
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS599_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:    43         4 - 46          4.90    13.33
  LONGEST_CONTINUOUS_SEGMENT:    43         5 - 47          4.84    13.32
  LONGEST_CONTINUOUS_SEGMENT:    43         6 - 48          4.94    13.23
  LCS_AVERAGE:     60.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32         7 - 38          1.94    13.39
  LONGEST_CONTINUOUS_SEGMENT:    32         8 - 39          1.58    13.66
  LCS_AVERAGE:     34.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        10 - 35          0.99    13.65
  LCS_AVERAGE:     25.77

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   29     3    3    3    3    3    4    5    8    9    9   15   15   17   17   22   25   26   28   38   38 
LCS_GDT     A       3     A       3      3    3   37     3    3    3    3    7    8    9    9   11   12   15   15   17   19   23   35   35   39   43   44 
LCS_GDT     K       4     K       4      3    3   43     3    3    3    3    7    8    9    9   11   15   25   28   34   37   39   40   40   41   43   44 
LCS_GDT     F       5     F       5      3    3   43     2    3    3    3    7    8    9    9   14   15   25   28   34   37   39   40   40   41   43   44 
LCS_GDT     L       6     L       6      3    3   43     2    3    3    4    5    6    9   10   20   23   31   36   36   38   39   40   40   41   43   44 
LCS_GDT     E       7     E       7      3   32   43     3    3    7   11   19   24   29   33   35   35   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     I       8     I       8      4   32   43     3    4    4    9   27   31   32   33   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     L       9     L       9     21   32   43     3    8   22   26   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     V      10     V      10     26   32   43     3   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     C      11     C      11     26   32   43     5   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     P      12     P      12     26   32   43     7   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     L      13     L      13     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     C      14     C      14     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     K      15     K      15     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     G      16     G      16     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     P      17     P      17     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     L      18     L      18     26   32   43     7   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     V      19     V      19     26   32   43     8   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     F      20     F      20     26   32   43     8   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     D      21     D      21     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     K      22     K      22     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     S      23     S      23     26   32   43     8   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     K      24     K      24     26   32   43     8   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     D      25     D      25     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     E      26     E      26     26   32   43     8   18   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     L      27     L      27     26   32   43     7   18   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     I      28     I      28     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     C      29     C      29     26   32   43     7   18   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     K      30     K      30     26   32   43     5   16   22   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     G      31     G      31     26   32   43     7   18   25   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     D      32     D      32     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     R      33     R      33     26   32   43     7   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     L      34     L      34     26   32   43     9   19   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     A      35     A      35     26   32   43     7   18   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     F      36     F      36     24   32   43     8   18   25   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     P      37     P      37     23   32   43     7   18   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     I      38     I      38     23   32   43     4   17   26   29   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     K      39     K      39      4   32   43     3    4   11   24   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     D      40     D      40      4    5   43     3    4    5    5    5    6    8    9   12   27   30   31   37   38   38   40   40   40   40   41 
LCS_GDT     G      41     G      41      4    5   43     3    4    5    5    5    5    8    9   11   13   18   24   26   36   38   40   40   40   40   42 
LCS_GDT     I      42     I      42      3    5   43     3    4    4   10   12   24   31   34   35   36   37   37   38   38   38   40   40   41   43   44 
LCS_GDT     P      43     P      43      3    5   43     3    4    4    4    6   13   30   34   35   36   36   37   38   38   38   40   40   41   43   43 
LCS_GDT     M      44     M      44      4    5   43     3    4    4    5   18   27   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     M      45     M      45      4    5   43     3    4   13   25   30   32   33   34   35   36   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     L      46     L      46      4    5   43     3    4    7   16   21   26   30   33   35   35   37   37   38   38   39   40   40   41   43   44 
LCS_GDT     E      47     E      47      4    5   43     4    4    6    7    8   13   15   18   23   25   27   33   36   37   39   39   40   41   43   44 
LCS_GDT     S      48     S      48      4    5   43     4    4    6    7    8    9   12   18   19   22   24   27   31   34   39   39   40   41   43   44 
LCS_GDT     E      49     E      49      4    5   19     4    4    6    7    8    9   10   16   19   22   24   25   27   29   32   37   40   41   43   44 
LCS_GDT     A      50     A      50      4    5   19     4    4    6    7    8   10   15   18   20   22   24   25   26   29   32   35   38   41   43   44 
LCS_GDT     R      51     R      51      3   12   19     3    4    4    5   11   13   15   18   20   22   24   25   26   27   32   35   38   40   43   43 
LCS_GDT     E      52     E      52     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     L      53     L      53     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     A      54     A      54     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     P      55     P      55     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     E      56     E      56     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     E      57     E      57     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     E      58     E      58     11   12   19     7   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     V      59     V      59     11   12   19     5   10   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     K      60     K      60     11   12   19     5    9   11   11   12   13   15   18   20   22   24   25   26   26   28   28   29   31   32   33 
LCS_GDT     L      61     L      61     11   12   19     5   10   11   11   12   13   15   17   20   22   24   25   26   26   28   28   29   30   32   33 
LCS_GDT     E      62     E      62     11   12   19     5   10   11   11   12   13   14   17   20   22   24   25   26   26   28   28   29   30   32   33 
LCS_AVERAGE  LCS_A:  40.28  (  25.77   34.13   60.92 )

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      9     19     26     29     30     32     33     34     35     36     37     37     38     38     39     40     40     41     43     44 
GDT PERCENT_CA  14.75  31.15  42.62  47.54  49.18  52.46  54.10  55.74  57.38  59.02  60.66  60.66  62.30  62.30  63.93  65.57  65.57  67.21  70.49  72.13
GDT RMS_LOCAL    0.29   0.66   0.92   1.07   1.19   1.43   1.68   1.90   2.06   2.27   2.58   2.58   2.76   2.76   4.08   4.19   3.50   4.45   5.53   5.57
GDT RMS_ALL_CA  13.34  13.50  13.75  13.83  13.74  13.68  13.67  13.69  13.63  13.65  13.36  13.36  13.40  13.40  12.94  13.01  13.63  12.90  12.06  12.34

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         28.982
LGA    A       3      A       3         24.745
LGA    K       4      K       4         19.501
LGA    F       5      F       5         18.159
LGA    L       6      L       6         14.361
LGA    E       7      E       7          8.925
LGA    I       8      I       8          6.215
LGA    L       9      L       9          3.238
LGA    V      10      V      10          1.593
LGA    C      11      C      11          2.214
LGA    P      12      P      12          1.953
LGA    L      13      L      13          2.471
LGA    C      14      C      14          2.208
LGA    K      15      K      15          0.996
LGA    G      16      G      16          0.870
LGA    P      17      P      17          0.463
LGA    L      18      L      18          0.757
LGA    V      19      V      19          0.381
LGA    F      20      F      20          0.759
LGA    D      21      D      21          1.199
LGA    K      22      K      22          1.693
LGA    S      23      S      23          2.337
LGA    K      24      K      24          2.499
LGA    D      25      D      25          1.900
LGA    E      26      E      26          2.028
LGA    L      27      L      27          1.714
LGA    I      28      I      28          1.161
LGA    C      29      C      29          2.182
LGA    K      30      K      30          2.730
LGA    G      31      G      31          3.058
LGA    D      32      D      32          2.251
LGA    R      33      R      33          1.579
LGA    L      34      L      34          1.692
LGA    A      35      A      35          2.166
LGA    F      36      F      36          2.921
LGA    P      37      P      37          3.147
LGA    I      38      I      38          1.586
LGA    K      39      K      39          1.376
LGA    D      40      D      40          8.326
LGA    G      41      G      41          9.149
LGA    I      42      I      42          3.989
LGA    P      43      P      43          4.764
LGA    M      44      M      44          3.395
LGA    M      45      M      45          2.314
LGA    L      46      L      46          8.352
LGA    E      47      E      47         14.727
LGA    S      48      S      48         19.314
LGA    E      49      E      49         20.013
LGA    A      50      A      50         17.619
LGA    R      51      R      51         19.892
LGA    E      52      E      52         26.060
LGA    L      53      L      53         25.693
LGA    A      54      A      54         29.492
LGA    P      55      P      55         29.179
LGA    E      56      E      56         29.710
LGA    E      57      E      57         26.588
LGA    E      58      E      58         23.767
LGA    V      59      V      59         24.011
LGA    K      60      K      60         22.467
LGA    L      61      L      61         19.641
LGA    E      62      E      62         19.488

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     34    1.90    50.000    47.726     1.703

LGA_LOCAL      RMSD =  1.897  Number of atoms =   34  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.818  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 10.966  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.108873 * X  +  -0.798637 * Y  +  -0.591884 * Z  +  12.588484
  Y_new =  -0.674304 * X  +   0.496822 * Y  +  -0.546335 * Z  +  32.351593
  Z_new =   0.730384 * X  +   0.339629 * Y  +  -0.592615 * Z  +  53.601929 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.621186   -0.520407  [ DEG:   150.1829    -29.8171 ]
  Theta =  -0.818884   -2.322709  [ DEG:   -46.9186   -133.0814 ]
  Phi   =  -1.730875    1.410718  [ DEG:   -99.1718     80.8282 ]
 
# 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_5                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS599_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   34   1.90  47.726    10.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS599_5
PFRMAT TS                                                                       
TARGET T0348                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      23.419  39.297  60.111  1.00  0.00              
ATOM      2  CA  ASP     2      20.312  39.077  62.929  1.00  0.00              
ATOM      3  CA  ALA     3      17.260  41.115  62.619  1.00  0.00              
ATOM      4  CA  LYS     4      17.082  41.206  58.892  1.00  0.00              
ATOM      5  CA  PHE     5      17.466  37.497  58.556  1.00  0.00              
ATOM      6  CA  LEU     6      14.729  36.862  61.163  1.00  0.00              
ATOM      7  CA  GLU     7      12.373  39.232  59.466  1.00  0.00              
ATOM      8  CA  ILE     8      13.093  37.832  56.063  1.00  0.00              
ATOM      9  CA  LEU     9      12.295  34.284  57.309  1.00  0.00              
ATOM     10  CA  VAL    10       9.091  34.303  59.358  1.00  0.00              
ATOM     11  CA  CYS    11       7.036  31.102  58.914  1.00  0.00              
ATOM     12  CA  PRO    12       3.296  31.265  59.241  1.00  0.00              
ATOM     13  CA  LEU    13       2.682  28.217  61.294  1.00  0.00              
ATOM     14  CA  CYS    14       5.265  28.314  64.005  1.00  0.00              
ATOM     15  CA  LYS    15       6.815  31.743  63.635  1.00  0.00              
ATOM     16  CA  GLY    16      10.311  30.368  63.576  1.00  0.00              
ATOM     17  CA  PRO    17      13.164  31.141  61.418  1.00  0.00              
ATOM     18  CA  LEU    18      13.085  30.197  57.752  1.00  0.00              
ATOM     19  CA  VAL    19      15.851  28.016  56.227  1.00  0.00              
ATOM     20  CA  PHE    20      16.634  28.271  52.556  1.00  0.00              
ATOM     21  CA  ASP    21      18.041  25.434  50.564  1.00  0.00              
ATOM     22  CA  LYS    22      19.759  27.177  47.574  1.00  0.00              
ATOM     23  CA  SER    23      20.252  24.142  45.464  1.00  0.00              
ATOM     24  CA  LYS    24      16.644  23.057  45.389  1.00  0.00              
ATOM     25  CA  ASP    25      15.004  26.496  45.624  1.00  0.00              
ATOM     26  CA  GLU    26      13.036  25.284  48.558  1.00  0.00              
ATOM     27  CA  LEU    27      12.123  27.001  51.767  1.00  0.00              
ATOM     28  CA  ILE    28      12.290  24.921  54.900  1.00  0.00              
ATOM     29  CA  CYS    29      10.339  25.885  57.948  1.00  0.00              
ATOM     30  CA  LYS    30      12.286  25.140  61.084  1.00  0.00              
ATOM     31  CA  GLY    31       9.650  24.192  63.624  1.00  0.00              
ATOM     32  CA  ASP    32       7.508  22.009  61.463  1.00  0.00              
ATOM     33  CA  ARG    33      10.219  20.590  59.152  1.00  0.00              
ATOM     34  CA  LEU    34       8.271  21.250  56.011  1.00  0.00              
ATOM     35  CA  ALA    35       9.959  21.486  52.663  1.00  0.00              
ATOM     36  CA  PHE    36       8.382  24.221  50.629  1.00  0.00              
ATOM     37  CA  PRO    37       9.127  25.082  47.035  1.00  0.00              
ATOM     38  CA  ILE    38       9.342  28.842  46.523  1.00  0.00              
ATOM     39  CA  LYS    39       5.769  29.682  45.619  1.00  0.00              
ATOM     40  CA  ASP    40       3.576  27.796  48.150  1.00  0.00              
ATOM     41  CA  GLY    41       5.950  28.626  50.978  1.00  0.00              
ATOM     42  CA  ILE    42       6.002  32.372  50.386  1.00  0.00              
ATOM     43  CA  PRO    43       2.196  32.768  50.449  1.00  0.00              
ATOM     44  CA  MET    44       1.804  30.751  53.660  1.00  0.00              
ATOM     45  CA  MET    45       4.459  32.686  55.492  1.00  0.00              
ATOM     46  CA  LEU    46       3.509  36.258  54.454  1.00  0.00              
ATOM     47  CA  GLU    47       5.003  39.291  56.203  1.00  0.00              
ATOM     48  CA  SER    48       4.155  42.024  53.670  1.00  0.00              
ATOM     49  CA  GLU    49       7.766  43.024  52.985  1.00  0.00              
ATOM     50  CA  ALA    50       8.896  39.431  52.395  1.00  0.00              
ATOM     51  CA  ARG    51       5.886  38.769  50.148  1.00  0.00              
ATOM     52  CA  GLU    52       6.769  41.726  47.877  1.00  0.00              
ATOM     53  CA  LEU    53      10.388  40.782  47.430  1.00  0.00              
ATOM     54  CA  ALA    54      11.401  40.371  43.869  1.00  0.00              
ATOM     55  CA  PRO    55      13.225  37.111  42.940  1.00  0.00              
ATOM     56  CA  GLU    56      16.500  38.995  42.612  1.00  0.00              
ATOM     57  CA  GLU    57      16.188  40.695  46.007  1.00  0.00              
ATOM     58  CA  GLU    58      15.410  37.301  47.598  1.00  0.00              
ATOM     59  CA  VAL    59      18.575  35.814  46.028  1.00  0.00              
ATOM     60  CA  LYS    60      20.621  38.802  47.339  1.00  0.00              
ATOM     61  CA  LEU    61      19.197  38.467  50.808  1.00  0.00              
ATOM     62  CA  GLU    62      19.967  34.726  50.925  1.00  0.00              
ATOM     63  CA  HIS    63      23.568  35.320  49.758  1.00  0.00              
ATOM     64  CA  HIS    64      24.388  38.192  52.092  1.00  0.00              
ATOM     65  CA  HIS    65      23.042  36.260  55.093  1.00  0.00              
ATOM     66  CA  HIS    66      24.850  33.207  54.471  1.00  0.00              
ATOM     67  CA  HIS    67      26.892  29.613  54.007  1.00  0.00              
ATOM     68  CA  HIS    68      26.571  27.502  50.437  1.00  0.00              
TER                                                                             
END
