
#######################################################
#                                                     #
#                        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 T0363TS168_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS168_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:    44        11 - 54          4.95     5.69
  LCS_AVERAGE:     94.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        35 - 46          1.87     8.60
  LONGEST_CONTINUOUS_SEGMENT:    12        38 - 49          1.96     9.10
  LCS_AVERAGE:     21.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        37 - 45          0.48     9.47
  LCS_AVERAGE:     10.82

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      3   10   44     2    3    6    7    9   13   20   23   28   31   33   37   38   40   42   42   43   43   44   45 
LCS_GDT     Q      12     Q      12      3   10   44     3    3    6    8   13   19   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     I      13     I      13      3   10   44     4    5    9   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     N      14     N      14      4   10   44     4    4   10   15   17   21   25   27   29   31   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     I      15     I      15      4   10   44     4    7   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     E      16     E      16      4   10   44     4    7   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     I      17     I      17      4   10   44     4    4    6    7   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     A      18     A      18      4   10   44     3    4   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     Y      19     Y      19      4   10   44     3    9   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     A      20     A      20      3   10   44     3    3    4    7    9   16   24   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     F      21     F      21      3    8   44     4    4   10   14   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     P      22     P      22      4    8   44     4    4    7   12   17   21   24   26   29   29   31   37   38   40   42   42   43   43   44   45 
LCS_GDT     E      23     E      23      4    8   44     4    7   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     R      24     R      24      4   10   44     3    4    5    9   11   17   18   24   28   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     Y      25     Y      25      4   10   44     3    4    6    9   12   17   21   25   28   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     Y      26     Y      26      4   10   44     3    4    5    7   10   13   17   21   26   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     L      27     L      27      4   10   44     3    4    6   11   14   19   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     K      28     K      28      4   10   44     3    4    6    9   11   13   18   21   26   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     S      29     S      29      4   10   44     3    4    6    9   11   13   17   21   25   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     F      30     F      30      4   10   44     3    4    6    9   11   13   17   20   25   29   33   36   38   40   42   42   43   43   44   45 
LCS_GDT     Q      31     Q      31      4   10   44     3    4    6    9    9   12   16   20   23   27   30   35   38   40   42   42   43   43   44   45 
LCS_GDT     V      32     V      32      4   10   44     3    4    6    9   11   13   17   21   26   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     D      33     D      33      4   10   44     3    4    6    7   10   13   17   20   25   29   33   36   38   40   42   42   43   43   44   45 
LCS_GDT     E      34     E      34      4    9   44     3    3    5    9   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     G      35     G      35      4   12   44     3    7   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     I      36     I      36      4   12   44     3    4   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     T      37     T      37      9   12   44     4    9   11   11   14   17   21   27   29   31   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     V      38     V      38      9   12   44     7    9   11   11   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     Q      39     Q      39      9   12   44     7    9   11   13   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     T      40     T      40      9   12   44     7    9   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     A      41     A      41      9   12   44     7    9   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     I      42     I      42      9   12   44     7    9   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     T      43     T      43      9   12   44     7    9   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     Q      44     Q      44      9   12   44     7    9   12   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     S      45     S      45      9   12   44     6    9   11   11   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     G      46     G      46      4   12   44     4    7   10   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     I      47     I      47      4   12   44     3    3    4    9   14   21   24   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     L      48     L      48      5   12   44     4    4    6    9   16   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     S      49     S      49      5   12   44     4    4   10   15   17   21   25   27   29   32   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     Q      50     Q      50      5    7   44     4    4    5    6    7    9   10   13   20   27   30   34   38   40   41   42   43   43   44   45 
LCS_GDT     F      51     F      51      5    7   44     4    4    5    6    7    9   10   18   18   23   23   33   36   40   42   42   43   43   44   45 
LCS_GDT     P      52     P      52      5    7   44     3    4    5    6    9   11   15   23   26   31   34   37   38   40   42   42   43   43   44   45 
LCS_GDT     E      53     E      53      4    7   44     3    3    4    5    8    9   13   19   23   27   31   36   38   40   42   42   43   43   44   45 
LCS_GDT     I      54     I      54      4    7   44     3    3    4    5    8   11   15   19   22   25   27   30   34   35   39   42   43   43   44   45 
LCS_GDT     D      55     D      55      4    4   33     3    3    4    5    8   12   15   20   23   25   27   30   34   35   37   40   41   42   44   45 
LCS_GDT     L      56     L      56      4    4   24     3    3    4    6    8   11   16   20   23   25   26   29   31   32   36   38   40   42   43   45 
LCS_AVERAGE  LCS_A:  42.19  (  10.82   21.55   94.19 )

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      7      9     12     15     17     21     25     27     29     32     34     37     38     40     42     42     43     43     44     45 
GDT PERCENT_CA  15.22  19.57  26.09  32.61  36.96  45.65  54.35  58.70  63.04  69.57  73.91  80.43  82.61  86.96  91.30  91.30  93.48  93.48  95.65  97.83
GDT RMS_LOCAL    0.32   0.48   1.07   1.30   1.54   1.93   2.39   2.55   2.71   3.43   3.52   3.82   4.06   4.25   4.59   4.51   4.70   4.70   4.95   5.40
GDT RMS_ALL_CA   9.01   9.47   7.38   7.13   7.00   7.01   6.70   6.58   6.63   6.24   6.29   6.10   5.98   6.10   5.74   6.01   5.82   5.82   5.69   5.56

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          6.567
LGA    Q      12      Q      12          3.895
LGA    I      13      I      13          1.514
LGA    N      14      N      14          2.913
LGA    I      15      I      15          2.199
LGA    E      16      E      16          1.349
LGA    I      17      I      17          3.748
LGA    A      18      A      18          1.406
LGA    Y      19      Y      19          1.198
LGA    A      20      A      20          3.893
LGA    F      21      F      21          2.950
LGA    P      22      P      22          4.718
LGA    E      23      E      23          0.558
LGA    R      24      R      24          6.459
LGA    Y      25      Y      25          5.635
LGA    Y      26      Y      26          6.685
LGA    L      27      L      27          3.825
LGA    K      28      K      28          7.821
LGA    S      29      S      29          8.123
LGA    F      30      F      30          9.659
LGA    Q      31      Q      31         10.250
LGA    V      32      V      32          6.832
LGA    D      33      D      33          8.860
LGA    E      34      E      34          2.901
LGA    G      35      G      35          1.598
LGA    I      36      I      36          1.702
LGA    T      37      T      37          4.882
LGA    V      38      V      38          3.578
LGA    Q      39      Q      39          2.881
LGA    T      40      T      40          0.802
LGA    A      41      A      41          0.839
LGA    I      42      I      42          1.068
LGA    T      43      T      43          2.169
LGA    Q      44      Q      44          2.352
LGA    S      45      S      45          3.594
LGA    G      46      G      46          0.551
LGA    I      47      I      47          3.702
LGA    L      48      L      48          3.551
LGA    S      49      S      49          2.705
LGA    Q      50      Q      50          6.556
LGA    F      51      F      51          7.971
LGA    P      52      P      52          7.018
LGA    E      53      E      53         11.637
LGA    I      54      I      54         13.622
LGA    D      55      D      55         17.236
LGA    L      56      L      56         17.437

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     27    2.55    50.543    45.319     1.019

LGA_LOCAL      RMSD =  2.550  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.460  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  5.553  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.029777 * X  +   0.975991 * Y  +   0.215765 * Z  +  22.523802
  Y_new =   0.992345 * X  +  -0.054749 * Y  +   0.110701 * Z  +  13.081594
  Z_new =   0.119856 * X  +   0.210816 * Y  +  -0.970150 * Z  +   4.464049 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.927616   -0.213976  [ DEG:   167.7401    -12.2599 ]
  Theta =  -0.120145   -3.021448  [ DEG:    -6.8838   -173.1162 ]
  Phi   =   1.540798   -1.600794  [ DEG:    88.2812    -91.7188 ]
 
# 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: T0363TS168_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS168_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   27   2.55  45.319     5.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS168_1-D1
PFRMAT TS
TARGET T0363
MODEL 1
PARENT N/A
ATOM     11  CA  ASN    11      11.924   0.759   6.664  1.00 25.00           C
ATOM     12  CA  GLN    12      13.965   3.885   7.278  1.00 25.00           C
ATOM     13  CA  ILE    13      16.270   6.922   7.480  1.00 25.00           C
ATOM     14  CA  ASN    14      19.902   6.941   6.406  1.00 25.00           C
ATOM     15  CA  ILE    15      21.631  10.263   5.650  1.00 25.00           C
ATOM     16  CA  GLU    16      21.227  13.385   3.429  1.00 25.00           C
ATOM     17  CA  ILE    17      22.852  15.940   1.068  1.00 25.00           C
ATOM     18  CA  ALA    18      25.544  17.997   2.818  1.00 25.00           C
ATOM     19  CA  TYR    19      27.677  21.192   2.926  1.00 25.00           C
ATOM     20  CA  ALA    20      30.177  20.905   0.074  1.00 25.00           C
ATOM     21  CA  PHE    21      29.378  22.362  -3.356  1.00 25.00           C
ATOM     22  CA  PRO    22      27.977  24.566  -6.081  1.00 25.00           C
ATOM     23  CA  GLU    23      30.190  27.151  -7.687  1.00 25.00           C
ATOM     24  CA  ARG    24      28.447  29.577  -5.355  1.00 25.00           C
ATOM     25  CA  TYR    25      28.382  27.648  -2.116  1.00 25.00           C
ATOM     26  CA  TYR    26      25.354  25.348  -1.556  1.00 25.00           C
ATOM     27  CA  LEU    27      24.385  21.661  -1.115  1.00 25.00           C
ATOM     28  CA  LYS    28      21.965  21.341   1.802  1.00 25.00           C
ATOM     29  CA  SER    29      20.969  19.078   4.729  1.00 25.00           C
ATOM     30  CA  PHE    30      20.116  16.429   7.332  1.00 25.00           C
ATOM     31  CA  GLN    31      20.915  13.710   9.828  1.00 25.00           C
ATOM     32  CA  VAL    32      19.968  10.018  10.395  1.00 25.00           C
ATOM     33  CA  ASP    33      20.809  10.006  14.098  1.00 25.00           C
ATOM     34  CA  GLU    34      20.915   6.205  14.278  1.00 25.00           C
ATOM     35  CA  GLY    35      23.897   3.887  15.046  1.00 25.00           C
ATOM     36  CA  ILE    36      25.954   7.020  14.360  1.00 25.00           C
ATOM     37  CA  THR    37      24.534   7.030  10.849  1.00 25.00           C
ATOM     38  CA  VAL    38      24.960  10.794  10.973  1.00 25.00           C
ATOM     39  CA  GLN    39      28.345  11.492  12.621  1.00 25.00           C
ATOM     40  CA  THR    40      29.776   8.283  11.099  1.00 25.00           C
ATOM     41  CA  ALA    41      28.462   9.304   7.649  1.00 25.00           C
ATOM     42  CA  ILE    42      30.058  12.764   8.039  1.00 25.00           C
ATOM     43  CA  THR    43      33.387  11.146   9.023  1.00 25.00           C
ATOM     44  CA  GLN    44      33.204   8.853   5.961  1.00 25.00           C
ATOM     45  CA  SER    45      32.508  11.872   3.710  1.00 25.00           C
ATOM     46  CA  GLY    46      32.994   9.776   0.588  1.00 25.00           C
ATOM     47  CA  ILE    47      32.714  12.354  -2.165  1.00 25.00           C
ATOM     48  CA  LEU    48      34.800  14.895  -0.231  1.00 25.00           C
ATOM     49  CA  SER    49      38.613  15.244  -0.272  1.00 25.00           C
ATOM     50  CA  GLN    50      38.775  14.173   3.403  1.00 25.00           C
ATOM     51  CA  PHE    51      37.659  10.663   2.567  1.00 25.00           C
ATOM     52  CA  PRO    52      40.661  10.553   0.156  1.00 25.00           C
ATOM     53  CA  GLU    53      41.212  11.322  -3.515  1.00 25.00           C
ATOM     54  CA  ILE    54      37.602  10.365  -4.415  1.00 25.00           C
ATOM     55  CA  ASP    55      38.399   6.918  -2.912  1.00 25.00           C
ATOM     56  CA  LEU    56      35.185   5.710  -1.352  1.00 25.00           C
TER
END
