
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0349TS599_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS599_3-D1.T0349_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:    31        27 - 72          4.89    14.25
  LCS_AVERAGE:     46.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        11 - 29          1.62    12.63
  LONGEST_CONTINUOUS_SEGMENT:    19        51 - 69          1.85    11.37
  LCS_AVERAGE:     26.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        12 - 28          0.95    12.42
  LCS_AVERAGE:     18.25

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:   57
LCS_GDT     M       1     M       1      3    4    8     3    3    3    3    6    8    8    8   10   10   12   13   17   20   21   23   24   24   31   31 
LCS_GDT     R       2     R       2      3    4    8     3    3    3    4    6    8    8    8   10   10   12   13   17   20   21   23   24   26   29   30 
LCS_GDT     E       3     E       3      3    4   10     3    3    3    5    5    5    6    6    7    9   10   13   17   20   21   23   24   26   29   30 
LCS_GDT     L       4     L       4      3    4   15     3    3    3    5    5    5    6    6    7    9   10   12   17   20   21   23   24   26   31   31 
LCS_GDT     L       5     L       5      3    4   21     3    3    3    5    5    5    6   10   12   17   18   19   20   20   21   23   24   27   31   34 
LCS_GDT     R       6     R       6      5    6   21     0    3    5    6    6    8   10   11   13   17   18   19   20   20   21   23   24   28   33   36 
LCS_GDT     T       7     T       7      5    6   23     4    5    5    6    6    8   10   11   13   17   18   19   20   24   29   33   38   40   43   46 
LCS_GDT     N       8     N       8      5    6   23     4    5    5    6    6    8   10   15   21   23   26   27   29   31   33   36   38   41   43   46 
LCS_GDT     D       9     D       9      5    6   23     4    5    5    6    6   15   18   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     A      10     A      10      5    6   23     4    6   10   14   15   15   18   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     V      11     V      11     14   19   23     3    7   11   15   18   18   20   20   22   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     L      12     L      12     17   19   23     4   14   16   17   18   18   20   20   22   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     L      13     L      13     17   19   23    12   14   16   17   18   18   20   20   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     S      14     S      14     17   19   23    12   14   16   17   18   18   20   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     A      15     A      15     17   19   23    12   14   16   17   18   18   20   20   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     V      16     V      16     17   19   23    12   14   16   17   18   18   20   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     G      17     G      17     17   19   23    12   14   16   17   18   18   20   20   22   23   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     A      18     A      18     17   19   23    12   14   16   17   18   18   20   20   22   23   26   28   31   34   37   38   40   41   43   46 
LCS_GDT     L      19     L      19     17   19   23    12   14   16   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     L      20     L      20     17   19   23    12   14   16   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     D      21     D      21     17   19   23    12   14   16   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     G      22     G      22     17   19   23    12   14   16   17   18   18   20   20   22   23   25   28   31   33   37   38   40   41   43   46 
LCS_GDT     A      23     A      23     17   19   23    12   14   16   17   18   18   20   20   22   23   25   28   31   33   37   38   40   41   43   46 
LCS_GDT     D      24     D      24     17   19   23    10   14   16   17   18   18   20   20   22   23   25   28   31   33   37   38   40   41   43   46 
LCS_GDT     I      25     I      25     17   19   23    12   14   16   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     G      26     G      26     17   19   23     3    5   12   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     H      27     H      27     17   19   31     3   10   16   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     L      28     L      28     17   19   31     4   10   16   17   18   18   20   20   22   23   25   28   31   34   37   38   40   41   43   46 
LCS_GDT     V      29     V      29      5   19   31     3    5    6    8    9   14   20   20   21   22   22   27   31   34   37   38   40   41   43   46 
LCS_GDT     P      45     P      45      3    3   31     0    3    3    3    3    5    6    8   16   19   21   23   25   26   28   30   30   31   31   31 
LCS_GDT     R      46     R      46      5   14   31     4    6    9   11   11   14   15   17   19   20   22   24   25   26   28   30   30   31   31   31 
LCS_GDT     R      47     R      47      5   14   31     4    5    9   11   11   12   15   16   17   19   20   23   24   26   28   30   30   31   31   31 
LCS_GDT     V      48     V      48      5   14   31     4    5    9   11   12   14   15   17   19   21   23   24   29   30   31   33   35   37   40   43 
LCS_GDT     L      49     L      49      8   14   31     4    6    8   11   11   18   20   20   21   23   24   28   31   34   37   38   40   41   43   46 
LCS_GDT     V      50     V      50      8   17   31     4    7    9   11   14   15   19   20   20   22   26   29   31   34   37   38   40   41   43   46 
LCS_GDT     H      51     H      51      8   19   31     3    7   10   13   15   18   19   21   23   26   27   29   30   34   37   38   40   41   43   46 
LCS_GDT     E      52     E      52      8   19   31     3    7   10   13   16   18   19   21   23   26   27   29   30   33   36   38   40   41   43   46 
LCS_GDT     D      53     D      53     13   19   31     4   11   13   15   16   18   19   21   23   26   27   29   30   31   33   34   38   40   43   46 
LCS_GDT     D      54     D      54     13   19   31     4   11   13   15   16   18   19   21   23   26   27   29   30   31   33   35   38   41   43   46 
LCS_GDT     L      55     L      55     13   19   31     5   11   13   15   16   18   19   21   23   26   27   29   30   34   37   38   40   41   43   46 
LCS_GDT     A      56     A      56     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   30   34   37   38   40   41   43   46 
LCS_GDT     G      57     G      57     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   30   34   36   38   40   41   43   46 
LCS_GDT     A      58     A      58     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   30   34   37   38   40   41   43   46 
LCS_GDT     R      59     R      59     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     R      60     R      60     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     L      61     L      61     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   30   34   37   38   40   41   43   46 
LCS_GDT     L      62     L      62     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     T      63     T      63     13   19   31     8   11   13   15   16   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     D      64     D      64     13   19   31     5   11   13   15   16   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     A      65     A      65     13   19   31     5    9   13   15   16   18   19   21   23   26   27   29   30   34   37   38   40   41   43   46 
LCS_GDT     G      66     G      66      4   19   31     3    4    6   11   15   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     L      67     L      67      3   19   31     3    3   13   15   16   18   19   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     A      68     A      68      4   19   31     3    4   10   15   16   18   20   21   23   26   27   29   31   34   37   38   40   41   43   46 
LCS_GDT     H      69     H      69      4   19   31     3    4   12   13   16   18   19   20   22   26   27   29   30   32   36   38   40   41   43   46 
LCS_GDT     E      70     E      70      4    5   31     3    4    4    5    6   13   16   19   20   21   23   24   26   30   31   31   35   39   43   46 
LCS_GDT     L      71     L      71      4    5   31     3    4    4    5    6    8   15   19   20   21   23   24   26   26   29   36   38   41   43   46 
LCS_GDT     R      72     R      72      3    5   31     3    3    3    3    4    8   10   13   16   20   22   24   25   25   28   30   31   36   42   45 
LCS_AVERAGE  LCS_A:  30.37  (  18.25   26.56   46.29 )

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     14     16     17     18     18     20     21     23     26     27     29     31     34     37     38     40     41     43     46 
GDT PERCENT_CA  21.05  24.56  28.07  29.82  31.58  31.58  35.09  36.84  40.35  45.61  47.37  50.88  54.39  59.65  64.91  66.67  70.18  71.93  75.44  80.70
GDT RMS_LOCAL    0.38   0.48   0.83   0.95   1.25   1.25   1.75   2.63   2.89   3.17   3.28   3.65   4.53   5.25   5.40   5.50   5.73   5.95   6.24   6.61
GDT RMS_ALL_CA  12.37  12.41  12.48  12.42  12.41  12.41  12.63  11.95  11.87  12.14  11.99  11.69  11.67  10.91  11.07  11.02  10.77  10.55  10.42  10.25

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         23.612
LGA    R       2      R       2         23.805
LGA    E       3      E       3         23.597
LGA    L       4      L       4         19.476
LGA    L       5      L       5         17.998
LGA    R       6      R       6         17.560
LGA    T       7      T       7         11.676
LGA    N       8      N       8          7.384
LGA    D       9      D       9          3.075
LGA    A      10      A      10          3.318
LGA    V      11      V      11          5.819
LGA    L      12      L      12          6.246
LGA    L      13      L      13          5.461
LGA    S      14      S      14          3.929
LGA    A      15      A      15          4.896
LGA    V      16      V      16          4.408
LGA    G      17      G      17          5.997
LGA    A      18      A      18          7.338
LGA    L      19      L      19          8.518
LGA    L      20      L      20          9.647
LGA    D      21      D      21         11.702
LGA    G      22      G      22         13.095
LGA    A      23      A      23         14.633
LGA    D      24      D      24         16.026
LGA    I      25      I      25         14.177
LGA    G      26      G      26         14.554
LGA    H      27      H      27         11.802
LGA    L      28      L      28         11.877
LGA    V      29      V      29         10.268
LGA    P      45      P      45         25.954
LGA    R      46      R      46         24.582
LGA    R      47      R      47         21.293
LGA    V      48      V      48         15.600
LGA    L      49      L      49         11.846
LGA    V      50      V      50          6.749
LGA    H      51      H      51          3.993
LGA    E      52      E      52          2.340
LGA    D      53      D      53          3.704
LGA    D      54      D      54          3.819
LGA    L      55      L      55          1.320
LGA    A      56      A      56          2.838
LGA    G      57      G      57          3.365
LGA    A      58      A      58          2.215
LGA    R      59      R      59          0.760
LGA    R      60      R      60          1.686
LGA    L      61      L      61          2.485
LGA    L      62      L      62          1.921
LGA    T      63      T      63          0.882
LGA    D      64      D      64          1.058
LGA    A      65      A      65          1.107
LGA    G      66      G      66          2.463
LGA    L      67      L      67          3.714
LGA    A      68      A      68          3.882
LGA    H      69      H      69          5.700
LGA    E      70      E      70         10.914
LGA    L      71      L      71         11.593
LGA    R      72      R      72         13.595

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     21    2.63    39.474    36.042     0.771

LGA_LOCAL      RMSD =  2.625  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.590  Number of atoms =   57 
Std_ALL_ATOMS  RMSD =  9.804  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.320458 * X  +   0.749873 * Y  +   0.578790 * Z  +  -2.243942
  Y_new =  -0.764354 * X  +  -0.565609 * Y  +   0.309597 * Z  +   4.311649
  Z_new =   0.559527 * X  +  -0.343188 * Y  +   0.754422 * Z  +   7.483804 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.426923    2.714670  [ DEG:   -24.4609    155.5391 ]
  Theta =  -0.593815   -2.547778  [ DEG:   -34.0231   -145.9769 ]
  Phi   =  -1.967790    1.173803  [ DEG:  -112.7460     67.2540 ]
 
# 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: T0349TS599_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_3-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   57   57   4.0   21   2.63  36.042     9.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_3-D1
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1     -10.510  -5.409   4.855  1.00  0.00              
ATOM      2  CA  ARG     2      -9.239  -8.751   3.223  1.00  0.00              
ATOM      3  CA  GLU     3     -10.221 -12.187   2.842  1.00  0.00              
ATOM      4  CA  LEU     4      -7.531 -10.022   3.820  1.00  0.00              
ATOM      5  CA  LEU     5      -7.880 -10.591   7.608  1.00  0.00              
ATOM      6  CA  ARG     6      -8.207 -14.321   7.280  1.00  0.00              
ATOM      7  CA  THR     7      -5.239 -14.908   5.062  1.00  0.00              
ATOM      8  CA  ASN     8      -2.774 -12.497   6.727  1.00  0.00              
ATOM      9  CA  ASP     9      -2.572 -10.406   3.538  1.00  0.00              
ATOM     10  CA  ALA    10      -3.218  -6.859   4.817  1.00  0.00              
ATOM     11  CA  VAL    11      -6.529  -5.324   3.686  1.00  0.00              
ATOM     12  CA  LEU    12      -6.073  -1.699   3.875  1.00  0.00              
ATOM     13  CA  LEU    13      -8.638   0.875   4.897  1.00  0.00              
ATOM     14  CA  SER    14     -10.075  -1.284   7.711  1.00  0.00              
ATOM     15  CA  ALA    15      -6.776  -2.547   9.034  1.00  0.00              
ATOM     16  CA  VAL    16      -5.288   0.883   9.169  1.00  0.00              
ATOM     17  CA  GLY    17      -8.195   2.352  11.033  1.00  0.00              
ATOM     18  CA  ALA    18      -8.253  -0.332  13.659  1.00  0.00              
ATOM     19  CA  LEU    19      -4.503  -0.083  14.331  1.00  0.00              
ATOM     20  CA  LEU    20      -4.552   3.674  14.650  1.00  0.00              
ATOM     21  CA  ASP    21      -7.600   3.648  16.995  1.00  0.00              
ATOM     22  CA  GLY    22      -6.020   1.057  19.223  1.00  0.00              
ATOM     23  CA  ALA    23      -2.845   3.030  19.727  1.00  0.00              
ATOM     24  CA  ASP    24      -4.732   6.366  20.168  1.00  0.00              
ATOM     25  CA  ILE    25      -2.886   7.901  17.258  1.00  0.00              
ATOM     26  CA  GLY    26      -4.842   9.906  14.730  1.00  0.00              
ATOM     27  CA  HIS    27      -2.575   9.710  11.696  1.00  0.00              
ATOM     28  CA  LEU    28      -3.788  10.990   8.363  1.00  0.00              
ATOM     29  CA  VAL    29      -1.789  10.276   5.261  1.00  0.00              
ATOM     45  CA  PRO    45      -6.767  13.928  11.751  1.00  0.00              
ATOM     46  CA  ARG    46      -4.289  14.385  14.603  1.00  0.00              
ATOM     47  CA  ARG    47      -1.052  14.028  12.768  1.00  0.00              
ATOM     48  CA  VAL    48      -1.100  14.688   9.090  1.00  0.00              
ATOM     49  CA  LEU    49       1.557  13.080   6.850  1.00  0.00              
ATOM     50  CA  VAL    50       1.919  14.090   3.349  1.00  0.00              
ATOM     51  CA  HIS    51       1.028  15.536   0.020  1.00  0.00              
ATOM     52  CA  GLU    52       1.951  13.407  -2.943  1.00  0.00              
ATOM     53  CA  ASP    53       4.734  15.768  -4.158  1.00  0.00              
ATOM     54  CA  ASP    54       6.265  15.627  -0.684  1.00  0.00              
ATOM     55  CA  LEU    55       6.154  11.811  -0.470  1.00  0.00              
ATOM     56  CA  ALA    56       9.677  11.508   1.037  1.00  0.00              
ATOM     57  CA  GLY    57       8.536  13.894   3.859  1.00  0.00              
ATOM     58  CA  ALA    58       5.344  11.843   4.337  1.00  0.00              
ATOM     59  CA  ARG    59       7.407   8.650   4.778  1.00  0.00              
ATOM     60  CA  ARG    60       9.487  10.423   7.423  1.00  0.00              
ATOM     61  CA  LEU    61       6.356  11.572   9.276  1.00  0.00              
ATOM     62  CA  LEU    62       4.894   8.011   9.226  1.00  0.00              
ATOM     63  CA  THR    63       8.148   6.638  10.503  1.00  0.00              
ATOM     64  CA  ASP    64       8.317   9.139  13.325  1.00  0.00              
ATOM     65  CA  ALA    65       4.735   8.274  14.317  1.00  0.00              
ATOM     66  CA  GLY    66       5.285   4.488  14.376  1.00  0.00              
ATOM     67  CA  LEU    67       2.944   3.543  11.593  1.00  0.00              
ATOM     68  CA  ALA    68       4.601   0.846   9.467  1.00  0.00              
ATOM     69  CA  HIS    69       5.492  -1.356  12.390  1.00  0.00              
ATOM     70  CA  GLU    70       2.038  -1.231  13.838  1.00  0.00              
ATOM     71  CA  LEU    71       0.139  -1.897  10.599  1.00  0.00              
ATOM     72  CA  ARG    72       2.503  -4.646   9.513  1.00  0.00              
TER                                                                             
END
