              
ATOM      3  CA  ALA     3      11.218  20.525  70.429  1.00  0.00              
ATOM      4  CA  LYS     4      15.159  19.823  69.109  1.00  0.00              
ATOM      5  CA  PHE     5      13.510  18.969  65.744  1.00  0.00              
ATOM      6  CA  LEU     6      11.459  22.121  65.704  1.00  0.00              
ATOM      7  CA  GLU     7      14.524  24.265  66.380  1.00  0.00              
ATOM      8  CA  ILE     8      16.426  22.698  63.459  1.00  0.00              
ATOM      9  CA  LEU     9      13.464  23.296  61.120  1.00  0.00              
ATOM     10  CA  VAL    10      12.114  26.815  61.695  1.00  0.00              
ATOM     11  CA  CYS    11       8.445  27.075  61.638  1.00  0.00              
ATOM     12  CA  PRO    12       4.987  28.370  61.136  1.00  0.00              
ATOM     13  CA  LEU    13       3.729  26.871  64.438  1.00  0.00              
ATOM     14  CA  CYS    14       6.299  28.076  66.977  1.00  0.00              
ATOM     15  CA  LYS    15       7.510  31.237  65.346  1.00  0.00              
ATOM     16  CA  GLY    16      11.223  30.262  65.200  1.00  0.00              
ATOM     17  CA  PRO    17      13.372  31.172  62.282  1.00  0.00              
ATOM     18  CA  LEU    18      12.516  30.579  58.695  1.00  0.00              
ATOM     19  CA  VAL    19      14.519  28.295  56.503  1.00  0.00              
ATOM     20  CA  PHE    20      15.252  28.282  52.907  1.00  0.00              
ATOM     21  CA  ASP    21      16.237  25.173  51.092  1.00  0.00              
ATOM     22  CA  LYS    22      18.449  26.286  48.166  1.00  0.00              
ATOM     23  CA  SER    23      18.949  22.740  46.897  1.00  0.00              
ATOM     24  CA  LYS    24      15.231  22.050  46.546  1.00  0.00              
ATOM     25  CA  ASP    25      14.242  25.507  45.504  1.00  0.00              
ATOM     26  CA  GLU    26      11.601  26.403  48.008  1.00  0.00              
ATOM     27  CA  LEU    27      11.719  29.670  49.880  1.00  0.00              
ATOM     28  CA  ILE    28       9.948  29.713  53.211  1.00  0.00              
ATOM     29  CA  CYS    29       9.949  32.522  55.686  1.00  0.00              
ATOM     30  CA  LYS    30       6.455  33.603  56.815  1.00  0.00              
ATOM     31  CA  GLY    31       7.335  37.187  57.481  1.00  0.00              
ATOM     32  CA  ASP    32       9.081  37.776  54.094  1.00  0.00              
ATOM     33  CA  ARG    33       6.587  35.961  51.920  1.00  0.00              
ATOM     34  CA  LEU    34       8.603  33.009  50.745  1.00  0.00              
ATOM     35  CA  ALA    35       6.767  30.026  49.402  1.00  0.00              
ATOM     36  CA  PHE    36       7.654  26.664  50.743  1.00  0.00              
ATOM     37  CA  PRO    37       7.621  23.333  49.172  1.00  0.00              
ATOM     38  CA  ILE    38       5.393  20.829  50.960  1.00  0.00              
ATOM     39  CA  LYS    39       7.566  17.722  50.571  1.00  0.00              
ATOM     40  CA  ASP    40      10.856  19.266  51.778  1.00  0.00              
ATOM     41  CA  GLY    41       9.132  20.988  54.637  1.00  0.00              
ATOM     42  CA  ILE    42       7.394  17.852  56.019  1.00  0.00              
ATOM     43  CA  PRO    43      10.617  15.780  55.997  1.00  0.00              
ATOM     44  CA  MET    44      12.597  18.495  57.853  1.00  0.00              
ATOM     45  CA  MET    45       9.854  18.724  60.478  1.00  0.00              
ATOM     46  CA  LEU    46       9.493  15.030  61.192  1.00  0.00              
ATOM     47  CA  GLU    47       7.780  13.412  64.127  1.00  0.00              
ATOM     48  CA  SER    48       6.665   9.968  62.998  1.00  0.00              
ATOM     49  CA  GLU    49       2.949  10.756  63.140  1.00  0.00              
ATOM     50  CA  ALA    50       3.353  13.970  61.138  1.00  0.00              
ATOM     51  CA  ARG    51       5.370  12.090  58.491  1.00  0.00              
ATOM     52  CA  GLU    52       2.511   9.623  57.937  1.00  0.00              
ATOM     53  CA  LEU    53      -0.166  12.267  57.480  1.00  0.00              
ATOM     54  CA  ALA    54      -2.058  12.012  54.266  1.00  0.00              
ATOM     55  CA  PRO    55      -1.730  14.679  51.600  1.00  0.00              
ATOM     56  CA  GLU    56      -5.048  16.189  52.464  1.00  0.00              
ATOM     57  CA  GLU    57      -4.261  16.386  56.157  1.00  0.00              
ATOM     58  CA  GLU    58      -0.855  18.036  55.399  1.00  0.00              
ATOM     59  CA  VAL    59      -2.560  20.733  53.336  1.00  0.00              
ATOM     60  CA  LYS    60      -5.026  21.294  56.185  1.00  0.00              
ATOM     61  CA  LEU    61      -2.261  21.548  58.794  1.00  0.00              
ATOM     62  CA  GLU    62      -0.328  24.074  56.654  1.00  0.00              
ATOM     63  CA  HIS    63      -3.466  26.224  56.167  1.00  0.00              
ATOM     64  CA  HIS    64      -4.647  26.201  59.805  1.00  0.00              
ATOM     65  CA  HIS    65      -1.189  27.137  60.933  1.00  0.00              
ATOM     66  CA  HIS    66      -0.598  29.924  58.754  1.00  0.00              
ATOM     67  CA  HIS    67       1.032  32.594  56.987  1.00  0.00              
ATOM     68  CA  HIS    68       3.594  31.059  54.042  1.00  0.00              
TER                                                                             
END
