
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0324TS393_2-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS393_2-D2.T0324_D2.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:    38        44 - 81          4.92    12.40
  LCS_AVERAGE:     47.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23        56 - 78          1.61    11.00
  LCS_AVERAGE:     24.54

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        62 - 78          0.82    10.92
  LCS_AVERAGE:     16.90

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:   65
LCS_GDT     S      17     S      17      3   15   21     0    3    6    8   11   16   17   19   22   26   30   33   35   38   41   42   43   44   46   47 
LCS_GDT     Q      18     Q      18     14   15   21     9   13   14   14   14   15   17   19   22   24   30   32   35   38   41   42   43   44   46   47 
LCS_GDT     P      19     P      19     14   15   21    10   13   14   14   14   16   17   19   21   24   30   33   35   38   41   42   43   44   46   47 
LCS_GDT     A      20     A      20     14   15   21    10   13   14   14   14   16   17   19   22   26   33   34   36   38   41   42   43   44   46   47 
LCS_GDT     Y      21     Y      21     14   15   21    10   13   14   14   14   19   24   26   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     T      22     T      22     14   15   21    10   13   14   19   20   21   24   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     T      23     T      23     14   15   21    10   13   14   14   14   16   26   28   29   30   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     V      24     V      24     14   15   21    10   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     M      25     M      25     14   15   21    10   13   14   14   14   16   17   19   23   26   29   32   36   40   41   41   42   44   46   47 
LCS_GDT     R      26     R      26     14   15   21    10   13   14   14   14   16   19   21   23   28   28   32   34   36   39   41   42   43   44   44 
LCS_GDT     E      27     E      27     14   15   21    10   13   14   14   14   16   17   19   21   24   24   26   30   31   35   39   40   42   44   44 
LCS_GDT     V      28     V      28     14   15   21    10   13   14   14   14   16   17   19   21   22   22   24   30   30   31   34   38   40   44   44 
LCS_GDT     L      29     L      29     14   15   21     9   13   14   14   14   16   17   19   21   22   22   23   24   27   31   34   34   36   37   43 
LCS_GDT     A      30     A      30     14   15   21     9   13   14   14   14   16   17   19   21   22   22   25   30   30   31   34   34   35   36   38 
LCS_GDT     T      31     T      31     14   15   21     4   10   14   14   14   16   17   19   21   22   22   23   24   27   28   29   31   33   35   37 
LCS_GDT     Y      32     Y      32      3   15   22     3    3    4    5    7    9   16   19   21   22   22   23   24   25   28   29   32   33   35   37 
LCS_GDT     G      33     G      33      3    6   22     3    3    5    8   11   16   17   19   21   22   22   23   24   27   28   29   31   33   34   37 
LCS_GDT     K      34     K      34      3    6   22     3    3    4    5    9   14   17   19   21   22   22   24   30   30   31   31   32   34   36   37 
LCS_GDT     P      35     P      35      3    6   22     3    3    4    5    7    9    9   11   13   21   21   24   30   30   31   31   32   34   34   37 
LCS_GDT     F      36     F      36      3    6   22     3    3    4    5    7    9   11   13   14   16   19   21   30   30   31   34   34   35   36   39 
LCS_GDT     S      37     S      37      3   11   22     3    3    4    9   10   12   12   13   14   16   18   20   23   28   31   34   34   36   38   40 
LCS_GDT     P      38     P      38      9   11   22     7    9    9   10   10   12   17   17   21   24   24   26   29   30   33   37   38   41   44   44 
LCS_GDT     A      39     A      39      9   11   22     7    9    9   10   10   13   18   18   20   24   24   27   32   35   37   39   40   42   44   44 
LCS_GDT     Q      40     Q      40      9   11   22     7    9    9   10   10   12   12   13   14   16   20   27   32   35   37   39   40   42   44   44 
LCS_GDT     A      41     A      41      9   11   22     7    9    9   10   10   12   12   14   23   24   27   31   34   36   38   41   42   43   44   44 
LCS_GDT     Q      42     Q      42      9   11   22     8   15   19   21   24   25   26   28   29   30   30   32   36   39   41   41   42   43   44   44 
LCS_GDT     K      43     K      43      9   11   22     7    9   14   18   19   22   24   28   29   30   31   36   38   40   41   41   42   43   44   46 
LCS_GDT     T      44     T      44      9   11   38     7    9    9   10   10   12   15   17   23   25   28   31   37   40   41   41   42   43   46   47 
LCS_GDT     F      45     F      45      9   11   38     4    9   13   19   20   21   23   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     P      46     P      46      9   11   38     3    9    9   14   19   21   24   26   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     M      47     M      47      3   11   38     3    3    5    7   19   21   23   26   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     A      48     A      48      3   10   38     3    3    5    5   10   11   12   13   14   16   19   22   34   37   40   41   43   44   46   47 
LCS_GDT     A      49     A      49      9   10   38     9    9    9    9    9   10   12   13   14   16   19   26   29   30   33   37   43   44   46   47 
LCS_GDT     E      50     E      50      9   10   38     9    9    9    9   10   11   11   12   14   22   24   26   29   30   31   32   33   41   45   47 
LCS_GDT     Q      51     Q      51      9   10   38     9    9    9    9   10   11   14   17   21   22   24   26   36   38   40   42   43   44   46   47 
LCS_GDT     A      52     A      52      9   10   38     9    9    9   14   19   21   24   26   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     M      53     M      53      9   10   38     9    9    9    9   10   11   19   23   26   29   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     T      54     T      54      9   10   38     9    9    9   16   20   21   24   26   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     E      55     E      55      9   10   38     9    9    9    9   10   11   11   12   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     L      56     L      56      9   23   38     9    9    9    9   24   25   26   28   29   30   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     G      57     G      57      9   23   38     9   10   19   21   24   25   26   28   29   30   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     I      58     I      58      5   23   38     3   10   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     A      59     A      59      5   23   38     3    3    6   10   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     A      60     A      60      5   23   38     4    4    7   16   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     S      61     S      61     14   23   38     4    4    6   12   20   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     E      62     E      62     17   23   38     9   14   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     F      63     F      63     17   23   38    12   15   18   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     D      64     D      64     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     H      65     H      65     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     F      66     F      66     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     Q      67     Q      67     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     A      68     A      68     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     Q      69     Q      69     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     Y      70     Y      70     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     E      71     E      71     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     D      72     D      72     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     V      73     V      73     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     M      74     M      74     17   23   38    12   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     A      75     A      75     17   23   38    10   15   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     S      76     S      76     17   23   38     4   14   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     H      77     H      77     17   23   38     4   14   19   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     Y      78     Y      78     17   23   38     3   13   18   21   24   25   26   28   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     D      79     D      79      4   19   38     3    4    4    7    9   14   20   23   29   32   33   36   38   40   41   42   43   44   46   47 
LCS_GDT     Q      80     Q      80      4   18   38     3    4    4    5    9   12   15   22   26   27   32   36   38   40   41   42   43   44   46   47 
LCS_GDT     I      81     I      81      3    6   38     3    3    4    4    7    9   14   19   26   32   33   36   38   40   41   42   43   44   46   47 
LCS_AVERAGE  LCS_A:  29.78  (  16.90   24.54   47.88 )

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     15     19     21     24     25     26     28     29     32     33     36     38     40     41     42     43     44     46     47 
GDT PERCENT_CA  18.46  23.08  29.23  32.31  36.92  38.46  40.00  43.08  44.62  49.23  50.77  55.38  58.46  61.54  63.08  64.62  66.15  67.69  70.77  72.31
GDT RMS_LOCAL    0.26   0.64   1.09   1.16   1.51   1.60   1.72   2.28   2.37   3.09   3.19   3.54   3.82   4.08   4.32   4.48   4.63   4.81   5.14   5.30
GDT RMS_ALL_CA  11.02  10.68  10.81  10.78  10.91  10.94  10.98  10.99  10.92  12.15  12.10  11.81  11.56  11.40  12.46  12.63  12.77  12.86  12.55  12.66

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17         14.945
LGA    Q      18      Q      18         15.301
LGA    P      19      P      19         12.280
LGA    A      20      A      20          9.596
LGA    Y      21      Y      21          7.880
LGA    T      22      T      22          3.986
LGA    T      23      T      23          3.643
LGA    V      24      V      24          2.058
LGA    M      25      M      25          7.006
LGA    R      26      R      26          7.577
LGA    E      27      E      27         10.651
LGA    V      28      V      28         13.465
LGA    L      29      L      29         15.932
LGA    A      30      A      30         18.486
LGA    T      31      T      31         21.676
LGA    Y      32      Y      32         21.125
LGA    G      33      G      33         26.687
LGA    K      34      K      34         22.503
LGA    P      35      P      35         24.814
LGA    F      36      F      36         19.552
LGA    S      37      S      37         20.109
LGA    P      38      P      38         15.180
LGA    A      39      A      39         12.002
LGA    Q      40      Q      40         11.985
LGA    A      41      A      41          8.980
LGA    Q      42      Q      42          3.916
LGA    K      43      K      43          3.991
LGA    T      44      T      44          8.830
LGA    F      45      F      45          5.492
LGA    P      46      P      46         10.301
LGA    M      47      M      47         10.747
LGA    A      48      A      48         17.108
LGA    A      49      A      49         16.147
LGA    E      50      E      50         17.053
LGA    Q      51      Q      51         14.874
LGA    A      52      A      52          8.630
LGA    M      53      M      53          7.416
LGA    T      54      T      54          7.359
LGA    E      55      E      55          6.901
LGA    L      56      L      56          2.543
LGA    G      57      G      57          2.869
LGA    I      58      I      58          1.864
LGA    A      59      A      59          3.283
LGA    A      60      A      60          3.160
LGA    S      61      S      61          3.325
LGA    E      62      E      62          1.293
LGA    F      63      F      63          1.906
LGA    D      64      D      64          1.700
LGA    H      65      H      65          1.319
LGA    F      66      F      66          1.456
LGA    Q      67      Q      67          1.775
LGA    A      68      A      68          1.708
LGA    Q      69      Q      69          1.603
LGA    Y      70      Y      70          1.856
LGA    E      71      E      71          1.971
LGA    D      72      D      72          2.069
LGA    V      73      V      73          2.399
LGA    M      74      M      74          2.015
LGA    A      75      A      75          1.635
LGA    S      76      S      76          1.271
LGA    H      77      H      77          0.826
LGA    Y      78      Y      78          0.648
LGA    D      79      D      79          4.856
LGA    Q      80      Q      80          6.677
LGA    I      81      I      81          7.242

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     28    2.17    40.769    37.708     1.234

LGA_LOCAL      RMSD =  2.168  Number of atoms =   28  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.957  Number of atoms =   65 
Std_ALL_ATOMS  RMSD = 10.434  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.799969 * X  +   0.458005 * Y  +  -0.387662 * Z  +  26.923298
  Y_new =   0.598993 * X  +   0.571364 * Y  +  -0.561027 * Z  +  15.894949
  Z_new =  -0.035457 * X  +  -0.681011 * Y  +  -0.731415 * Z  +  -4.226102 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.391865    0.749727  [ DEG:  -137.0438     42.9562 ]
  Theta =   0.035464    3.106129  [ DEG:     2.0319    177.9681 ]
  Phi   =   2.498879   -0.642714  [ DEG:   143.1752    -36.8248 ]
 
# 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: T0324TS393_2-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0324TS393_2-D2.T0324_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   65   65   4.0   28   2.17  37.708    10.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS393_2-D2
PFRMAT TS
TARGET T0324
MODEL 2
PARENT N/A
ATOM     17  CA  SER    17      25.265  14.100  -0.603  1.00 25.00           C
ATOM     18  CA  GLN    18      22.615  11.318  -0.790  1.00 25.00           C
ATOM     19  CA  PRO    19      19.317  11.996   1.035  1.00 25.00           C
ATOM     20  CA  ALA    20      20.655  10.234   4.160  1.00 25.00           C
ATOM     21  CA  TYR    21      23.855  12.331   4.003  1.00 25.00           C
ATOM     22  CA  THR    22      21.773  15.529   3.684  1.00 25.00           C
ATOM     23  CA  THR    23      19.663  14.485   6.705  1.00 25.00           C
ATOM     24  CA  VAL    24      22.845  13.815   8.727  1.00 25.00           C
ATOM     25  CA  MET    25      24.217  17.257   7.757  1.00 25.00           C
ATOM     26  CA  ARG    26      20.925  18.897   8.825  1.00 25.00           C
ATOM     27  CA  GLU    27      21.064  17.049  12.177  1.00 25.00           C
ATOM     28  CA  VAL    28      24.674  18.216  12.697  1.00 25.00           C
ATOM     29  CA  LEU    29      23.648  21.822  11.917  1.00 25.00           C
ATOM     30  CA  ALA    30      20.760  21.568  14.421  1.00 25.00           C
ATOM     31  CA  THR    31      23.157  20.214  17.085  1.00 25.00           C
ATOM     32  CA  TYR    32      19.958  20.174  19.191  1.00 25.00           C
ATOM     33  CA  GLY    33      20.516  23.371  21.257  1.00 25.00           C
ATOM     34  CA  LYS    34      19.848  25.467  18.188  1.00 25.00           C
ATOM     35  CA  PRO    35      22.319  27.901  19.881  1.00 25.00           C
ATOM     36  CA  PHE    36      24.552  27.344  16.813  1.00 25.00           C
ATOM     37  CA  SER    37      25.744  30.759  15.829  1.00 25.00           C
ATOM     38  CA  PRO    38      22.034  31.369  15.014  1.00 25.00           C
ATOM     39  CA  ALA    39      18.464  32.049  13.805  1.00 25.00           C
ATOM     40  CA  GLN    40      19.715  32.338  10.197  1.00 25.00           C
ATOM     41  CA  ALA    41      21.599  29.023  10.559  1.00 25.00           C
ATOM     42  CA  GLN    42      18.443  27.351  11.940  1.00 25.00           C
ATOM     43  CA  LYS    43      16.404  28.713   8.998  1.00 25.00           C
ATOM     44  CA  THR    44      19.017  27.378   6.537  1.00 25.00           C
ATOM     45  CA  PHE    45      18.898  23.947   8.233  1.00 25.00           C
ATOM     46  CA  PRO    46      15.532  23.312   6.581  1.00 25.00           C
ATOM     47  CA  MET    47      12.575  25.507   7.534  1.00 25.00           C
ATOM     48  CA  ALA    48      10.531  25.164   4.413  1.00 25.00           C
ATOM     49  CA  ALA    49      11.703  21.769   3.217  1.00 25.00           C
ATOM     50  CA  GLU    50       7.936  21.093   3.098  1.00 25.00           C
ATOM     51  CA  GLN    51       8.591  17.321   3.003  1.00 25.00           C
ATOM     52  CA  ALA    52      10.940  17.628   6.011  1.00 25.00           C
ATOM     53  CA  MET    53       8.280  19.615   7.918  1.00 25.00           C
ATOM     54  CA  THR    54       5.663  16.939   7.105  1.00 25.00           C
ATOM     55  CA  GLU    55       8.043  14.203   8.338  1.00 25.00           C
ATOM     56  CA  LEU    56       8.642  16.150  11.580  1.00 25.00           C
ATOM     57  CA  GLY    57       4.901  16.434  12.353  1.00 25.00           C
ATOM     58  CA  ILE    58       5.024  12.624  12.086  1.00 25.00           C
ATOM     59  CA  ALA    59       3.758  10.936  15.321  1.00 25.00           C
ATOM     60  CA  ALA    60       4.534   8.075  17.719  1.00 25.00           C
ATOM     61  CA  SER    61       6.390   4.815  16.952  1.00 25.00           C
ATOM     62  CA  GLU    62       7.187   6.069  13.423  1.00 25.00           C
ATOM     63  CA  PHE    63       8.499   9.366  14.865  1.00 25.00           C
ATOM     64  CA  ASP    64      10.692   7.438  17.343  1.00 25.00           C
ATOM     65  CA  HIS    65      12.064   5.283  14.491  1.00 25.00           C
ATOM     66  CA  PHE    66      12.840   8.431  12.452  1.00 25.00           C
ATOM     67  CA  GLN    67      14.644   9.965  15.462  1.00 25.00           C
ATOM     68  CA  ALA    68      16.687   6.756  15.904  1.00 25.00           C
ATOM     69  CA  GLN    69      17.619   6.808  12.190  1.00 25.00           C
ATOM     70  CA  TYR    70      18.698  10.470  12.488  1.00 25.00           C
ATOM     71  CA  GLU    71      20.836   9.619  15.548  1.00 25.00           C
ATOM     72  CA  ASP    72      22.460   6.723  13.638  1.00 25.00           C
ATOM     73  CA  VAL    73      23.203   9.053  10.690  1.00 25.00           C
ATOM     74  CA  MET    74      24.766  11.611  13.073  1.00 25.00           C
ATOM     75  CA  ALA    75      26.927   8.865  14.643  1.00 25.00           C
ATOM     76  CA  SER    76      28.058   7.732  11.164  1.00 25.00           C
ATOM     77  CA  HIS    77      28.951  11.343  10.252  1.00 25.00           C
ATOM     78  CA  TYR    78      30.955  11.694  13.497  1.00 25.00           C
ATOM     79  CA  ASP    79      32.812   8.432  12.731  1.00 25.00           C
ATOM     80  CA  GLN    80      35.648   9.691  10.528  1.00 25.00           C
ATOM     81  CA  ILE    81      33.585  11.548   7.958  1.00 25.00           C
TER
END
