
#######################################################
#                                                     #
#                        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   61 (   61),  selected   61 , name T0381TS393_1-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS393_1-D1.T0381_D1.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:    33        17 - 49          4.72    14.44
  LCS_AVERAGE:     48.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        46 - 65          1.93    14.66
  LCS_AVERAGE:     26.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        49 - 63          1.00    16.13
  LCS_AVERAGE:     16.64

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     V      17     V      17     14   19   33     6   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     Q      18     Q      18     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     S      19     S      19     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     L      20     L      20     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     A      21     A      21     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     R      22     R      22     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     G      23     G      23     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   38   39 
LCS_GDT     L      24     L      24     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   37   39 
LCS_GDT     A      25     A      25     14   19   33    12   13   14   16   18   19   21   22   24   25   29   31   31   32   33   33   34   37   37   39 
LCS_GDT     V      26     V      26     14   19   33    12   13   14   16   18   19   21   23   25   25   29   31   31   33   34   36   38   38   40   43 
LCS_GDT     I      27     I      27     14   19   33    12   13   14   16   18   19   21   23   24   25   29   31   31   32   33   35   35   37   38   41 
LCS_GDT     R      28     R      28     14   19   33    12   13   14   16   18   19   21   23   24   25   29   31   31   32   33   35   35   37   38   41 
LCS_GDT     C      29     C      29     14   19   33    12   13   14   16   18   19   21   22   25   28   30   31   32   33   35   36   38   40   42   43 
LCS_GDT     F      30     F      30     14   19   33     3    4   13   16   18   19   21   23   26   28   30   31   32   33   35   36   38   41   42   43 
LCS_GDT     D      31     D      31      4   19   33     0    4    6   11   18   19   21   22   26   28   30   31   32   33   35   36   38   38   40   43 
LCS_GDT     H      32     H      32      3   19   33     3    3    3    8   18   19   21   23   26   28   30   31   32   33   35   36   38   41   42   43 
LCS_GDT     R      33     R      33      3   19   33     3    6   11   14   18   19   21   22   24   25   29   31   31   33   35   36   38   41   42   43 
LCS_GDT     N      34     N      34      3   19   33     3    3    3    4    8   10   12   20   24   25   29   31   31   33   35   36   38   41   42   43 
LCS_GDT     Q      35     Q      35      3   19   33     3    4    4   14   17   19   21   22   24   25   29   31   31   33   35   36   38   41   42   43 
LCS_GDT     R      36     R      36      4    8   33     3    4    4    5    8   12   15   21   24   25   29   31   31   33   35   36   38   41   42   43 
LCS_GDT     R      37     R      37      4   11   33     3    4    5   10   15   17   21   22   24   25   26   29   31   33   35   36   38   41   42   43 
LCS_GDT     T      38     T      38     10   11   33     4   10   11   12   15   16   18   21   24   25   26   27   29   31   33   36   37   38   39   39 
LCS_GDT     L      39     L      39     10   11   33     8   10   11   12   15   16   18   19   21   24   26   27   29   31   35   36   37   41   42   43 
LCS_GDT     S      40     S      40     10   11   33     8   10   11   12   15   16   18   19   21   23   26   27   29   31   35   36   37   41   42   43 
LCS_GDT     D      41     D      41     10   11   33     8   10   11   12   15   16   18   20   21   24   26   29   31   33   35   36   38   41   42   43 
LCS_GDT     V      42     V      42     10   11   33     8   10   11   12   15   16   18   22   22   26   29   30   32   33   35   36   38   41   42   43 
LCS_GDT     A      43     A      43     10   11   33     8   10   11   12   15   16   18   19   21   24   29   30   32   33   35   36   38   41   42   43 
LCS_GDT     R      44     R      44     10   11   33     8   10   11   12   15   16   18   23   25   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     A      45     A      45     10   11   33     8   10   11   12   15   16   18   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     T      46     T      46     10   20   33     8   10   11   14   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     D      47     D      47     10   20   33     4   10   13   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     L      48     L      48      4   20   33     3    5    5    6   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     T      49     T      49     15   20   33     3    5    5   14   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     R      50     R      50     15   20   28     3   11   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     A      51     A      51     15   20   28    11   12   14   16   18   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     T      52     T      52     15   20   28     9   12   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     A      53     A      53     15   20   28    11   12   14   16   18   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     R      54     R      54     15   20   28    11   12   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     R      55     R      55     15   20   28    11   12   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     F      56     F      56     15   20   28    11   12   14   15   17   19   21   23   26   28   30   31   32   33   35   36   38   41   42   43 
LCS_GDT     L      57     L      57     15   20   28    11   12   14   15   17   19   21   23   26   28   30   31   32   33   35   36   38   41   42   43 
LCS_GDT     L      58     L      58     15   20   28    11   12   14   15   17   19   21   23   26   28   30   31   32   33   35   36   38   41   42   43 
LCS_GDT     T      59     T      59     15   20   28    11   12   14   15   17   19   21   23   26   28   30   31   32   33   35   36   38   41   42   43 
LCS_GDT     L      60     L      60     15   20   28    11   12   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     V      61     V      61     15   20   28    11   12   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     E      62     E      62     15   20   28    11   12   14   15   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     L      63     L      63     15   20   28     3    4   14   15   16   18   21   23   25   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     G      64     G      64      6   20   28     3    4    8   13   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     Y      65     Y      65      6   20   28     3    9   11   13   17   19   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     V      66     V      66      6   10   28     3    9   11   12   14   15   18   22   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     A      67     A      67      6   10   28     3    5    8    9   11   13   17   17   20   22   24   27   31   33   35   36   38   41   42   43 
LCS_GDT     T      68     T      68      6   10   22     3    5    8    9   11   13   13   16   23   24   29   31   31   32   32   33   34   37   39   39 
LCS_GDT     D      69     D      69      6   10   22     3    5    7    9   11   13   13   15   23   25   29   31   31   32   32   33   34   37   38   38 
LCS_GDT     G      70     G      70      6   10   22     3    5    7    8   11   13   13   16   23   25   29   31   31   32   32   33   34   37   37   38 
LCS_GDT     S      71     S      71      4   10   22     3    4    8    9   11   13   13   21   24   25   29   31   31   32   32   33   34   37   38   38 
LCS_GDT     A      72     A      72      4   10   20     3    4    8    9   11   14   18   21   24   25   29   31   31   32   32   33   35   37   39   39 
LCS_GDT     F      73     F      73      4   10   20     3    4   11   12   14   15   18   21   24   25   29   31   31   33   35   36   38   41   42   43 
LCS_GDT     W      74     W      74      4   10   20     3    4    7   12   15   16   18   20   23   24   28   31   31   33   35   36   38   41   42   43 
LCS_GDT     L      75     L      75      4   10   20     3    4    7    8   15   16   18   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     T      76     T      76      4   10   20     3    4    7   12   15   16   19   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_GDT     P      77     P      77      4   10   20     0    4    7    7   14   18   21   23   26   28   30   30   32   33   35   36   38   41   42   43 
LCS_AVERAGE  LCS_A:  30.53  (  16.64   26.55   48.40 )

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     13     14     16     18     19     21     23     26     28     30     31     32     33     35     36     38     41     42     43 
GDT PERCENT_CA  19.67  21.31  22.95  26.23  29.51  31.15  34.43  37.70  42.62  45.90  49.18  50.82  52.46  54.10  57.38  59.02  62.30  67.21  68.85  70.49
GDT RMS_LOCAL    0.23   0.32   0.65   0.93   1.38   1.48   1.92   2.19   2.98   3.17   3.39   3.99   3.69   3.86   4.55   4.55   4.90   5.63   5.73   5.87
GDT RMS_ALL_CA  13.78  13.76  13.56  13.60  13.53  13.53  15.15  14.83  12.76  12.75  12.65  12.93  12.54  12.58  11.98  12.06  12.03  11.77  11.77  11.84

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17         28.768
LGA    Q      18      Q      18         23.381
LGA    S      19      S      19         19.426
LGA    L      20      L      20         20.090
LGA    A      21      A      21         17.868
LGA    R      22      R      22         12.037
LGA    G      23      G      23         10.727
LGA    L      24      L      24         10.006
LGA    A      25      A      25          7.713
LGA    V      26      V      26          1.919
LGA    I      27      I      27          3.664
LGA    R      28      R      28          3.846
LGA    C      29      C      29          7.908
LGA    F      30      F      30          9.379
LGA    D      31      D      31         10.809
LGA    H      32      H      32         17.440
LGA    R      33      R      33         23.241
LGA    N      34      N      34         23.238
LGA    Q      35      Q      35         23.365
LGA    R      36      R      36         25.780
LGA    R      37      R      37         22.929
LGA    T      38      T      38         24.651
LGA    L      39      L      39         19.778
LGA    S      40      S      40         20.034
LGA    D      41      D      41         18.779
LGA    V      42      V      42         12.651
LGA    A      43      A      43         10.139
LGA    R      44      R      44         10.990
LGA    A      45      A      45         10.656
LGA    T      46      T      46          3.719
LGA    D      47      D      47          1.708
LGA    L      48      L      48          3.181
LGA    T      49      T      49          2.463
LGA    R      50      R      50          2.225
LGA    A      51      A      51          1.556
LGA    T      52      T      52          1.335
LGA    A      53      A      53          0.159
LGA    R      54      R      54          0.456
LGA    R      55      R      55          0.323
LGA    F      56      F      56          0.800
LGA    L      57      L      57          1.035
LGA    L      58      L      58          0.469
LGA    T      59      T      59          0.684
LGA    L      60      L      60          1.362
LGA    V      61      V      61          1.079
LGA    E      62      E      62          0.259
LGA    L      63      L      63          3.518
LGA    G      64      G      64          2.570
LGA    Y      65      Y      65          3.508
LGA    V      66      V      66          9.336
LGA    A      67      A      67         14.781
LGA    T      68      T      68         20.524
LGA    D      69      D      69         27.686
LGA    G      70      G      70         29.844
LGA    S      71      S      71         30.211
LGA    A      72      A      72         25.696
LGA    F      73      F      73         18.726
LGA    W      74      W      74         17.540
LGA    L      75      L      75         11.830
LGA    T      76      T      76         11.412
LGA    P      77      P      77          6.742

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   61   61    4.0     23    2.19    36.066    34.507     1.005

LGA_LOCAL      RMSD =  2.188  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.917  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 10.412  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.801405 * X  +   0.267743 * Y  +  -0.534850 * Z  +   7.287393
  Y_new =   0.522876 * X  +  -0.120599 * Y  +  -0.843835 * Z  +  40.518028
  Z_new =  -0.290433 * X  +  -0.955913 * Y  +  -0.043347 * Z  +   6.853588 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.616112    1.525481  [ DEG:   -92.5964     87.4036 ]
  Theta =   0.294680    2.846913  [ DEG:    16.8839    163.1161 ]
  Phi   =   2.563498   -0.578095  [ DEG:   146.8776    -33.1224 ]
 
# 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: T0381TS393_1-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS393_1-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   61   61   4.0   23   2.19  34.507    10.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS393_1-D1
PFRMAT TS
TARGET T0381
MODEL 1
PARENT N/A
ATOM     17  CA  VAL    17      11.647  58.860   6.935  1.00 25.00           C
ATOM     18  CA  GLN    18      11.765  60.727  10.278  1.00 25.00           C
ATOM     19  CA  SER    19       8.290  59.388  11.176  1.00 25.00           C
ATOM     20  CA  LEU    20       9.409  55.831  10.305  1.00 25.00           C
ATOM     21  CA  ALA    21      12.524  56.249  12.493  1.00 25.00           C
ATOM     22  CA  ARG    22      10.353  57.505  15.387  1.00 25.00           C
ATOM     23  CA  GLY    23       8.021  54.495  14.978  1.00 25.00           C
ATOM     24  CA  LEU    24      11.031  52.128  15.009  1.00 25.00           C
ATOM     25  CA  ALA    25      12.346  53.805  18.192  1.00 25.00           C
ATOM     26  CA  VAL    26       8.908  53.433  19.837  1.00 25.00           C
ATOM     27  CA  ILE    27       8.816  49.730  18.868  1.00 25.00           C
ATOM     28  CA  ARG    28      12.315  49.231  20.342  1.00 25.00           C
ATOM     29  CA  CYS    29      11.222  50.952  23.583  1.00 25.00           C
ATOM     30  CA  PHE    30       8.131  48.697  23.767  1.00 25.00           C
ATOM     31  CA  ASP    31      10.328  45.604  23.245  1.00 25.00           C
ATOM     32  CA  HIS    32      12.038  44.054  26.299  1.00 25.00           C
ATOM     33  CA  ARG    33      14.488  43.230  29.083  1.00 25.00           C
ATOM     34  CA  ASN    34      11.423  41.420  30.526  1.00 25.00           C
ATOM     35  CA  GLN    35       8.936  44.225  31.252  1.00 25.00           C
ATOM     36  CA  ARG    36      11.331  46.409  33.238  1.00 25.00           C
ATOM     37  CA  ARG    37       9.135  49.300  32.272  1.00 25.00           C
ATOM     38  CA  THR    38       5.440  49.514  32.968  1.00 25.00           C
ATOM     39  CA  LEU    39       5.195  49.489  29.170  1.00 25.00           C
ATOM     40  CA  SER    40       1.423  49.687  29.799  1.00 25.00           C
ATOM     41  CA  ASP    41       1.852  53.116  31.448  1.00 25.00           C
ATOM     42  CA  VAL    42       3.913  54.325  28.454  1.00 25.00           C
ATOM     43  CA  ALA    43       1.205  53.073  26.053  1.00 25.00           C
ATOM     44  CA  ARG    44      -1.478  54.896  28.089  1.00 25.00           C
ATOM     45  CA  ALA    45       0.599  58.113  27.991  1.00 25.00           C
ATOM     46  CA  THR    46       0.998  57.769  24.198  1.00 25.00           C
ATOM     47  CA  ASP    47      -2.681  58.099  23.286  1.00 25.00           C
ATOM     48  CA  LEU    48      -2.173  61.731  22.473  1.00 25.00           C
ATOM     49  CA  THR    49       0.266  62.515  19.605  1.00 25.00           C
ATOM     50  CA  ARG    50       2.084  65.454  21.256  1.00 25.00           C
ATOM     51  CA  ALA    51       4.755  67.284  23.301  1.00 25.00           C
ATOM     52  CA  THR    52       5.874  63.968  24.854  1.00 25.00           C
ATOM     53  CA  ALA    53       6.097  62.385  21.374  1.00 25.00           C
ATOM     54  CA  ARG    54       8.183  65.347  20.132  1.00 25.00           C
ATOM     55  CA  ARG    55      10.519  64.997  23.148  1.00 25.00           C
ATOM     56  CA  PHE    56      10.904  61.251  22.445  1.00 25.00           C
ATOM     57  CA  LEU    57      11.717  61.998  18.778  1.00 25.00           C
ATOM     58  CA  LEU    58      14.332  64.580  19.857  1.00 25.00           C
ATOM     59  CA  THR    59      15.893  62.032  22.253  1.00 25.00           C
ATOM     60  CA  LEU    60      16.019  59.432  19.446  1.00 25.00           C
ATOM     61  CA  VAL    61      17.697  61.977  17.129  1.00 25.00           C
ATOM     62  CA  GLU    62      20.271  62.790  19.845  1.00 25.00           C
ATOM     63  CA  LEU    63      22.123  59.817  18.253  1.00 25.00           C
ATOM     64  CA  GLY    64      21.943  56.664  20.323  1.00 25.00           C
ATOM     65  CA  TYR    65      18.590  55.589  21.904  1.00 25.00           C
ATOM     66  CA  VAL    66      16.777  56.056  25.252  1.00 25.00           C
ATOM     67  CA  ALA    67      19.027  58.134  27.412  1.00 25.00           C
ATOM     68  CA  THR    68      17.902  58.517  31.071  1.00 25.00           C
ATOM     69  CA  ASP    69      19.522  58.315  34.505  1.00 25.00           C
ATOM     70  CA  GLY    70      17.248  57.931  37.531  1.00 25.00           C
ATOM     71  CA  SER    71      16.043  54.606  36.297  1.00 25.00           C
ATOM     72  CA  ALA    72      13.260  54.448  33.736  1.00 25.00           C
ATOM     73  CA  PHE    73      13.451  54.212  29.917  1.00 25.00           C
ATOM     74  CA  TRP    74      15.848  51.481  28.733  1.00 25.00           C
ATOM     75  CA  LEU    75      17.672  51.058  25.356  1.00 25.00           C
ATOM     76  CA  THR    76      21.389  51.596  24.701  1.00 25.00           C
ATOM     77  CA  PRO    77      21.682  51.143  20.933  1.00 25.00           C
TER
END
