
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS599_2.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          4.80    14.74
  LONGEST_CONTINUOUS_SEGMENT:    43         5 - 47          4.72    14.68
  LONGEST_CONTINUOUS_SEGMENT:    43         6 - 48          4.85    14.56
  LCS_AVERAGE:     61.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32         7 - 38          1.89    14.69
  LONGEST_CONTINUOUS_SEGMENT:    32         8 - 39          1.55    14.89
  LCS_AVERAGE:     34.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25        10 - 34          0.96    14.77
  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    6    8    9    9   11   14   15   16   18   25   28   29   30   34 
LCS_GDT     A       3     A       3      3    3   37     3    3    5    5    5    5    5    8   10   11   12   14   15   20   23   25   30   35   41   43 
LCS_GDT     K       4     K       4      3    3   43     3    3    5    5    5    5    6    8   11   14   23   29   35   38   39   40   41   42   42   43 
LCS_GDT     F       5     F       5      3    3   43     3    3    5    5    5    5    6    8   13   16   23   33   34   38   39   40   41   42   42   43 
LCS_GDT     L       6     L       6      3    3   43     3    3    3    3    5    8    8   10   20   25   30   36   37   38   39   40   41   42   42   43 
LCS_GDT     E       7     E       7      3   32   43     3    3    6   12   20   25   30   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     I       8     I       8      4   32   43     4    4    4   17   27   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     L       9     L       9     21   32   43     4    9   22   26   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     V      10     V      10     25   32   43     5   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     C      11     C      11     25   32   43     7   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     P      12     P      12     25   32   43     8   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     L      13     L      13     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     C      14     C      14     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     K      15     K      15     25   32   43     9   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     G      16     G      16     25   32   43     9   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     P      17     P      17     25   32   43     9   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     L      18     L      18     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     V      19     V      19     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     F      20     F      20     25   32   43     8   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     D      21     D      21     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     K      22     K      22     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     S      23     S      23     25   32   43     8   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     K      24     K      24     25   32   43     8   17   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     D      25     D      25     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     E      26     E      26     25   32   43     8   17   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     L      27     L      27     25   32   43     7   16   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     I      28     I      28     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     C      29     C      29     25   32   43     8   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     K      30     K      30     25   32   43     5   15   22   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     G      31     G      31     25   32   43     8   16   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     D      32     D      32     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     R      33     R      33     25   32   43     8   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     L      34     L      34     25   32   43    10   19   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     A      35     A      35     23   32   43     7   16   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     F      36     F      36     22   32   43     8   16   24   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     P      37     P      37     22   32   43     8   16   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     I      38     I      38     22   32   43     5   17   25   28   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     K      39     K      39      4   32   43     3    4   11   25   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     D      40     D      40      4    5   43     3    4    5    5    5    6    8    9   12   27   29   31   37   38   39   40   40   40   40   41 
LCS_GDT     G      41     G      41      4    5   43     3    4    5    5    5    5    8   11   12   14   18   24   31   35   38   40   40   40   40   42 
LCS_GDT     I      42     I      42      3    5   43     3    4    4   11   13   23   32   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     P      43     P      43      3    5   43     3    4    4    4    5   14   30   34   35   36   36   37   38   38   39   40   40   42   42   43 
LCS_GDT     M      44     M      44      4    5   43     4    4    4    5   20   28   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     M      45     M      45      4    5   43     4    5   14   25   30   32   33   34   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     L      46     L      46      4    5   43     4    4   11   15   22   25   29   33   35   36   37   37   38   38   39   40   41   42   42   43 
LCS_GDT     E      47     E      47      4    5   43     4    4    5    8   13   15   16   19   23   26   31   33   36   38   39   40   41   42   42   43 
LCS_GDT     S      48     S      48      4    5   43     4    4    5    8    9    9   15   18   20   24   27   28   30   36   38   39   40   41   42   43 
LCS_GDT     E      49     E      49      4    5   21     4    4    5    8    9    9   10   17   20   24   24   24   26   27   31   33   38   39   41   42 
LCS_GDT     A      50     A      50      4    5   21     4    4    5    8    9   12   15   19   20   24   24   24   25   27   31   33   36   39   41   42 
LCS_GDT     R      51     R      51      3   12   21     3    3    4    8    9   11   16   19   20   24   24   24   25   27   31   33   34   38   40   42 
LCS_GDT     E      52     E      52     11   12   21     7   11   12   13   14   15   16   19   20   24   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   24   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   24   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   24   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   24   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   24   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   24   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   24   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   24   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   24   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   24   24   24   25   26   28   28   30   30   32   33 
LCS_AVERAGE  LCS_A:  40.20  (  24.91   34.13   61.54 )

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     25     28     30     32     33     34     35     36     37     37     38     38     39     40     41     42     42     43 
GDT PERCENT_CA  16.39  31.15  40.98  45.90  49.18  52.46  54.10  55.74  57.38  59.02  60.66  60.66  62.30  62.30  63.93  65.57  67.21  68.85  68.85  70.49
GDT RMS_LOCAL    0.38   0.67   0.90   1.03   1.20   1.43   1.60   1.89   2.03   2.24   2.54   2.54   2.72   2.72   3.13   4.08   4.32   4.48   4.48   4.85
GDT RMS_ALL_CA  14.91  14.65  14.86  14.98  14.93  14.87  14.84  14.88  14.85  14.86  14.65  14.65  14.67  14.67  14.77  14.48  14.38  14.41  14.41  14.27

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         29.104
LGA    A       3      A       3         24.777
LGA    K       4      K       4         18.810
LGA    F       5      F       5         17.448
LGA    L       6      L       6         14.115
LGA    E       7      E       7          8.654
LGA    I       8      I       8          5.896
LGA    L       9      L       9          3.187
LGA    V      10      V      10          1.668
LGA    C      11      C      11          2.216
LGA    P      12      P      12          2.073
LGA    L      13      L      13          2.523
LGA    C      14      C      14          2.228
LGA    K      15      K      15          0.956
LGA    G      16      G      16          0.792
LGA    P      17      P      17          0.511
LGA    L      18      L      18          0.686
LGA    V      19      V      19          0.397
LGA    F      20      F      20          0.660
LGA    D      21      D      21          1.135
LGA    K      22      K      22          1.713
LGA    S      23      S      23          2.420
LGA    K      24      K      24          2.537
LGA    D      25      D      25          1.914
LGA    E      26      E      26          2.033
LGA    L      27      L      27          1.704
LGA    I      28      I      28          1.132
LGA    C      29      C      29          2.152
LGA    K      30      K      30          2.808
LGA    G      31      G      31          3.073
LGA    D      32      D      32          2.216
LGA    R      33      R      33          1.580
LGA    L      34      L      34          1.682
LGA    A      35      A      35          2.123
LGA    F      36      F      36          2.892
LGA    P      37      P      37          3.150
LGA    I      38      I      38          1.592
LGA    K      39      K      39          1.338
LGA    D      40      D      40          8.341
LGA    G      41      G      41          9.101
LGA    I      42      I      42          3.908
LGA    P      43      P      43          4.732
LGA    M      44      M      44          3.297
LGA    M      45      M      45          2.385
LGA    L      46      L      46          8.355
LGA    E      47      E      47         14.051
LGA    S      48      S      48         19.099
LGA    E      49      E      49         20.534
LGA    A      50      A      50         18.515
LGA    R      51      R      51         21.099
LGA    E      52      E      52         27.402
LGA    L      53      L      53         27.888
LGA    A      54      A      54         33.635
LGA    P      55      P      55         34.761
LGA    E      56      E      56         35.150
LGA    E      57      E      57         29.618
LGA    E      58      E      58         26.860
LGA    V      59      V      59         28.518
LGA    K      60      K      60         25.211
LGA    L      61      L      61         20.496
LGA    E      62      E      62         22.204

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     34    1.89    49.590    47.517     1.710

LGA_LOCAL      RMSD =  1.889  Number of atoms =   34  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.967  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 12.317  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.484733 * X  +   0.861664 * Y  +   0.150228 * Z  +  12.592828
  Y_new =  -0.868925 * X  +   0.494037 * Y  +  -0.029935 * Z  +  33.095440
  Z_new =  -0.100012 * X  +  -0.116026 * Y  +   0.988198 * Z  +  53.654148 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.116877    3.024716  [ DEG:    -6.6965    173.3035 ]
  Theta =   0.100180    3.041413  [ DEG:     5.7399    174.2601 ]
  Phi   =  -1.061943    2.079649  [ DEG:   -60.8449    119.1551 ]
 
# 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_2                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS599_2.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   1.89  47.517    12.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS599_2
PFRMAT TS                                                                       
TARGET T0348                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      23.644  37.566  58.478  1.00  0.00              
ATOM      2  CA  ASP     2      20.902  38.215  61.600  1.00  0.00              
ATOM      3  CA  ALA     3      17.548  40.703  62.093  1.00  0.00              
ATOM      4  CA  LYS     4      16.764  41.354  58.154  1.00  0.00              
ATOM      5  CA  PHE     5      17.261  37.675  57.558  1.00  0.00              
ATOM      6  CA  LEU     6      14.919  36.768  60.453  1.00  0.00              
ATOM      7  CA  GLU     7      12.300  39.159  59.071  1.00  0.00              
ATOM      8  CA  ILE     8      12.613  37.754  55.614  1.00  0.00              
ATOM      9  CA  LEU     9      12.217  34.150  56.915  1.00  0.00              
ATOM     10  CA  VAL    10       9.210  34.279  59.243  1.00  0.00              
ATOM     11  CA  CYS    11       7.070  31.094  58.901  1.00  0.00              
ATOM     12  CA  PRO    12       3.369  31.424  59.244  1.00  0.00              
ATOM     13  CA  LEU    13       2.722  28.339  61.270  1.00  0.00              
ATOM     14  CA  CYS    14       5.238  28.422  64.008  1.00  0.00              
ATOM     15  CA  LYS    15       6.927  31.754  63.666  1.00  0.00              
ATOM     16  CA  GLY    16      10.397  30.149  63.771  1.00  0.00              
ATOM     17  CA  PRO    17      13.129  31.085  61.424  1.00  0.00              
ATOM     18  CA  LEU    18      13.080  30.134  57.790  1.00  0.00              
ATOM     19  CA  VAL    19      15.835  28.051  56.183  1.00  0.00              
ATOM     20  CA  PHE    20      16.537  28.344  52.485  1.00  0.00              
ATOM     21  CA  ASP    21      18.021  25.578  50.450  1.00  0.00              
ATOM     22  CA  LYS    22      19.791  27.266  47.496  1.00  0.00              
ATOM     23  CA  SER    23      20.318  24.211  45.366  1.00  0.00              
ATOM     24  CA  LYS    24      16.657  23.086  45.327  1.00  0.00              
ATOM     25  CA  ASP    25      15.055  26.463  45.701  1.00  0.00              
ATOM     26  CA  GLU    26      13.057  25.202  48.621  1.00  0.00              
ATOM     27  CA  LEU    27      12.096  26.973  51.783  1.00  0.00              
ATOM     28  CA  ILE    28      12.305  24.924  54.928  1.00  0.00              
ATOM     29  CA  CYS    29      10.341  25.881  57.984  1.00  0.00              
ATOM     30  CA  LYS    30      12.207  25.188  61.151  1.00  0.00              
ATOM     31  CA  GLY    31       9.645  24.267  63.689  1.00  0.00              
ATOM     32  CA  ASP    32       7.516  22.078  61.526  1.00  0.00              
ATOM     33  CA  ARG    33      10.131  20.568  59.169  1.00  0.00              
ATOM     34  CA  LEU    34       8.169  21.302  56.036  1.00  0.00              
ATOM     35  CA  ALA    35       9.854  21.473  52.687  1.00  0.00              
ATOM     36  CA  PHE    36       8.343  24.245  50.631  1.00  0.00              
ATOM     37  CA  PRO    37       9.129  25.037  47.054  1.00  0.00              
ATOM     38  CA  ILE    38       9.317  28.755  46.509  1.00  0.00              
ATOM     39  CA  LYS    39       5.748  29.651  45.586  1.00  0.00              
ATOM     40  CA  ASP    40       3.545  27.800  48.160  1.00  0.00              
ATOM     41  CA  GLY    41       5.977  28.648  50.943  1.00  0.00              
ATOM     42  CA  ILE    42       5.999  32.422  50.317  1.00  0.00              
ATOM     43  CA  PRO    43       2.208  32.654  50.411  1.00  0.00              
ATOM     44  CA  MET    44       1.949  30.698  53.641  1.00  0.00              
ATOM     45  CA  MET    45       4.560  32.743  55.439  1.00  0.00              
ATOM     46  CA  LEU    46       3.515  36.253  54.401  1.00  0.00              
ATOM     47  CA  GLU    47       3.959  38.940  57.091  1.00  0.00              
ATOM     48  CA  SER    48       3.155  42.111  55.144  1.00  0.00              
ATOM     49  CA  GLU    49       6.601  43.662  55.534  1.00  0.00              
ATOM     50  CA  ALA    50       8.522  40.566  54.362  1.00  0.00              
ATOM     51  CA  ARG    51       6.398  40.130  51.264  1.00  0.00              
ATOM     52  CA  GLU    52       6.850  43.805  50.305  1.00  0.00              
ATOM     53  CA  LEU    53      10.695  43.851  50.415  1.00  0.00              
ATOM     54  CA  ALA    54      11.827  45.817  47.407  1.00  0.00              
ATOM     55  CA  PRO    55      14.030  44.178  44.803  1.00  0.00              
ATOM     56  CA  GLU    56      17.115  45.867  46.090  1.00  0.00              
ATOM     57  CA  GLU    57      16.525  44.697  49.664  1.00  0.00              
ATOM     58  CA  GLU    58      15.933  41.098  48.495  1.00  0.00              
ATOM     59  CA  VAL    59      19.187  41.106  46.515  1.00  0.00              
ATOM     60  CA  LYS    60      21.134  42.438  49.545  1.00  0.00              
ATOM     61  CA  LEU    61      19.569  39.741  51.676  1.00  0.00              
ATOM     62  CA  GLU    62      20.477  36.951  49.229  1.00  0.00              
ATOM     63  CA  HIS    63      24.104  38.092  48.933  1.00  0.00              
ATOM     64  CA  HIS    64      24.717  38.300  52.724  1.00  0.00              
ATOM     65  CA  HIS    65      22.975  34.946  53.122  1.00  0.00              
ATOM     66  CA  HIS    66      25.411  33.035  50.532  1.00  0.00              
ATOM     67  CA  HIS    67      26.262  30.601  48.021  1.00  0.00              
ATOM     68  CA  HIS    68      23.734  30.777  44.686  1.00  0.00              
TER                                                                             
END
