
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS599_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:    45         3 - 47          4.97    13.64
  LCS_AVERAGE:     63.83

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32         8 - 39          1.77    13.94
  LCS_AVERAGE:     33.40

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29        10 - 38          0.86    14.26
  LCS_AVERAGE:     28.41

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      0    3   40     0    0    0    0    6    8    8    9    9   10   12   13   14   14   22   23   38   40   43   43 
LCS_GDT     A       3     A       3      3    3   45     0    3    3    3    6    8    8    9    9   11   22   27   33   38   39   40   42   43   44   44 
LCS_GDT     K       4     K       4      3    3   45     3    3    3    3    5    8    8   11   16   28   32   34   37   38   40   41   42   43   44   44 
LCS_GDT     F       5     F       5      3    3   45     3    3    3    3    5    8    8    9   16   29   33   39   39   39   40   41   42   43   44   44 
LCS_GDT     L       6     L       6      3    3   45     3    3    3    3    5    7   17   22   32   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     E       7     E       7      4    5   45     3    4    4    4    9   10   16   24   33   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     I       8     I       8      4   32   45     3    4    7   15   21   28   32   33   34   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     L       9     L       9     26   32   45     3    6   20   28   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     V      10     V      10     29   32   45     4   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     C      11     C      11     29   32   45     5   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     P      12     P      12     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     L      13     L      13     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     C      14     C      14     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     K      15     K      15     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     G      16     G      16     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     P      17     P      17     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     L      18     L      18     29   32   45     6   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     V      19     V      19     29   32   45    10   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     F      20     F      20     29   32   45     8   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     D      21     D      21     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     K      22     K      22     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     S      23     S      23     29   32   45     8   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     K      24     K      24     29   32   45     8   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     D      25     D      25     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     E      26     E      26     29   32   45     8   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     L      27     L      27     29   32   45     8   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     I      28     I      28     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     C      29     C      29     29   32   45     8   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     K      30     K      30     29   32   45     5   17   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     G      31     G      31     29   32   45     7   18   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     D      32     D      32     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     R      33     R      33     29   32   45     7   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     L      34     L      34     29   32   45    12   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     A      35     A      35     29   32   45     8   15   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     F      36     F      36     29   32   45     7   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     P      37     P      37     29   32   45    10   24   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     I      38     I      38     29   32   45     3   17   28   29   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     K      39     K      39      4   32   45     3    4    8   15   29   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     D      40     D      40      4    5   45     3    4    4    5    5    5    7   10   11   17   29   31   36   37   38   40   40   42   42   42 
LCS_GDT     G      41     G      41      4    5   45     3    4    4    5    6    8    8   10   11   17   18   24   32   34   38   39   40   42   42   43 
LCS_GDT     I      42     I      42      3    5   45     3    4    4    7   13   18   31   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     P      43     P      43      3    5   45     3    4    4    4    6   10   22   35   35   35   36   37   37   38   40   41   42   43   44   44 
LCS_GDT     M      44     M      44      4    5   45     3    4    5    5   14   22   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     M      45     M      45      4    5   45     3    4    8   17   30   32   33   35   35   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     L      46     L      46      4    5   45     3    4    5    8   15   21   28   33   34   35   36   39   39   39   40   41   42   43   44   44 
LCS_GDT     E      47     E      47      4    5   45     4    4    6    7   10   12   15   18   22   23   28   31   35   37   39   40   42   43   44   44 
LCS_GDT     S      48     S      48      4    5   44     4    4    6    7    8    8   12   17   19   23   25   28   30   34   37   40   41   43   44   44 
LCS_GDT     E      49     E      49      4    5   19     4    4    6    7    8    8   10   14   19   22   25   25   26   28   31   36   40   41   42   44 
LCS_GDT     A      50     A      50      4    5   19     4    4    6    7    8   10   14   18   21   23   25   25   26   28   29   34   39   41   42   43 
LCS_GDT     R      51     R      51      3   12   19     3    4    4    5    8   13   16   18   21   23   25   25   26   28   29   34   37   41   42   42 
LCS_GDT     E      52     E      52     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     L      53     L      53     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     A      54     A      54     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     P      55     P      55     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     E      56     E      56     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     E      57     E      57     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     E      58     E      58     11   12   19     7    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     V      59     V      59     11   12   19     6    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     K      60     K      60     11   12   19     4    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     L      61     L      61     11   12   19     4    7   11   12   13   14   16   18   20   23   25   25   26   28   29   30   31   32   33   33 
LCS_GDT     E      62     E      62     11   12   19     4    9   11   12   13   14   16   18   21   23   25   25   26   28   29   30   31   32   33   33 
LCS_AVERAGE  LCS_A:  41.88  (  28.41   33.40   63.83 )

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     12     24     28     29     30     32     33     35     35     35     36     39     39     39     40     41     42     43     44     44 
GDT PERCENT_CA  19.67  39.34  45.90  47.54  49.18  52.46  54.10  57.38  57.38  57.38  59.02  63.93  63.93  63.93  65.57  67.21  68.85  70.49  72.13  72.13
GDT RMS_LOCAL    0.31   0.64   0.81   0.86   1.04   1.47   1.78   2.22   2.22   2.22   2.62   3.30   3.30   3.30   3.48   3.80   4.26   4.43   4.80   4.80
GDT RMS_ALL_CA  14.08  14.19  14.28  14.26  14.17  14.03  14.00  14.02  14.02  14.02  13.67  13.56  13.56  13.56  13.58  13.49  13.39  13.40  13.24  13.24

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         23.275
LGA    A       3      A       3         20.008
LGA    K       4      K       4         17.380
LGA    F       5      F       5         12.553
LGA    L       6      L       6         11.114
LGA    E       7      E       7         13.023
LGA    I       8      I       8          8.246
LGA    L       9      L       9          3.925
LGA    V      10      V      10          3.019
LGA    C      11      C      11          3.331
LGA    P      12      P      12          3.481
LGA    L      13      L      13          3.705
LGA    C      14      C      14          3.498
LGA    K      15      K      15          2.882
LGA    G      16      G      16          1.973
LGA    P      17      P      17          1.018
LGA    L      18      L      18          1.400
LGA    V      19      V      19          0.510
LGA    F      20      F      20          1.815
LGA    D      21      D      21          2.384
LGA    K      22      K      22          3.340
LGA    S      23      S      23          3.753
LGA    K      24      K      24          3.590
LGA    D      25      D      25          3.428
LGA    E      26      E      26          2.976
LGA    L      27      L      27          2.364
LGA    I      28      I      28          1.281
LGA    C      29      C      29          2.190
LGA    K      30      K      30          2.708
LGA    G      31      G      31          3.803
LGA    D      32      D      32          2.784
LGA    R      33      R      33          1.835
LGA    L      34      L      34          1.777
LGA    A      35      A      35          2.214
LGA    F      36      F      36          3.047
LGA    P      37      P      37          3.465
LGA    I      38      I      38          2.428
LGA    K      39      K      39          1.666
LGA    D      40      D      40          7.608
LGA    G      41      G      41          8.328
LGA    I      42      I      42          3.241
LGA    P      43      P      43          3.866
LGA    M      44      M      44          2.900
LGA    M      45      M      45          3.838
LGA    L      46      L      46          9.872
LGA    E      47      E      47         16.387
LGA    S      48      S      48         20.491
LGA    E      49      E      49         21.124
LGA    A      50      A      50         19.106
LGA    R      51      R      51         20.934
LGA    E      52      E      52         27.194
LGA    L      53      L      53         27.225
LGA    A      54      A      54         31.712
LGA    P      55      P      55         32.289
LGA    E      56      E      56         32.247
LGA    E      57      E      57         28.008
LGA    E      58      E      58         25.762
LGA    V      59      V      59         26.521
LGA    K      60      K      60         23.838
LGA    L      61      L      61         20.552
LGA    E      62      E      62         21.583

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     35    2.22    52.869    48.738     1.507

LGA_LOCAL      RMSD =  2.222  Number of atoms =   35  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.252  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 11.246  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.754290 * X  +  -0.132949 * Y  +  -0.642939 * Z  +  12.763596
  Y_new =   0.253671 * X  +  -0.962249 * Y  +  -0.098627 * Z  +  32.563274
  Z_new =  -0.605555 * X  +  -0.237489 * Y  +   0.759541 * Z  +  51.759758 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.303044    2.838549  [ DEG:   -17.3631    162.6369 ]
  Theta =   0.650463    2.491130  [ DEG:    37.2688    142.7312 ]
  Phi   =   2.817171   -0.324422  [ DEG:   161.4120    -18.5880 ]
 
# 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_3                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS599_3.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   35   2.22  48.738    11.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS599_3
PFRMAT TS                                                                       
TARGET T0348                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      17.683  42.035  59.896  1.00  0.00              
ATOM      2  CA  ASP     2      18.678  41.806  55.815  1.00  0.00              
ATOM      3  CA  ALA     3      17.194  42.223  51.904  1.00  0.00              
ATOM      4  CA  LYS     4      16.740  42.461  55.711  1.00  0.00              
ATOM      5  CA  PHE     5      13.374  40.610  55.453  1.00  0.00              
ATOM      6  CA  LEU     6      14.837  37.880  53.328  1.00  0.00              
ATOM      7  CA  GLU     7      17.729  37.372  55.782  1.00  0.00              
ATOM      8  CA  ILE     8      15.187  36.985  58.599  1.00  0.00              
ATOM      9  CA  LEU     9      13.039  34.448  56.788  1.00  0.00              
ATOM     10  CA  VAL    10       9.319  34.619  57.674  1.00  0.00              
ATOM     11  CA  CYS    11       7.524  31.294  57.659  1.00  0.00              
ATOM     12  CA  PRO    12       3.826  31.230  57.394  1.00  0.00              
ATOM     13  CA  LEU    13       2.985  28.774  60.099  1.00  0.00              
ATOM     14  CA  CYS    14       5.302  29.522  62.909  1.00  0.00              
ATOM     15  CA  LYS    15       6.886  32.813  61.990  1.00  0.00              
ATOM     16  CA  GLY    16      10.359  31.501  62.569  1.00  0.00              
ATOM     17  CA  PRO    17      13.438  31.868  60.601  1.00  0.00              
ATOM     18  CA  LEU    18      13.726  30.351  57.168  1.00  0.00              
ATOM     19  CA  VAL    19      16.491  27.886  56.132  1.00  0.00              
ATOM     20  CA  PHE    20      17.511  27.622  52.494  1.00  0.00              
ATOM     21  CA  ASP    21      18.803  24.459  50.922  1.00  0.00              
ATOM     22  CA  LYS    22      20.999  25.549  47.991  1.00  0.00              
ATOM     23  CA  SER    23      21.349  22.207  46.348  1.00  0.00              
ATOM     24  CA  LYS    24      17.672  21.623  45.934  1.00  0.00              
ATOM     25  CA  ASP    25      16.386  25.197  45.817  1.00  0.00              
ATOM     26  CA  GLU    26      13.935  24.541  48.614  1.00  0.00              
ATOM     27  CA  LEU    27      13.023  26.608  51.604  1.00  0.00              
ATOM     28  CA  ILE    28      12.859  24.794  54.878  1.00  0.00              
ATOM     29  CA  CYS    29      10.856  26.062  57.777  1.00  0.00              
ATOM     30  CA  LYS    30      12.533  25.299  61.058  1.00  0.00              
ATOM     31  CA  GLY    31       9.502  25.115  63.243  1.00  0.00              
ATOM     32  CA  ASP    32       7.354  22.805  61.223  1.00  0.00              
ATOM     33  CA  ARG    33      10.030  20.936  59.213  1.00  0.00              
ATOM     34  CA  LEU    34       8.317  21.465  55.939  1.00  0.00              
ATOM     35  CA  ALA    35      10.044  21.521  52.613  1.00  0.00              
ATOM     36  CA  PHE    36       8.834  24.529  50.605  1.00  0.00              
ATOM     37  CA  PRO    37       9.573  25.156  46.997  1.00  0.00              
ATOM     38  CA  ILE    38      10.254  28.872  46.489  1.00  0.00              
ATOM     39  CA  LYS    39       6.778  30.002  45.348  1.00  0.00              
ATOM     40  CA  ASP    40       4.472  28.454  47.977  1.00  0.00              
ATOM     41  CA  GLY    41       6.910  29.338  50.752  1.00  0.00              
ATOM     42  CA  ILE    42       7.098  33.035  49.744  1.00  0.00              
ATOM     43  CA  PRO    43       3.297  33.419  49.675  1.00  0.00              
ATOM     44  CA  MET    44       2.794  31.805  53.124  1.00  0.00              
ATOM     45  CA  MET    45       5.436  34.093  54.709  1.00  0.00              
ATOM     46  CA  LEU    46       4.340  37.382  53.250  1.00  0.00              
ATOM     47  CA  GLU    47       5.343  40.749  54.722  1.00  0.00              
ATOM     48  CA  SER    48       4.236  43.059  51.879  1.00  0.00              
ATOM     49  CA  GLU    49       7.724  44.189  50.802  1.00  0.00              
ATOM     50  CA  ALA    50       9.073  40.666  50.613  1.00  0.00              
ATOM     51  CA  ARG    51       6.123  39.486  48.556  1.00  0.00              
ATOM     52  CA  GLU    52       6.517  42.233  46.009  1.00  0.00              
ATOM     53  CA  LEU    53      10.175  41.611  45.307  1.00  0.00              
ATOM     54  CA  ALA    54      10.743  41.774  41.570  1.00  0.00              
ATOM     55  CA  PRO    55      12.128  38.753  39.776  1.00  0.00              
ATOM     56  CA  GLU    56      15.559  40.276  39.459  1.00  0.00              
ATOM     57  CA  GLU    57      15.742  41.100  43.126  1.00  0.00              
ATOM     58  CA  GLU    58      14.687  37.526  44.072  1.00  0.00              
ATOM     59  CA  VAL    59      17.478  36.066  41.956  1.00  0.00              
ATOM     60  CA  LYS    60      19.994  38.392  43.557  1.00  0.00              
ATOM     61  CA  LEU    61      18.728  37.387  46.984  1.00  0.00              
ATOM     62  CA  GLU    62      18.994  33.658  46.223  1.00  0.00              
ATOM     63  CA  HIS    63      22.570  34.022  44.935  1.00  0.00              
ATOM     64  CA  HIS    64      23.757  36.186  47.858  1.00  0.00              
ATOM     65  CA  HIS    65      22.195  33.581  50.150  1.00  0.00              
ATOM     66  CA  HIS    66      24.137  30.539  48.805  1.00  0.00              
ATOM     67  CA  HIS    67      26.760  27.746  47.077  1.00  0.00              
ATOM     68  CA  HIS    68      29.979  27.737  44.415  1.00  0.00              
TER                                                                             
END
