
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0311TS168_2-D1
# Molecule2: number of CA atoms   64 (  486),  selected   64 , name T0311_D1.pdb
# PARAMETERS: T0311TS168_2-D1.T0311_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:    62         8 - 69          4.89     5.42
  LCS_AVERAGE:     94.63

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29        22 - 50          1.96     6.92
  LCS_AVERAGE:     34.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        47 - 60          0.84     8.66
  LONGEST_CONTINUOUS_SEGMENT:    14        48 - 61          0.98     8.93
  LCS_AVERAGE:     17.72

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:   64
LCS_GDT     R       8     R       8      3   16   62     0    3    3    6   12   27   33   37   45   51   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     P       9     P       9     12   16   62    12   12   12   14   14   28   35   40   47   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     G      10     G      10     12   16   62    12   12   15   22   28   32   38   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     D      11     D      11     12   16   62    12   12   12   21   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     I      12     I      12     12   16   62    12   12   12   14   23   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     I      13     I      13     12   16   62    12   12   12   16   26   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     Q      14     Q      14     12   16   62    12   12   12   20   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     E      15     E      15     12   16   62    12   12   12   14   18   28   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     S      16     S      16     12   16   62    12   12   12   14   18   28   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      17     L      17     12   16   62    12   12   12   19   26   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     D      18     D      18     12   16   62    12   12   12   14   16   21   28   37   47   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     E      19     E      19     12   16   62    12   12   12   14   16   21   27   34   39   49   53   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      20     L      20     12   16   62    12   12   12   14   18   26   32   40   47   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     N      21     N      21      4   24   62     3    4    8   16   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     V      22     V      22     10   29   62     3    4   16   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     S      23     S      23     13   29   62     3   11   16   22   26   32   38   43   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      24     L      24     13   29   62     8   12   18   22   26   31   38   42   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     R      25     R      25     13   29   62     8   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     E      26     E      26     13   29   62     8   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     F      27     F      27     13   29   62     8   13   18   22   28   33   38   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      28     A      28     13   29   62     8   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     R      29     R      29     13   29   62     8   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      30     A      30     13   29   62     8   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     M      31     M      31     13   29   62     8   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     E      32     E      32     13   29   62     4   11   16   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     I      33     I      33     13   29   62     4    7   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      34     A      34     13   29   62     4    4   14   20   26   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     P      35     P      35     13   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     S      36     S      36     11   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     T      37     T      37     11   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      38     A      38     11   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     S      39     S      39     11   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     R      40     R      40     11   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      41     L      41     11   29   62     9   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      42     L      42     11   29   62     9   10   16   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     T      43     T      43     11   29   62     9   10   15   22   28   33   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     G      44     G      44      3   29   62     3    3    3   10   18   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     K      45     K      45      3   29   62     3   10   15   21   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      46     A      46     10   29   62     4    6   10   13   17   27   36   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      47     A      47     14   29   62     4    9   16   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      48     L      48     14   29   62     6   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     T      49     T      49     14   29   62     7   13   18   22   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     P      50     P      50     14   29   62     9   12   14   15   24   33   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     E      51     E      51     14   19   62     9   12   14   15   20   31   38   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     M      52     M      52     14   19   62     9   12   14   15   24   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     A      53     A      53     14   19   62     9   12   14   15   24   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     I      54     I      54     14   19   62     9   12   14   15   18   26   34   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     K      55     K      55     14   19   62     9   12   14   15   17   24   32   39   47   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     L      56     L      56     14   19   62     9   12   14   15   18   26   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     S      57     S      57     14   19   62     9   12   14   15   17   26   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     V      58     V      58     14   19   62     9   12   14   15   17   22   29   35   44   50   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     V      59     V      59     14   19   62     9   12   14   15   17   19   28   34   41   49   54   57   57   58   58   59   60   60   61   62 
LCS_GDT     I      60     I      60     14   19   62     4   11   14   15   21   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     G      61     G      61     14   19   62     4    5   12   15   18   26   36   44   48   52   55   57   57   58   58   59   60   60   61   61 
LCS_GDT     S      62     S      62     13   19   62     4   10   12   15   17   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     S      63     S      63      5   19   62     4    5   12   19   28   34   39   44   48   52   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     P      64     P      64      8   19   62     8    8    8    8   13   22   29   37   46   51   55   57   57   58   58   59   60   60   61   62 
LCS_GDT     Q      65     Q      65      8    8   62     8    8    8    8   10   12   12   14   23   30   32   40   50   52   57   59   60   60   61   62 
LCS_GDT     M      66     M      66      8    8   62     8    8    8    8   10   12   12   14   18   25   32   37   43   51   54   58   60   60   61   62 
LCS_GDT     W      67     W      67      8    8   62     8    8    8    8   10   12   12   21   34   41   49   55   56   58   58   59   60   60   61   62 
LCS_GDT     L      68     L      68      8    8   62     8    8    8    8   10   12   12   14   16   19   20   24   25   37   44   45   58   60   61   62 
LCS_GDT     N      69     N      69      8    8   62     8    8    8    8   10   12   12   14   16   16   20   24   24   26   28   31   31   37   40   53 
LCS_GDT     L      70     L      70      8    8   16     8    8    8    8   10   12   12   14   16   16   20   24   24   26   28   31   31   60   60   62 
LCS_GDT     Q      71     Q      71      8    8   16     8    8    8    8   10   12   12   14   16   16   19   24   24   26   28   31   31   36   48   62 
LCS_AVERAGE  LCS_A:  48.80  (  17.72   34.06   94.63 )

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     18     22     28     34     39     44     48     52     55     57     57     58     58     59     60     60     61     62 
GDT PERCENT_CA  18.75  20.31  28.12  34.38  43.75  53.12  60.94  68.75  75.00  81.25  85.94  89.06  89.06  90.62  90.62  92.19  93.75  93.75  95.31  96.88
GDT RMS_LOCAL    0.23   0.68   0.97   1.19   1.76   2.29   2.55   2.75   2.90   3.14   3.38   3.51   3.51   3.68   3.68   3.97   4.22   4.22   4.49   5.05
GDT RMS_ALL_CA  11.55   7.21   7.26   7.17   6.28   6.25   6.22   6.24   6.22   6.09   5.91   5.89   5.89   5.79   5.79   5.66   5.57   5.57   5.50   5.39

#      Molecule1      Molecule2       DISTANCE
LGA    R       8      R       8          7.065
LGA    P       9      P       9          5.330
LGA    G      10      G      10          4.711
LGA    D      11      D      11          1.488
LGA    I      12      I      12          2.329
LGA    I      13      I      13          2.704
LGA    Q      14      Q      14          1.665
LGA    E      15      E      15          3.190
LGA    S      16      S      16          3.447
LGA    L      17      L      17          0.932
LGA    D      18      D      18          4.557
LGA    E      19      E      19          6.084
LGA    L      20      L      20          4.638
LGA    N      21      N      21          2.755
LGA    V      22      V      22          3.675
LGA    S      23      S      23          4.626
LGA    L      24      L      24          5.078
LGA    R      25      R      25          3.203
LGA    E      26      E      26          3.265
LGA    F      27      F      27          3.878
LGA    A      28      A      28          2.440
LGA    R      29      R      29          1.684
LGA    A      30      A      30          2.733
LGA    M      31      M      31          2.245
LGA    E      32      E      32          1.761
LGA    I      33      I      33          1.189
LGA    A      34      A      34          3.388
LGA    P      35      P      35          3.410
LGA    S      36      S      36          2.869
LGA    T      37      T      37          2.176
LGA    A      38      A      38          2.626
LGA    S      39      S      39          2.920
LGA    R      40      R      40          2.330
LGA    L      41      L      41          2.452
LGA    L      42      L      42          3.111
LGA    T      43      T      43          3.436
LGA    G      44      G      44          2.271
LGA    K      45      K      45          2.835
LGA    A      46      A      46          4.756
LGA    A      47      A      47          2.850
LGA    L      48      L      48          1.375
LGA    T      49      T      49          1.028
LGA    P      50      P      50          3.506
LGA    E      51      E      51          3.670
LGA    M      52      M      52          2.658
LGA    A      53      A      53          2.297
LGA    I      54      I      54          3.962
LGA    K      55      K      55          4.517
LGA    L      56      L      56          3.329
LGA    S      57      S      57          3.352
LGA    V      58      V      58          5.382
LGA    V      59      V      59          5.519
LGA    I      60      I      60          2.453
LGA    G      61      G      61          3.921
LGA    S      62      S      62          3.103
LGA    S      63      S      63          2.275
LGA    P      64      P      64          7.129
LGA    Q      65      Q      65         13.790
LGA    M      66      M      66         14.047
LGA    W      67      W      67         10.043
LGA    L      68      L      68         15.146
LGA    N      69      N      69         19.490
LGA    L      70      L      70         16.802
LGA    Q      71      Q      71         17.683

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   64   64    4.0     44    2.75    53.906    52.758     1.544

LGA_LOCAL      RMSD =  2.750  Number of atoms =   44  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.146  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  5.384  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.942645 * X  +   0.216509 * Y  +  -0.254055 * Z  +  31.344357
  Y_new =  -0.190577 * X  +   0.275779 * Y  +   0.942139 * Z  +   5.075263
  Z_new =   0.274045 * X  +   0.936520 * Y  +  -0.218700 * Z  +  13.736865 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.800209   -1.341384  [ DEG:   103.1444    -76.8556 ]
  Theta =  -0.277597   -2.863996  [ DEG:   -15.9051   -164.0949 ]
  Phi   =  -2.942109    0.199484  [ DEG:  -168.5704     11.4296 ]
 
# 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: T0311TS168_2-D1                               
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311TS168_2-D1.T0311_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   64   64   4.0   44   2.75  52.758     5.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS168_2-D1
PFRMAT TS
TARGET T0311
MODEL 2
PARENT N/A
ATOM      8  CA  ARG     8      40.933   7.852  10.883  1.00 25.00           C
ATOM      9  CA  PRO     9      37.647   7.008  12.717  1.00 25.00           C
ATOM     10  CA  GLY    10      35.785   3.836  11.652  1.00 25.00           C
ATOM     11  CA  ASP    11      36.398   2.288  15.100  1.00 25.00           C
ATOM     12  CA  ILE    12      35.081   5.464  16.787  1.00 25.00           C
ATOM     13  CA  ILE    13      31.957   5.374  14.572  1.00 25.00           C
ATOM     14  CA  GLN    14      31.393   1.695  15.473  1.00 25.00           C
ATOM     15  CA  GLU    15      31.745   2.527  19.194  1.00 25.00           C
ATOM     16  CA  SER    16      29.220   5.383  18.820  1.00 25.00           C
ATOM     17  CA  LEU    17      26.778   3.025  17.047  1.00 25.00           C
ATOM     18  CA  ASP    18      27.184   0.453  19.857  1.00 25.00           C
ATOM     19  CA  GLU    19      26.518   3.170  22.473  1.00 25.00           C
ATOM     20  CA  LEU    20      23.030   3.537  20.924  1.00 25.00           C
ATOM     21  CA  ASN    21      19.721   5.195  20.212  1.00 25.00           C
ATOM     22  CA  VAL    22      20.788   4.942  16.558  1.00 25.00           C
ATOM     23  CA  SER    23      20.109   1.244  17.093  1.00 25.00           C
ATOM     24  CA  LEU    24      23.130  -0.085  15.158  1.00 25.00           C
ATOM     25  CA  ARG    25      21.268  -3.406  14.744  1.00 25.00           C
ATOM     26  CA  GLU    26      18.662  -1.696  12.519  1.00 25.00           C
ATOM     27  CA  PHE    27      21.450  -0.159  10.391  1.00 25.00           C
ATOM     28  CA  ALA    28      23.109  -3.593  10.041  1.00 25.00           C
ATOM     29  CA  ARG    29      19.766  -5.127   8.977  1.00 25.00           C
ATOM     30  CA  ALA    30      19.289  -2.350   6.383  1.00 25.00           C
ATOM     31  CA  MET    31      22.820  -2.969   5.035  1.00 25.00           C
ATOM     32  CA  GLU    32      23.462  -6.599   5.672  1.00 25.00           C
ATOM     33  CA  ILE    33      24.551  -8.914   8.419  1.00 25.00           C
ATOM     34  CA  ALA    34      23.353  -8.705  12.005  1.00 25.00           C
ATOM     35  CA  PRO    35      25.837  -6.829  14.186  1.00 25.00           C
ATOM     36  CA  SER    36      28.822  -9.218  13.968  1.00 25.00           C
ATOM     37  CA  THR    37      29.546  -8.029  10.400  1.00 25.00           C
ATOM     38  CA  ALA    38      29.395  -4.381  11.560  1.00 25.00           C
ATOM     39  CA  SER    39      31.809  -5.167  14.427  1.00 25.00           C
ATOM     40  CA  ARG    40      34.206  -6.871  11.975  1.00 25.00           C
ATOM     41  CA  LEU    41      34.045  -3.823   9.660  1.00 25.00           C
ATOM     42  CA  LEU    42      34.788  -1.508  12.620  1.00 25.00           C
ATOM     43  CA  THR    43      37.777  -3.689  13.608  1.00 25.00           C
ATOM     44  CA  GLY    44      39.323  -7.166  13.890  1.00 25.00           C
ATOM     45  CA  LYS    45      39.408  -7.862  10.168  1.00 25.00           C
ATOM     46  CA  ALA    46      39.971  -4.359   8.797  1.00 25.00           C
ATOM     47  CA  ALA    47      40.034  -3.943   5.052  1.00 25.00           C
ATOM     48  CA  LEU    48      36.577  -2.625   4.250  1.00 25.00           C
ATOM     49  CA  THR    49      35.148  -4.051   1.060  1.00 25.00           C
ATOM     50  CA  PRO    50      31.790  -3.963  -0.797  1.00 25.00           C
ATOM     51  CA  GLU    51      29.351  -5.631   1.640  1.00 25.00           C
ATOM     52  CA  MET    52      31.615  -4.695   4.585  1.00 25.00           C
ATOM     53  CA  ALA    53      31.764  -1.073   3.349  1.00 25.00           C
ATOM     54  CA  ILE    54      27.947  -0.988   3.059  1.00 25.00           C
ATOM     55  CA  LYS    55      27.620  -2.361   6.619  1.00 25.00           C
ATOM     56  CA  LEU    56      30.049   0.310   7.898  1.00 25.00           C
ATOM     57  CA  SER    57      28.029   3.033   6.117  1.00 25.00           C
ATOM     58  CA  VAL    58      24.800   1.696   7.681  1.00 25.00           C
ATOM     59  CA  VAL    59      26.439   1.715  11.143  1.00 25.00           C
ATOM     60  CA  ILE    60      27.597   5.326  10.601  1.00 25.00           C
ATOM     61  CA  GLY    61      30.283   6.987   8.382  1.00 25.00           C
ATOM     62  CA  SER    62      31.106   7.478   4.660  1.00 25.00           C
ATOM     63  CA  SER    63      29.046   8.708   1.670  1.00 25.00           C
ATOM     64  CA  PRO    64      25.576   7.248   1.313  1.00 25.00           C
ATOM     65  CA  GLN    65      22.566   9.345   2.417  1.00 25.00           C
ATOM     66  CA  MET    66      22.151   7.152   5.531  1.00 25.00           C
ATOM     67  CA  TRP    67      25.869   7.566   6.347  1.00 25.00           C
ATOM     68  CA  LEU    68      25.558  11.363   5.954  1.00 25.00           C
ATOM     69  CA  ASN    69      22.514  11.379   8.277  1.00 25.00           C
ATOM     70  CA  LEU    70      24.447   9.325  10.867  1.00 25.00           C
ATOM     71  CA  GLN    71      27.387  11.771  10.648  1.00 25.00           C
TER
END
