
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS599_1.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:    44         4 - 47          4.99    14.64
  LCS_AVERAGE:     62.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32         7 - 38          1.91    14.70
  LONGEST_CONTINUOUS_SEGMENT:    32         8 - 39          1.52    14.90
  LCS_AVERAGE:     34.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25        10 - 34          1.00    14.82
  LCS_AVERAGE:     24.91

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   28     3    3    3    3    3    3    5    8    9    9   12   14   15   16   18   25   29   29   30   34 
LCS_GDT     A       3     A       3      3    3   38     3    3    4    5    5    5    6    7    9    9   12   14   15   20   23   25   30   36   42   43 
LCS_GDT     K       4     K       4      3    3   44     3    3    4    5    5    5    6   10   11   14   23   34   36   39   40   40   41   42   42   43 
LCS_GDT     F       5     F       5      3    3   44     3    3    3    5    5    5    6    8   13   16   26   34   36   39   40   40   41   42   42   43 
LCS_GDT     L       6     L       6      3    3   44     3    3    3    3    4    6    8   10   20   25   30   36   37   39   40   40   41   42   42   43 
LCS_GDT     E       7     E       7      3   32   44     3    3    5   11   18   25   30   33   34   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     I       8     I       8      4   32   44     4    4    4   21   28   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     L       9     L       9     18   32   44     4    9   22   27   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     V      10     V      10     25   32   44     4   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     C      11     C      11     25   32   44     4   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     P      12     P      12     25   32   44     7   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     L      13     L      13     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     C      14     C      14     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     K      15     K      15     25   32   44    10   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     G      16     G      16     25   32   44    10   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     P      17     P      17     25   32   44    10   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     L      18     L      18     25   32   44     4   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     V      19     V      19     25   32   44     7   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     F      20     F      20     25   32   44     7   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     D      21     D      21     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     K      22     K      22     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     S      23     S      23     25   32   44     7   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     K      24     K      24     25   32   44     7   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     D      25     D      25     25   32   44     8   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     E      26     E      26     25   32   44     7   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     L      27     L      27     25   32   44     6   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     I      28     I      28     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     C      29     C      29     25   32   44     8   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     K      30     K      30     25   32   44     5   15   23   28   30   32   33   34   35   36   37   37   38   38   40   40   41   42   42   43 
LCS_GDT     G      31     G      31     25   32   44     8   18   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     D      32     D      32     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     R      33     R      33     25   32   44     8   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     L      34     L      34     25   32   44    10   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     A      35     A      35     23   32   44     6   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     F      36     F      36     23   32   44     8   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     P      37     P      37     23   32   44     8   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     I      38     I      38     23   32   44     3   19   28   28   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     K      39     K      39      4   32   44     3    4   13   24   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     D      40     D      40      4    5   44     3    4    5    5    5    7    9   11   14   26   30   31   37   38   39   40   40   40   40   41 
LCS_GDT     G      41     G      41      4    5   44     3    4    5    5    5    5    9   10   13   14   19   20   32   37   38   40   40   40   40   42 
LCS_GDT     I      42     I      42      3    5   44     3    4    4   11   13   20   32   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     P      43     P      43      3    5   44     3    4    4    4    5   16   32   34   35   36   36   37   38   38   39   40   40   42   42   43 
LCS_GDT     M      44     M      44      4    5   44     3    4    4    5   19   29   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     M      45     M      45      4    5   44     3    4   14   25   30   32   33   34   35   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     L      46     L      46      4    5   44     3    4    9   14   21   25   30   33   34   36   37   37   38   39   40   40   41   42   42   43 
LCS_GDT     E      47     E      47      4    5   44     4    4    5    8   12   15   16   19   23   26   31   35   36   38   40   40   41   42   42   43 
LCS_GDT     S      48     S      48      4    5   43     4    4    5    8    8    9   14   17   20   23   27   27   32   36   38   39   40   42   42   43 
LCS_GDT     E      49     E      49      4    5   21     4    4    5    8    8    9    9   14   19   23   24   24   26   27   30   33   38   39   41   42 
LCS_GDT     A      50     A      50      4    5   21     4    4    5    8    8   11   15   19   20   23   24   24   25   26   30   33   37   39   41   42 
LCS_GDT     R      51     R      51      3   12   21     3    3    4    8    8   11   16   19   20   23   24   24   25   26   30   33   35   38   40   41 
LCS_GDT     E      52     E      52     11   12   21     7   10   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     L      53     L      53     11   12   21     7   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     A      54     A      54     11   12   21     7   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     P      55     P      55     11   12   21     7   11   12   13   14   15   16   19   20   22   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     E      56     E      56     11   12   21     7   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     E      57     E      57     11   12   21     7   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     E      58     E      58     11   12   21     7   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     V      59     V      59     11   12   20     5   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     K      60     K      60     11   12   20     4   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     L      61     L      61     11   12   20     4   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_GDT     E      62     E      62     11   12   20     4   11   12   13   14   15   16   19   20   23   24   24   25   26   28   28   30   30   32   33 
LCS_AVERAGE  LCS_A:  40.60  (  24.91   34.13   62.75 )

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     10     19     28     28     30     32     33     34     35     36     37     37     38     39     40     40     41     42     42     43 
GDT PERCENT_CA  16.39  31.15  45.90  45.90  49.18  52.46  54.10  55.74  57.38  59.02  60.66  60.66  62.30  63.93  65.57  65.57  67.21  68.85  68.85  70.49
GDT RMS_LOCAL    0.36   0.72   1.02   1.02   1.18   1.41   1.58   1.87   2.00   2.20   2.53   2.53   2.71   4.04   4.06   4.06   4.30   4.45   4.45   4.82
GDT RMS_ALL_CA  14.65  15.28  15.00  15.00  14.96  14.89  14.85  14.89  14.86  14.88  14.65  14.65  14.68  14.50  14.48  14.48  14.38  14.41  14.41  14.27

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         29.118
LGA    A       3      A       3         24.793
LGA    K       4      K       4         18.655
LGA    F       5      F       5         17.410
LGA    L       6      L       6         14.247
LGA    E       7      E       7          8.858
LGA    I       8      I       8          5.732
LGA    L       9      L       9          3.134
LGA    V      10      V      10          1.566
LGA    C      11      C      11          2.144
LGA    P      12      P      12          1.987
LGA    L      13      L      13          2.476
LGA    C      14      C      14          2.204
LGA    K      15      K      15          0.846
LGA    G      16      G      16          0.817
LGA    P      17      P      17          0.408
LGA    L      18      L      18          0.760
LGA    V      19      V      19          0.425
LGA    F      20      F      20          0.583
LGA    D      21      D      21          1.144
LGA    K      22      K      22          1.560
LGA    S      23      S      23          2.577
LGA    K      24      K      24          2.770
LGA    D      25      D      25          1.962
LGA    E      26      E      26          2.121
LGA    L      27      L      27          1.812
LGA    I      28      I      28          1.165
LGA    C      29      C      29          2.165
LGA    K      30      K      30          2.720
LGA    G      31      G      31          2.940
LGA    D      32      D      32          2.120
LGA    R      33      R      33          1.610
LGA    L      34      L      34          1.652
LGA    A      35      A      35          2.000
LGA    F      36      F      36          2.610
LGA    P      37      P      37          2.968
LGA    I      38      I      38          1.650
LGA    K      39      K      39          1.334
LGA    D      40      D      40          8.158
LGA    G      41      G      41          9.120
LGA    I      42      I      42          3.934
LGA    P      43      P      43          4.576
LGA    M      44      M      44          3.283
LGA    M      45      M      45          2.362
LGA    L      46      L      46          8.320
LGA    E      47      E      47         14.003
LGA    S      48      S      48         19.081
LGA    E      49      E      49         20.533
LGA    A      50      A      50         18.476
LGA    R      51      R      51         21.110
LGA    E      52      E      52         27.401
LGA    L      53      L      53         27.932
LGA    A      54      A      54         33.694
LGA    P      55      P      55         34.806
LGA    E      56      E      56         35.205
LGA    E      57      E      57         29.666
LGA    E      58      E      58         26.938
LGA    V      59      V      59         28.546
LGA    K      60      K      60         25.261
LGA    L      61      L      61         20.551
LGA    E      62      E      62         22.255

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     34    1.87    49.590    47.963     1.729

LGA_LOCAL      RMSD =  1.866  Number of atoms =   34  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.977  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 12.311  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.825091 * X  +   0.401855 * Y  +   0.397162 * Z  +  12.576700
  Y_new =  -0.536551 * X  +   0.337050 * Y  +   0.773634 * Z  +  33.104370
  Z_new =   0.177026 * X  +  -0.851416 * Y  +   0.493713 * Z  +  53.655308 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.045308    2.096285  [ DEG:   -59.8917    120.1083 ]
  Theta =  -0.177963   -2.963629  [ DEG:   -10.1966   -169.8035 ]
  Phi   =  -0.576581    2.565012  [ DEG:   -33.0357    146.9643 ]
 
# 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_1                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS599_1.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   34   1.87  47.963    12.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS599_1
PFRMAT TS                                                                       
TARGET T0348                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      23.668  37.590  58.404  1.00  0.00              
ATOM      2  CA  ASP     2      21.021  38.355  61.577  1.00  0.00              
ATOM      3  CA  ALA     3      17.641  40.805  62.045  1.00  0.00              
ATOM      4  CA  LYS     4      16.678  41.475  58.045  1.00  0.00              
ATOM      5  CA  PHE     5      17.282  37.813  57.511  1.00  0.00              
ATOM      6  CA  LEU     6      15.086  36.751  60.457  1.00  0.00              
ATOM      7  CA  GLU     7      12.380  39.132  59.333  1.00  0.00              
ATOM      8  CA  ILE     8      12.512  37.880  55.796  1.00  0.00              
ATOM      9  CA  LEU     9      12.187  34.233  56.958  1.00  0.00              
ATOM     10  CA  VAL    10       9.220  34.193  59.320  1.00  0.00              
ATOM     11  CA  CYS    11       7.023  31.048  58.959  1.00  0.00              
ATOM     12  CA  PRO    12       3.325  31.368  59.312  1.00  0.00              
ATOM     13  CA  LEU    13       2.671  28.249  61.304  1.00  0.00              
ATOM     14  CA  CYS    14       5.257  28.270  64.010  1.00  0.00              
ATOM     15  CA  LYS    15       6.877  31.664  63.771  1.00  0.00              
ATOM     16  CA  GLY    16      10.378  30.111  63.778  1.00  0.00              
ATOM     17  CA  PRO    17      13.067  31.188  61.408  1.00  0.00              
ATOM     18  CA  LEU    18      13.006  30.199  57.774  1.00  0.00              
ATOM     19  CA  VAL    19      15.788  28.123  56.168  1.00  0.00              
ATOM     20  CA  PHE    20      16.476  28.400  52.492  1.00  0.00              
ATOM     21  CA  ASP    21      18.040  25.615  50.520  1.00  0.00              
ATOM     22  CA  LYS    22      19.629  27.331  47.460  1.00  0.00              
ATOM     23  CA  SER    23      20.466  24.269  45.499  1.00  0.00              
ATOM     24  CA  LYS    24      16.974  22.872  45.487  1.00  0.00              
ATOM     25  CA  ASP    25      14.973  26.124  45.536  1.00  0.00              
ATOM     26  CA  GLU    26      13.037  25.063  48.556  1.00  0.00              
ATOM     27  CA  LEU    27      12.102  26.882  51.706  1.00  0.00              
ATOM     28  CA  ILE    28      12.320  24.917  54.893  1.00  0.00              
ATOM     29  CA  CYS    29      10.368  25.870  57.946  1.00  0.00              
ATOM     30  CA  LYS    30      12.320  25.158  61.092  1.00  0.00              
ATOM     31  CA  GLY    31       9.765  24.179  63.676  1.00  0.00              
ATOM     32  CA  ASP    32       7.627  22.066  61.554  1.00  0.00              
ATOM     33  CA  ARG    33      10.118  20.571  59.137  1.00  0.00              
ATOM     34  CA  LEU    34       8.099  21.421  56.090  1.00  0.00              
ATOM     35  CA  ALA    35       9.678  21.624  52.677  1.00  0.00              
ATOM     36  CA  PHE    36       8.193  24.517  50.760  1.00  0.00              
ATOM     37  CA  PRO    37       8.811  25.034  47.026  1.00  0.00              
ATOM     38  CA  ILE    38       9.332  28.734  46.425  1.00  0.00              
ATOM     39  CA  LYS    39       5.783  29.828  45.551  1.00  0.00              
ATOM     40  CA  ASP    40       3.521  27.988  48.040  1.00  0.00              
ATOM     41  CA  GLY    41       5.921  28.642  50.940  1.00  0.00              
ATOM     42  CA  ILE    42       6.169  32.401  50.350  1.00  0.00              
ATOM     43  CA  PRO    43       2.357  32.597  50.396  1.00  0.00              
ATOM     44  CA  MET    44       2.014  30.625  53.674  1.00  0.00              
ATOM     45  CA  MET    45       4.562  32.680  55.515  1.00  0.00              
ATOM     46  CA  LEU    46       3.589  36.188  54.427  1.00  0.00              
ATOM     47  CA  GLU    47       4.088  38.855  57.142  1.00  0.00              
ATOM     48  CA  SER    48       3.328  42.042  55.273  1.00  0.00              
ATOM     49  CA  GLU    49       6.742  43.602  55.634  1.00  0.00              
ATOM     50  CA  ALA    50       8.633  40.495  54.416  1.00  0.00              
ATOM     51  CA  ARG    51       6.418  40.146  51.322  1.00  0.00              
ATOM     52  CA  GLU    52       6.840  43.824  50.390  1.00  0.00              
ATOM     53  CA  LEU    53      10.671  43.896  50.417  1.00  0.00              
ATOM     54  CA  ALA    54      11.757  45.878  47.412  1.00  0.00              
ATOM     55  CA  PRO    55      13.934  44.212  44.770  1.00  0.00              
ATOM     56  CA  GLU    56      17.050  45.903  46.005  1.00  0.00              
ATOM     57  CA  GLU    57      16.510  44.736  49.595  1.00  0.00              
ATOM     58  CA  GLU    58      15.866  41.159  48.442  1.00  0.00              
ATOM     59  CA  VAL    59      19.111  41.106  46.453  1.00  0.00              
ATOM     60  CA  LYS    60      21.066  42.457  49.426  1.00  0.00              
ATOM     61  CA  LEU    61      19.523  39.789  51.650  1.00  0.00              
ATOM     62  CA  GLU    62      20.376  36.982  49.198  1.00  0.00              
ATOM     63  CA  HIS    63      24.000  38.104  48.898  1.00  0.00              
ATOM     64  CA  HIS    64      24.644  38.358  52.629  1.00  0.00              
ATOM     65  CA  HIS    65      22.912  35.003  53.088  1.00  0.00              
ATOM     66  CA  HIS    66      25.320  33.066  50.508  1.00  0.00              
ATOM     67  CA  HIS    67      25.695  30.493  48.021  1.00  0.00              
ATOM     68  CA  HIS    68      23.421  30.942  44.518  1.00  0.00              
TER                                                                             
END
