
#######################################################
#                                                     #
#                        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   46 (   46),  selected   46 , name T0363TS599_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS599_1-D1.T0363_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:    46        11 - 56          3.08     3.08
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        11 - 36          1.94     4.34
  LCS_AVERAGE:     54.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        11 - 26          0.92     5.51
  LONGEST_CONTINUOUS_SEGMENT:    16        12 - 27          0.99     5.23
  LONGEST_CONTINUOUS_SEGMENT:    16        40 - 55          0.95     5.31
  LONGEST_CONTINUOUS_SEGMENT:    16        41 - 56          0.96     5.36
  LCS_AVERAGE:     32.56

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:   46
LCS_GDT     N      11     N      11     16   26   46     5   10   17   21   28   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      12     Q      12     16   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      13     I      13     16   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     N      14     N      14     16   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      15     I      15     16   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      16     E      16     16   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      17     I      17     16   26   46     4   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      18     A      18     16   26   46     4   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      19     Y      19     16   26   46     3   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      20     A      20     16   26   46     3   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      21     F      21     16   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     P      22     P      22     16   26   46     3    7   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      23     E      23     16   26   46     3    8   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     R      24     R      24     16   26   46     3   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      25     Y      25     16   26   46     3   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      26     Y      26     16   26   46     3   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      27     L      27     16   26   46     4   10   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     K      28     K      28      8   26   46     4   10   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      29     S      29      8   26   46     3   10   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      30     F      30      8   26   46     3    7   15   20   24   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      31     Q      31      8   26   46     3   10   15   20   24   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     V      32     V      32      8   26   46     3    9   15   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     D      33     D      33     15   26   46     5   11   17   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      34     E      34     15   26   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     G      35     G      35     15   26   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      36     I      36     15   26   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      37     T      37     15   24   46     8   12   15   20   28   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     V      38     V      38     15   24   46     8   12   15   20   28   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      39     Q      39     15   24   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      40     T      40     16   24   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      41     A      41     16   24   46     8   12   15   20   28   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      42     I      42     16   24   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      43     T      43     16   24   46     8   12   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      44     Q      44     16   24   46     8   12   15   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      45     S      45     16   24   46     8   12   15   21   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     G      46     G      46     16   24   46     6   11   15   20   30   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      47     I      47     16   24   46     7   11   15   19   23   35   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      48     L      48     16   24   46     7   11   15   19   23   31   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      49     S      49     16   24   46     7   11   15   19   23   31   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      50     Q      50     16   24   46     7   11   15   19   23   31   40   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      51     F      51     16   24   46     7   11   15   19   21   28   36   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     P      52     P      52     16   24   46     7   11   15   19   21   28   35   42   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      53     E      53     16   24   46     7   11   15   19   21   25   31   36   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      54     I      54     16   24   46     4   11   15   19   21   25   32   40   43   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     D      55     D      55     16   24   46     4    4   15   17   18   23   26   36   41   45   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      56     L      56     16   24   46     3    3    6   17   18   23   26   36   41   45   46   46   46   46   46   46   46   46   46   46 
LCS_AVERAGE  LCS_A:  62.40  (  32.56   54.63  100.00 )

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      8     12     17     21     30     35     40     42     43     45     46     46     46     46     46     46     46     46     46     46 
GDT PERCENT_CA  17.39  26.09  36.96  45.65  65.22  76.09  86.96  91.30  93.48  97.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.52   0.91   1.34   2.04   2.21   2.54   2.72   2.81   3.00   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08
GDT RMS_ALL_CA   4.56   3.77   5.46   4.52   3.87   3.77   3.36   3.19   3.14   3.09   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          3.759
LGA    Q      12      Q      12          3.223
LGA    I      13      I      13          3.640
LGA    N      14      N      14          2.991
LGA    I      15      I      15          2.834
LGA    E      16      E      16          1.886
LGA    I      17      I      17          2.172
LGA    A      18      A      18          2.461
LGA    Y      19      Y      19          3.421
LGA    A      20      A      20          2.956
LGA    F      21      F      21          3.581
LGA    P      22      P      22          3.732
LGA    E      23      E      23          2.550
LGA    R      24      R      24          3.047
LGA    Y      25      Y      25          2.795
LGA    Y      26      Y      26          3.206
LGA    L      27      L      27          1.715
LGA    K      28      K      28          2.061
LGA    S      29      S      29          2.189
LGA    F      30      F      30          3.400
LGA    Q      31      Q      31          3.363
LGA    V      32      V      32          2.693
LGA    D      33      D      33          1.015
LGA    E      34      E      34          1.361
LGA    G      35      G      35          2.492
LGA    I      36      I      36          2.692
LGA    T      37      T      37          3.310
LGA    V      38      V      38          3.194
LGA    Q      39      Q      39          3.047
LGA    T      40      T      40          2.991
LGA    A      41      A      41          2.844
LGA    I      42      I      42          2.557
LGA    T      43      T      43          2.667
LGA    Q      44      Q      44          2.426
LGA    S      45      S      45          1.601
LGA    G      46      G      46          0.645
LGA    I      47      I      47          2.117
LGA    L      48      L      48          2.471
LGA    S      49      S      49          2.229
LGA    Q      50      Q      50          2.648
LGA    F      51      F      51          3.545
LGA    P      52      P      52          3.901
LGA    E      53      E      53          5.139
LGA    I      54      I      54          4.426
LGA    D      55      D      55          5.824
LGA    L      56      L      56          5.473

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     42    2.72    65.761    68.940     1.487

LGA_LOCAL      RMSD =  2.724  Number of atoms =   42  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.089  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  3.085  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.617556 * X  +  -0.358847 * Y  +  -0.699895 * Z  +  24.638004
  Y_new =  -0.468595 * X  +   0.546822 * Y  +  -0.693832 * Z  +  18.274210
  Z_new =   0.631698 * X  +   0.756448 * Y  +   0.169540 * Z  +   6.106805 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.350314   -1.791279  [ DEG:    77.3673   -102.6327 ]
  Theta =  -0.683742   -2.457851  [ DEG:   -39.1755   -140.8245 ]
  Phi   =  -0.649103    2.492490  [ DEG:   -37.1908    142.8092 ]
 
# 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: T0363TS599_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS599_1-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   46   46   4.0   42   2.72  68.940     3.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS599_1-D1
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     11  CA  ASN    11      16.657   3.306  12.564  1.00  0.00              
ATOM     12  CA  GLN    12      17.320   5.216   9.412  1.00  0.00              
ATOM     13  CA  ILE    13      19.054   8.523   9.823  1.00  0.00              
ATOM     14  CA  ASN    14      19.386  10.788   6.844  1.00  0.00              
ATOM     15  CA  ILE    15      22.139  13.305   6.578  1.00  0.00              
ATOM     16  CA  GLU    16      22.218  15.955   3.969  1.00  0.00              
ATOM     17  CA  ILE    17      25.352  17.555   2.895  1.00  0.00              
ATOM     18  CA  ALA    18      25.464  20.528   0.630  1.00  0.00              
ATOM     19  CA  TYR    19      28.526  21.378  -1.332  1.00  0.00              
ATOM     20  CA  ALA    20      28.878  24.601  -3.034  1.00  0.00              
ATOM     21  CA  PHE    21      31.068  24.911  -6.025  1.00  0.00              
ATOM     22  CA  PRO    22      31.498  28.298  -7.609  1.00  0.00              
ATOM     23  CA  GLU    23      27.902  28.471  -8.873  1.00  0.00              
ATOM     24  CA  ARG    24      26.965  24.816  -8.863  1.00  0.00              
ATOM     25  CA  TYR    25      25.334  23.230  -5.892  1.00  0.00              
ATOM     26  CA  TYR    26      26.132  19.825  -5.120  1.00  0.00              
ATOM     27  CA  LEU    27      23.879  17.808  -2.924  1.00  0.00              
ATOM     28  CA  LYS    28      25.259  14.917  -1.069  1.00  0.00              
ATOM     29  CA  SER    29      22.998  12.563   0.813  1.00  0.00              
ATOM     30  CA  PHE    30      24.371  10.445   3.587  1.00  0.00              
ATOM     31  CA  GLN    31      22.491   7.623   4.988  1.00  0.00              
ATOM     32  CA  VAL    32      23.238   6.423   8.423  1.00  0.00              
ATOM     33  CA  ASP    33      21.885   3.101   9.648  1.00  0.00              
ATOM     34  CA  GLU    34      20.767   2.874  13.154  1.00  0.00              
ATOM     35  CA  GLY    35      23.513   2.208  15.490  1.00  0.00              
ATOM     36  CA  ILE    36      26.275   3.588  13.326  1.00  0.00              
ATOM     37  CA  THR    37      28.517   6.453  14.558  1.00  0.00              
ATOM     38  CA  VAL    38      28.564   9.560  12.424  1.00  0.00              
ATOM     39  CA  GLN    39      32.313   8.947  11.742  1.00  0.00              
ATOM     40  CA  THR    40      31.592   5.537  10.274  1.00  0.00              
ATOM     41  CA  ALA    41      28.551   6.649   8.234  1.00  0.00              
ATOM     42  CA  ILE    42      30.412   9.629   6.889  1.00  0.00              
ATOM     43  CA  THR    43      33.447   7.634   5.841  1.00  0.00              
ATOM     44  CA  GLN    44      31.349   5.186   3.934  1.00  0.00              
ATOM     45  CA  SER    45      29.678   7.963   2.026  1.00  0.00              
ATOM     46  CA  GLY    46      32.988   9.735   1.189  1.00  0.00              
ATOM     47  CA  ILE    47      31.963  12.931   2.897  1.00  0.00              
ATOM     48  CA  LEU    48      35.150  13.361   4.971  1.00  0.00              
ATOM     49  CA  SER    49      37.313  12.808   1.938  1.00  0.00              
ATOM     50  CA  GLN    50      35.371  15.440  -0.048  1.00  0.00              
ATOM     51  CA  PHE    51      35.133  18.080   2.687  1.00  0.00              
ATOM     52  CA  PRO    52      38.286  17.935   4.822  1.00  0.00              
ATOM     53  CA  GLU    53      37.395  20.784   7.198  1.00  0.00              
ATOM     54  CA  ILE    54      34.148  19.013   8.223  1.00  0.00              
ATOM     55  CA  ASP    55      34.198  17.329  11.553  1.00  0.00              
ATOM     56  CA  LEU    56      32.535  13.965  11.690  1.00  0.00              
TER                                                                             
END
