
#######################################################
#                                                     #
#                        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 T0381TS168_4-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS168_4-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:    32        36 - 67          4.98     9.66
  LCS_AVERAGE:     48.27

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        17 - 34          1.67    16.37
  LCS_AVERAGE:     22.39

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        17 - 30          0.64    16.20
  LONGEST_CONTINUOUS_SEGMENT:    14        49 - 62          0.87    10.57
  LCS_AVERAGE:     14.97

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   18   29     6   13   13   14   16   18   19   21   22   23   29   33   37   41   42   43   44   47   48   49 
LCS_GDT     Q      18     Q      18     14   18   29    12   13   13   14   16   18   20   24   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     S      19     S      19     14   18   29    12   13   13   14   16   18   19   21   22   23   27   30   37   41   42   43   44   47   48   49 
LCS_GDT     L      20     L      20     14   18   29    12   13   13   14   16   18   19   21   22   23   26   28   31   33   37   43   44   47   48   49 
LCS_GDT     A      21     A      21     14   18   29    12   13   13   14   16   18   19   21   25   30   31   34   37   41   42   43   44   47   48   49 
LCS_GDT     R      22     R      22     14   18   29    12   13   13   14   16   18   19   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     G      23     G      23     14   18   29    12   13   13   14   16   18   19   21   22   23   23   28   30   41   42   43   44   47   48   49 
LCS_GDT     L      24     L      24     14   18   29    12   13   13   14   16   18   19   21   22   23   23   28   37   41   42   43   44   47   48   49 
LCS_GDT     A      25     A      25     14   18   29    12   13   13   14   16   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     V      26     V      26     14   18   29    12   13   13   14   16   18   19   21   25   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     I      27     I      27     14   18   29    12   13   13   14   16   18   19   21   22   23   23   34   34   41   42   43   44   44   48   49 
LCS_GDT     R      28     R      28     14   18   29    12   13   13   14   16   18   19   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     C      29     C      29     14   18   29    12   13   13   14   16   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     F      30     F      30     14   18   29     3    4   13   14   16   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     D      31     D      31      4   18   29     0    3    4   10   16   18   19   21   22   30   32   34   37   41   42   43   44   44   46   48 
LCS_GDT     H      32     H      32      3   18   29     3    3    4   10   16   18   19   21   22   30   32   34   37   41   42   43   44   44   46   48 
LCS_GDT     R      33     R      33      3   18   29     3    3    5   10   15   18   19   21   22   23   23   28   37   41   42   43   44   44   46   49 
LCS_GDT     N      34     N      34      3   18   29     3    3    4    7   11   18   19   21   26   27   31   33   37   41   42   43   44   47   48   49 
LCS_GDT     Q      35     Q      35      3    7   29     3    3    4    7   12   14   19   21   26   27   30   33   36   39   42   43   44   47   48   49 
LCS_GDT     R      36     R      36      4    7   32     3    4    4    7   12   14   16   18   22   25   28   30   34   38   40   41   44   47   48   49 
LCS_GDT     R      37     R      37      4    7   32     3    4    6    7    8   11   18   21   22   25   28   29   31   38   40   41   44   47   48   49 
LCS_GDT     T      38     T      38      4   10   32     3    4    5    9   11   12   18   21   22   23   25   28   31   33   35   39   41   45   47   49 
LCS_GDT     L      39     L      39      8   10   32     8    9    9   10   11   13   15   20   22   23   25   28   31   33   35   39   41   45   47   49 
LCS_GDT     S      40     S      40      8   10   32     8    9    9   10   11   12   15   18   20   22   25   27   31   33   35   38   41   45   47   49 
LCS_GDT     D      41     D      41      8   10   32     8    9    9   10   11   13   15   17   20   22   25   28   31   33   35   39   41   45   47   49 
LCS_GDT     V      42     V      42      8   10   32     8    9    9   10   11   13   15   18   21   25   28   29   31   33   40   41   44   47   48   49 
LCS_GDT     A      43     A      43      8   10   32     8    9    9   10   11   18   19   20   20   25   28   29   32   38   40   41   44   47   48   49 
LCS_GDT     R      44     R      44      8   10   32     8    9    9   13   14   17   18   20   21   25   28   29   33   38   40   41   44   47   48   49 
LCS_GDT     A      45     A      45      8   10   32     8    9    9   10   11   14   16   19   21   25   28   30   34   38   40   41   44   47   48   49 
LCS_GDT     T      46     T      46      8   10   32     8    9    9   10   11   15   19   22   26   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     D      47     D      47      5   16   32     2    4    5    7   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     L      48     L      48      5   16   32     3    4    5    6   10   17   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     T      49     T      49     14   16   32     3    4   10   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     R      50     R      50     14   16   32     3    9   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     A      51     A      51     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     T      52     T      52     14   16   32     4   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     A      53     A      53     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     R      54     R      54     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     R      55     R      55     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     F      56     F      56     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     L      57     L      57     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     L      58     L      58     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     T      59     T      59     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     L      60     L      60     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     V      61     V      61     14   16   32    11   12   13   15   15   18   20   23   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     E      62     E      62     14   16   32    11   12   13   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     L      63     L      63      4   15   32     3    4    7    8   12   14   16   20   23   25   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     G      64     G      64      4    8   32     3    4    5    7   11   13   16   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     Y      65     Y      65      4    8   32     3    4    5    6   13   17   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     V      66     V      66      5   10   32     3    5   10   15   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     A      67     A      67      5   10   32     3    5    7   14   15   15   18   19   21   25   28   30   32   38   40   41   44   47   48   49 
LCS_GDT     T      68     T      68      5   10   29     3    9    9   10   12   14   16   18   19   22   25   28   31   33   35   39   41   45   47   49 
LCS_GDT     D      69     D      69      5   10   23     3    5    9   10   12   14   16   18   19   22   24   28   30   32   34   36   37   39   41   43 
LCS_GDT     G      70     G      70      5   10   22     3    5    6    7   12   14   16   18   19   21   22   28   30   30   32   34   36   38   39   41 
LCS_GDT     S      71     S      71      4   10   21     3    5    5    8   12   14   16   18   19   21   22   28   30   30   34   36   37   39   41   43 
LCS_GDT     A      72     A      72      4   10   21     3    5    7    8   12   14   16   18   19   22   25   28   31   33   35   39   41   45   47   49 
LCS_GDT     F      73     F      73      4   10   21     3    5    7    8   12   14   16   18   21   25   28   30   31   38   40   41   44   47   48   49 
LCS_GDT     W      74     W      74      4   10   21     3    3    6    8   12   15   19   21   26   27   30   33   36   41   42   43   44   47   48   49 
LCS_GDT     L      75     L      75      4   10   21     3    3    6    8   15   18   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     T      76     T      76      3    6   21     2    3    4    6    9   16   20   25   27   30   32   34   37   41   42   43   44   47   48   49 
LCS_GDT     P      77     P      77      3    5   21     0    3    4    4   10   13   16   18   19   21   21   23   25   26   28   30   38   44   46   47 
LCS_AVERAGE  LCS_A:  28.54  (  14.97   22.39   48.27 )

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     13     15     16     18     20     25     27     30     32     34     37     41     42     43     44     47     48     49 
GDT PERCENT_CA  19.67  21.31  21.31  24.59  26.23  29.51  32.79  40.98  44.26  49.18  52.46  55.74  60.66  67.21  68.85  70.49  72.13  77.05  78.69  80.33
GDT RMS_LOCAL    0.23   0.32   0.32   1.29   1.23   1.63   2.28   2.89   3.07   3.27   3.46   3.69   4.21   4.63   4.75   4.86   4.99   5.85   5.95   6.07
GDT RMS_ALL_CA  15.98  15.99  15.99   9.79  16.34  16.43   9.89  10.79  10.67  10.80  10.81  10.92  10.50  10.42  10.23  10.24  10.14   8.99   9.04   9.11

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17          9.534
LGA    Q      18      Q      18          4.441
LGA    S      19      S      19          8.789
LGA    L      20      L      20         10.225
LGA    A      21      A      21          5.646
LGA    R      22      R      22          3.823
LGA    G      23      G      23          8.002
LGA    L      24      L      24          6.726
LGA    A      25      A      25          1.308
LGA    V      26      V      26          4.525
LGA    I      27      I      27          5.986
LGA    R      28      R      28          3.683
LGA    C      29      C      29          2.097
LGA    F      30      F      30          2.625
LGA    D      31      D      31          4.607
LGA    H      32      H      32          5.087
LGA    R      33      R      33          8.510
LGA    N      34      N      34          8.922
LGA    Q      35      Q      35         11.020
LGA    R      36      R      36         15.712
LGA    R      37      R      37         16.665
LGA    T      38      T      38         22.019
LGA    L      39      L      39         18.705
LGA    S      40      S      40         20.979
LGA    D      41      D      41         19.651
LGA    V      42      V      42         13.530
LGA    A      43      A      43         12.814
LGA    R      44      R      44         14.471
LGA    A      45      A      45         11.648
LGA    T      46      T      46          5.493
LGA    D      47      D      47          3.777
LGA    L      48      L      48          3.286
LGA    T      49      T      49          2.953
LGA    R      50      R      50          3.743
LGA    A      51      A      51          3.284
LGA    T      52      T      52          2.762
LGA    A      53      A      53          2.949
LGA    R      54      R      54          3.150
LGA    R      55      R      55          2.591
LGA    F      56      F      56          2.682
LGA    L      57      L      57          3.552
LGA    L      58      L      58          2.622
LGA    T      59      T      59          1.901
LGA    L      60      L      60          3.995
LGA    V      61      V      61          4.220
LGA    E      62      E      62          1.964
LGA    L      63      L      63          5.317
LGA    G      64      G      64          3.829
LGA    Y      65      Y      65          2.597
LGA    V      66      V      66          3.889
LGA    A      67      A      67         10.669
LGA    T      68      T      68         17.440
LGA    D      69      D      69         24.504
LGA    G      70      G      70         28.050
LGA    S      71      S      71         26.713
LGA    A      72      A      72         21.393
LGA    F      73      F      73         14.431
LGA    W      74      W      74          9.635
LGA    L      75      L      75          2.369
LGA    T      76      T      76          2.774
LGA    P      77      P      77          9.442

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   61   61    4.0     25    2.89    39.344    34.824     0.835

LGA_LOCAL      RMSD =  2.894  Number of atoms =   25  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.987  Number of atoms =   61 
Std_ALL_ATOMS  RMSD =  8.728  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.165200 * X  +   0.666348 * Y  +  -0.727110 * Z  +  -3.784128
  Y_new =   0.786619 * X  +   0.355694 * Y  +   0.504691 * Z  +  60.603596
  Z_new =   0.594928 * X  +  -0.655333 * Y  +  -0.465402 * Z  +   4.242048 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.188319    0.953274  [ DEG:  -125.3814     54.6186 ]
  Theta =  -0.637176   -2.504416  [ DEG:   -36.5075   -143.4925 ]
  Phi   =   1.363792   -1.777801  [ DEG:    78.1395   -101.8605 ]
 
# 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: T0381TS168_4-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS168_4-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   25   2.89  34.824     8.73
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS168_4-D1
PFRMAT TS
TARGET T0381
MODEL 4
PARENT N/A
ATOM     17  CA  VAL    17       4.520  62.986  30.574  1.00 25.00           C
ATOM     18  CA  GLN    18       3.386  59.348  30.961  1.00 25.00           C
ATOM     19  CA  SER    19       1.090  59.714  27.919  1.00 25.00           C
ATOM     20  CA  LEU    20       3.981  61.184  25.883  1.00 25.00           C
ATOM     21  CA  ALA    21       6.232  58.268  26.929  1.00 25.00           C
ATOM     22  CA  ARG    22       3.518  55.770  25.896  1.00 25.00           C
ATOM     23  CA  GLY    23       3.169  57.513  22.505  1.00 25.00           C
ATOM     24  CA  LEU    24       6.964  57.365  22.010  1.00 25.00           C
ATOM     25  CA  ALA    25       6.954  53.633  22.869  1.00 25.00           C
ATOM     26  CA  VAL    26       4.122  53.038  20.361  1.00 25.00           C
ATOM     27  CA  ILE    27       6.075  54.936  17.668  1.00 25.00           C
ATOM     28  CA  ARG    28       9.188  52.833  18.408  1.00 25.00           C
ATOM     29  CA  CYS    29       7.114  49.624  18.138  1.00 25.00           C
ATOM     30  CA  PHE    30       5.681  50.802  14.789  1.00 25.00           C
ATOM     31  CA  ASP    31       9.213  51.561  13.517  1.00 25.00           C
ATOM     32  CA  HIS    32      10.715  48.567  11.625  1.00 25.00           C
ATOM     33  CA  ARG    33      12.470  46.263   9.160  1.00 25.00           C
ATOM     34  CA  ASN    34      10.704  43.525  11.122  1.00 25.00           C
ATOM     35  CA  GLN    35      11.996  42.016  14.298  1.00 25.00           C
ATOM     36  CA  ARG    36      14.795  42.561  16.788  1.00 25.00           C
ATOM     37  CA  ARG    37      13.196  44.611  19.601  1.00 25.00           C
ATOM     38  CA  THR    38      12.107  43.612  23.126  1.00 25.00           C
ATOM     39  CA  LEU    39       9.773  46.690  23.107  1.00 25.00           C
ATOM     40  CA  SER    40       6.866  44.197  23.174  1.00 25.00           C
ATOM     41  CA  ASP    41       6.191  45.045  26.847  1.00 25.00           C
ATOM     42  CA  VAL    42       6.208  48.783  26.014  1.00 25.00           C
ATOM     43  CA  ALA    43       3.751  48.177  23.138  1.00 25.00           C
ATOM     44  CA  ARG    44       1.463  46.190  25.480  1.00 25.00           C
ATOM     45  CA  ALA    45       1.590  49.026  28.051  1.00 25.00           C
ATOM     46  CA  THR    46       0.708  51.568  25.326  1.00 25.00           C
ATOM     47  CA  ASP    47      -1.854  54.390  25.372  1.00 25.00           C
ATOM     48  CA  LEU    48      -1.392  57.881  23.928  1.00 25.00           C
ATOM     49  CA  THR    49       0.129  61.109  22.675  1.00 25.00           C
ATOM     50  CA  ARG    50       3.370  62.660  21.379  1.00 25.00           C
ATOM     51  CA  ALA    51       5.645  65.372  19.918  1.00 25.00           C
ATOM     52  CA  THR    52       7.298  65.862  23.338  1.00 25.00           C
ATOM     53  CA  ALA    53       7.855  62.085  23.638  1.00 25.00           C
ATOM     54  CA  ARG    54       9.414  62.013  20.140  1.00 25.00           C
ATOM     55  CA  ARG    55      11.721  64.921  21.082  1.00 25.00           C
ATOM     56  CA  PHE    56      12.767  63.089  24.277  1.00 25.00           C
ATOM     57  CA  LEU    57      13.501  59.923  22.253  1.00 25.00           C
ATOM     58  CA  LEU    58      15.605  61.960  19.785  1.00 25.00           C
ATOM     59  CA  THR    59      17.545  63.524  22.693  1.00 25.00           C
ATOM     60  CA  LEU    60      18.172  60.050  24.176  1.00 25.00           C
ATOM     61  CA  VAL    61      19.421  58.798  20.779  1.00 25.00           C
ATOM     62  CA  GLU    62      21.766  61.814  20.502  1.00 25.00           C
ATOM     63  CA  LEU    63      20.314  62.060  17.009  1.00 25.00           C
ATOM     64  CA  GLY    64      20.029  58.995  14.744  1.00 25.00           C
ATOM     65  CA  TYR    65      20.657  55.808  16.813  1.00 25.00           C
ATOM     66  CA  VAL    66      17.478  54.187  18.228  1.00 25.00           C
ATOM     67  CA  ALA    67      17.334  53.659  22.002  1.00 25.00           C
ATOM     68  CA  THR    68      18.907  50.903  24.169  1.00 25.00           C
ATOM     69  CA  ASP    69      21.522  49.330  26.440  1.00 25.00           C
ATOM     70  CA  GLY    70      22.772  45.860  25.475  1.00 25.00           C
ATOM     71  CA  SER    71      23.471  46.264  21.787  1.00 25.00           C
ATOM     72  CA  ALA    72      19.768  46.335  21.119  1.00 25.00           C
ATOM     73  CA  PHE    73      16.735  48.366  20.098  1.00 25.00           C
ATOM     74  CA  TRP    74      17.422  48.280  16.391  1.00 25.00           C
ATOM     75  CA  LEU    75      16.396  51.311  14.261  1.00 25.00           C
ATOM     76  CA  THR    76      17.133  54.468  12.207  1.00 25.00           C
ATOM     77  CA  PRO    77      14.257  56.293  13.902  1.00 25.00           C
TER
END
