
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS599_3-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          3.23     3.23
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24        11 - 34          1.74     4.42
  LONGEST_CONTINUOUS_SEGMENT:    24        31 - 54          1.97     4.92
  LCS_AVERAGE:     52.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        33 - 47          0.95     4.49
  LONGEST_CONTINUOUS_SEGMENT:    15        34 - 48          1.00     4.46
  LONGEST_CONTINUOUS_SEGMENT:    15        39 - 53          0.97     5.64
  LONGEST_CONTINUOUS_SEGMENT:    15        40 - 54          0.87     5.57
  LONGEST_CONTINUOUS_SEGMENT:    15        41 - 55          0.96     5.44
  LCS_AVERAGE:     27.32

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     10   24   46     5    8   16   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      12     Q      12     10   24   46     5    8   16   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      13     I      13     10   24   46     5   11   17   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     N      14     N      14     10   24   46     5   11   17   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      15     I      15     10   24   46     4   11   17   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      16     E      16     11   24   46     4   11   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      17     I      17     11   24   46     3   11   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      18     A      18     11   24   46     4   11   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      19     Y      19     11   24   46     3    9   16   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      20     A      20     11   24   46     4   11   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      21     F      21     11   24   46     3   10   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     P      22     P      22     11   24   46     3    7   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      23     E      23     11   24   46     3    6   16   20   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     R      24     R      24     11   24   46     4    9   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      25     Y      25     11   24   46     4   11   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Y      26     Y      26     11   24   46     4    9   16   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      27     L      27     10   24   46     5    9   17   21   23   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     K      28     K      28      7   24   46     3    9   17   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      29     S      29      7   24   46     3   11   17   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      30     F      30      8   24   46     3   11   17   21   24   26   36   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      31     Q      31      8   24   46     3   11   17   21   24   29   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     V      32     V      32      8   24   46     3    8   17   21   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     D      33     D      33     15   24   46     4    8   16   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      34     E      34     15   24   46     4   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     G      35     G      35     15   24   46     8   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      36     I      36     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      37     T      37     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     V      38     V      38     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      39     Q      39     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      40     T      40     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     A      41     A      41     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      42     I      42     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     T      43     T      43     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      44     Q      44     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      45     S      45     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     G      46     G      46     15   24   46    10   12   15   19   24   32   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      47     I      47     15   24   46    10   11   15   19   21   27   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      48     L      48     15   24   46    10   11   15   19   21   27   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     S      49     S      49     15   24   46    10   11   15   19   23   31   38   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     Q      50     Q      50     15   24   46    10   11   15   19   21   27   37   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     F      51     F      51     15   24   46    10   11   15   19   21   23   31   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     P      52     P      52     15   24   46    10   11   15   19   21   23   33   42   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     E      53     E      53     15   24   46    10   11   15   19   21   22   28   37   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     I      54     I      54     15   24   46     4   11   15   19   21   22   31   40   44   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     D      55     D      55     15   23   46     4   11   13   16   17   21   28   30   39   44   46   46   46   46   46   46   46   46   46   46 
LCS_GDT     L      56     L      56     14   23   46     3    3    4   13   16   18   28   30   38   43   46   46   46   46   46   46   46   46   46   46 
LCS_AVERAGE  LCS_A:  59.80  (  27.32   52.08  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     10     12     17     21     24     32     38     42     44     44     46     46     46     46     46     46     46     46     46     46 
GDT PERCENT_CA  21.74  26.09  36.96  45.65  52.17  69.57  82.61  91.30  95.65  95.65 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.48   1.05   1.33   1.68   2.32   2.62   2.89   3.05   3.05   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23
GDT RMS_ALL_CA   5.59   4.18   5.65   5.30   4.99   3.90   3.56   3.33   3.25   3.25   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          3.798
LGA    Q      12      Q      12          3.634
LGA    I      13      I      13          3.827
LGA    N      14      N      14          3.102
LGA    I      15      I      15          2.969
LGA    E      16      E      16          1.984
LGA    I      17      I      17          2.660
LGA    A      18      A      18          3.159
LGA    Y      19      Y      19          3.533
LGA    A      20      A      20          3.379
LGA    F      21      F      21          3.348
LGA    P      22      P      22          3.676
LGA    E      23      E      23          2.555
LGA    R      24      R      24          2.189
LGA    Y      25      Y      25          3.159
LGA    Y      26      Y      26          2.926
LGA    L      27      L      27          2.473
LGA    K      28      K      28          2.820
LGA    S      29      S      29          2.867
LGA    F      30      F      30          3.950
LGA    Q      31      Q      31          3.735
LGA    V      32      V      32          3.094
LGA    D      33      D      33          1.175
LGA    E      34      E      34          1.478
LGA    G      35      G      35          2.449
LGA    I      36      I      36          2.721
LGA    T      37      T      37          3.759
LGA    V      38      V      38          3.515
LGA    Q      39      Q      39          3.516
LGA    T      40      T      40          3.161
LGA    A      41      A      41          2.542
LGA    I      42      I      42          2.366
LGA    T      43      T      43          2.868
LGA    Q      44      Q      44          2.525
LGA    S      45      S      45          1.775
LGA    G      46      G      46          1.379
LGA    I      47      I      47          2.546
LGA    L      48      L      48          2.361
LGA    S      49      S      49          2.021
LGA    Q      50      Q      50          3.042
LGA    F      51      F      51          3.919
LGA    P      52      P      52          3.646
LGA    E      53      E      53          4.842
LGA    I      54      I      54          4.252
LGA    D      55      D      55          5.704
LGA    L      56      L      56          5.690

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     42    2.89    65.761    66.805     1.405

LGA_LOCAL      RMSD =  2.890  Number of atoms =   42  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.229  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  3.226  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.174391 * X  +   0.848785 * Y  +  -0.499151 * Z  +  26.407513
  Y_new =   0.840542 * X  +   0.135730 * Y  +   0.524468 * Z  +  19.307171
  Z_new =   0.512910 * X  +  -0.511020 * Y  +  -0.689769 * Z  +   7.098382 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.503969    0.637624  [ DEG:  -143.4668     36.5332 ]
  Theta =  -0.538571   -2.603022  [ DEG:   -30.8578   -149.1422 ]
  Phi   =   1.366224   -1.775369  [ DEG:    78.2789   -101.7211 ]
 
# 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_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS599_3-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   2.89  66.805     3.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS599_3-D1
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM     11  CA  ASN    11      16.901   3.367  12.449  1.00  0.00              
ATOM     12  CA  GLN    12      17.079   5.626   9.462  1.00  0.00              
ATOM     13  CA  ILE    13      18.985   8.848   9.784  1.00  0.00              
ATOM     14  CA  ASN    14      19.361  10.983   6.783  1.00  0.00              
ATOM     15  CA  ILE    15      21.942  13.699   6.542  1.00  0.00              
ATOM     16  CA  GLU    16      21.970  16.012   3.582  1.00  0.00              
ATOM     17  CA  ILE    17      24.845  18.095   2.733  1.00  0.00              
ATOM     18  CA  ALA    18      24.764  20.664  -0.010  1.00  0.00              
ATOM     19  CA  TYR    19      27.860  22.275  -1.264  1.00  0.00              
ATOM     20  CA  ALA    20      27.807  25.325  -3.262  1.00  0.00              
ATOM     21  CA  PHE    21      30.905  26.444  -5.015  1.00  0.00              
ATOM     22  CA  PRO    22      30.785  29.442  -7.241  1.00  0.00              
ATOM     23  CA  GLU    23      27.994  27.905  -9.356  1.00  0.00              
ATOM     24  CA  ARG    24      28.629  24.197  -9.122  1.00  0.00              
ATOM     25  CA  TYR    25      26.310  22.352  -6.985  1.00  0.00              
ATOM     26  CA  TYR    26      27.457  19.415  -5.184  1.00  0.00              
ATOM     27  CA  LEU    27      24.968  17.247  -3.384  1.00  0.00              
ATOM     28  CA  LYS    28      26.077  14.959  -0.678  1.00  0.00              
ATOM     29  CA  SER    29      23.701  12.589   0.859  1.00  0.00              
ATOM     30  CA  PHE    30      24.649  10.766   3.993  1.00  0.00              
ATOM     31  CA  GLN    31      22.723   7.807   5.251  1.00  0.00              
ATOM     32  CA  VAL    32      23.281   6.684   8.776  1.00  0.00              
ATOM     33  CA  ASP    33      22.077   3.310   9.977  1.00  0.00              
ATOM     34  CA  GLU    34      20.923   3.040  13.521  1.00  0.00              
ATOM     35  CA  GLY    35      23.685   2.366  15.940  1.00  0.00              
ATOM     36  CA  ILE    36      26.428   3.687  13.752  1.00  0.00              
ATOM     37  CA  THR    37      28.972   6.230  14.841  1.00  0.00              
ATOM     38  CA  VAL    38      29.182   9.465  12.921  1.00  0.00              
ATOM     39  CA  GLN    39      32.702   8.585  11.772  1.00  0.00              
ATOM     40  CA  THR    40      31.559   5.354  10.222  1.00  0.00              
ATOM     41  CA  ALA    41      28.488   6.944   8.534  1.00  0.00              
ATOM     42  CA  ILE    42      30.469   9.778   7.172  1.00  0.00              
ATOM     43  CA  THR    43      33.122   7.535   5.709  1.00  0.00              
ATOM     44  CA  GLN    44      30.710   5.264   4.015  1.00  0.00              
ATOM     45  CA  SER    45      28.881   8.148   2.427  1.00  0.00              
ATOM     46  CA  GLY    46      32.046   9.842   1.120  1.00  0.00              
ATOM     47  CA  ILE    47      31.417  12.984   3.128  1.00  0.00              
ATOM     48  CA  LEU    48      34.957  13.176   4.621  1.00  0.00              
ATOM     49  CA  SER    49      36.539  12.761   1.245  1.00  0.00              
ATOM     50  CA  GLN    50      34.440  15.651  -0.105  1.00  0.00              
ATOM     51  CA  PHE    51      34.697  18.009   2.853  1.00  0.00              
ATOM     52  CA  PRO    52      38.121  17.483   4.454  1.00  0.00              
ATOM     53  CA  GLU    53      37.922  20.200   7.080  1.00  0.00              
ATOM     54  CA  ILE    54      34.557  19.133   8.406  1.00  0.00              
ATOM     55  CA  ASP    55      34.464  17.174  11.608  1.00  0.00              
ATOM     56  CA  LEU    56      31.813  14.445  11.246  1.00  0.00              
TER                                                                             
END
