
#######################################################
#                                                     #
#                        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 T0363TS393_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS393_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:    33        24 - 56          4.98     6.17
  LCS_AVERAGE:     69.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        24 - 36          1.93    12.78
  LCS_AVERAGE:     21.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        37 - 45          0.96    11.54
  LCS_AVERAGE:     12.95

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      5   11   28     0    3    7    8    9   10   12   13   17   18   21   30   35   37   40   41   42   43   45   45 
LCS_GDT     Q      12     Q      12      7   11   28     3    4    7    8    9   11   12   16   21   24   30   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      13     I      13      7   11   29     3    5    7    9   11   14   18   20   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     N      14     N      14      7   11   29     3    5    7    8    9   14   18   20   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      15     I      15      7   11   29     3    6    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     E      16     E      16      7   11   29     3    6    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      17     I      17      7   11   29     3    5    7    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     A      18     A      18      7   11   29     3    5    7    9   12   16   19   21   23   27   31   32   36   38   40   41   42   43   45   45 
LCS_GDT     Y      19     Y      19      5   11   29     3    5    7    9   11   16   18   21   23   26   31   32   36   38   40   41   42   43   45   45 
LCS_GDT     A      20     A      20      3   11   29     3    3    6    9    9   14   15   19   21   23   24   27   32   35   38   40   42   43   45   45 
LCS_GDT     F      21     F      21      4   11   29     3    4    4    6    9   12   13   19   21   24   26   27   32   36   39   41   42   43   45   45 
LCS_GDT     P      22     P      22      4    7   29     3    4    4    6    9   12   14   17   20   22   26   27   30   35   36   40   42   43   45   45 
LCS_GDT     E      23     E      23      4    9   29     3    4    6    8    9   11   15   19   23   27   31   32   36   38   40   41   42   43   45   45 
LCS_GDT     R      24     R      24      4   13   33     3    4    7   10   11   17   18   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     Y      25     Y      25      5   13   33     3    4    7   10   11   14   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     Y      26     Y      26      5   13   33     3    4    5    8    9   13   16   19   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     L      27     L      27      5   13   33     3    5    7   10   11   15   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     K      28     K      28      5   13   33     3    5    7   10   11   13   16   20   24   28   30   34   36   38   40   41   42   43   45   45 
LCS_GDT     S      29     S      29      5   13   33     3    5    7   10   11   13   14   19   22   26   30   34   35   38   40   41   42   43   45   45 
LCS_GDT     F      30     F      30      7   13   33     3    5    7   10   11   13   14   19   21   26   30   34   36   38   40   41   42   43   45   45 
LCS_GDT     Q      31     Q      31      7   13   33     3    5    7   10   11   13   14   19   21   22   23   25   27   30   36   39   41   41   44   45 
LCS_GDT     V      32     V      32      7   13   33     4    5    7    9   11   13   14   19   21   24   30   34   36   38   40   41   42   43   45   45 
LCS_GDT     D      33     D      33      7   13   33     4    5    7    9   11   13   18   20   24   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     E      34     E      34      7   13   33     4    5    7    9   11   13   14   19   24   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     G      35     G      35      7   13   33     4    5    7    9   11   13   15   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      36     I      36      7   13   33     3    5    7    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     T      37     T      37      9   10   33     3    4    8    9   11   16   19   21   22   26   29   31   31   33   36   38   41   43   45   45 
LCS_GDT     V      38     V      38      9   10   33     7    8    8    9   11   16   18   21   22   26   29   31   31   33   36   38   41   43   45   45 
LCS_GDT     Q      39     Q      39      9   10   33     7    8    8    9   11   16   19   21   23   26   29   31   34   38   40   41   42   43   45   45 
LCS_GDT     T      40     T      40      9   10   33     7    8    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     A      41     A      41      9   10   33     7    8    8    9   12   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      42     I      42      9   10   33     7    8    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     T      43     T      43      9   10   33     7    8    8    9   12   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     Q      44     Q      44      9   10   33     7    8    8   10   12   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     S      45     S      45      9   10   33     6    8    8    9   10   12   14   18   24   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     G      46     G      46      4   10   33     3    6    8   10   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      47     I      47      4    5   33     3    4    4    7   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     L      48     L      48      4    5   33     3    4    4   10   11   13   18   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     S      49     S      49      4    5   33     3    6    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     Q      50     Q      50      4    5   33     3    4    5    5   11   12   14   18   22   26   29   31   35   38   40   41   41   43   45   45 
LCS_GDT     F      51     F      51      4    5   33     3    4    5    7   11   16   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     P      52     P      52      4    5   33     3    3    5    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     E      53     E      53      4    5   33     3    3    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     I      54     I      54      3    5   33     3    3    5    5    9   14   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     D      55     D      55      3    5   33     3    6    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_GDT     L      56     L      56      3    5   33     3    5    8    9   13   17   19   23   25   28   31   34   36   38   40   41   42   43   45   45 
LCS_AVERAGE  LCS_A:  34.56  (  12.95   21.55   69.19 )

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      8      8     10     13     17     19     23     25     28     31     34     36     38     40     41     42     43     45     45 
GDT PERCENT_CA  15.22  17.39  17.39  21.74  28.26  36.96  41.30  50.00  54.35  60.87  67.39  73.91  78.26  82.61  86.96  89.13  91.30  93.48  97.83  97.83
GDT RMS_LOCAL    0.32   0.39   0.39   1.38   1.84   2.21   2.43   2.79   3.08   3.42   3.77   4.05   4.29   4.48   4.71   4.86   5.10   5.18   5.45   5.45
GDT RMS_ALL_CA  11.89  12.16  12.16   9.42   6.42   6.33   6.50   6.34   6.08   5.92   5.76   5.94   5.68   5.73   5.71   5.66   5.62   5.62   5.62   5.62

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11         13.610
LGA    Q      12      Q      12         11.443
LGA    I      13      I      13          7.065
LGA    N      14      N      14          7.438
LGA    I      15      I      15          2.257
LGA    E      16      E      16          2.145
LGA    I      17      I      17          3.039
LGA    A      18      A      18          5.181
LGA    Y      19      Y      19          6.304
LGA    A      20      A      20         10.628
LGA    F      21      F      21          9.590
LGA    P      22      P      22         11.025
LGA    E      23      E      23          7.406
LGA    R      24      R      24          3.970
LGA    Y      25      Y      25          3.554
LGA    Y      26      Y      26          4.350
LGA    L      27      L      27          3.678
LGA    K      28      K      28          6.994
LGA    S      29      S      29          8.894
LGA    F      30      F      30          8.361
LGA    Q      31      Q      31         12.883
LGA    V      32      V      32          9.877
LGA    D      33      D      33          8.675
LGA    E      34      E      34          7.292
LGA    G      35      G      35          3.584
LGA    I      36      I      36          2.326
LGA    T      37      T      37          6.931
LGA    V      38      V      38          6.965
LGA    Q      39      Q      39          5.572
LGA    T      40      T      40          2.830
LGA    A      41      A      41          2.556
LGA    I      42      I      42          1.161
LGA    T      43      T      43          3.004
LGA    Q      44      Q      44          2.781
LGA    S      45      S      45          4.873
LGA    G      46      G      46          1.802
LGA    I      47      I      47          2.897
LGA    L      48      L      48          3.955
LGA    S      49      S      49          2.713
LGA    Q      50      Q      50          6.780
LGA    F      51      F      51          3.848
LGA    P      52      P      52          1.417
LGA    E      53      E      53          0.794
LGA    I      54      I      54          3.493
LGA    D      55      D      55          1.510
LGA    L      56      L      56          1.602

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     23    2.79    44.565    39.741     0.797

LGA_LOCAL      RMSD =  2.788  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.353  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  5.611  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.593919 * X  +  -0.763339 * Y  +   0.254115 * Z  +  20.871336
  Y_new =  -0.582203 * X  +   0.189803 * Y  +  -0.790579 * Z  +  14.224737
  Z_new =   0.555248 * X  +  -0.617486 * Y  +  -0.557146 * Z  +   5.422729 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.304870    0.836722  [ DEG:  -132.0593     47.9407 ]
  Theta =  -0.588661   -2.552932  [ DEG:   -33.7278   -146.2722 ]
  Phi   =  -2.366156    0.775437  [ DEG:  -135.5707     44.4293 ]
 
# 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: T0363TS393_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_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   23   2.79  39.741     5.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_3-D1
PFRMAT TS
TARGET T0363
MODEL 3
PARENT N/A
ATOM     11  CA  ASN    11       9.858   9.561  18.027  1.00 25.00           C
ATOM     12  CA  GLN    12      12.851   9.786  15.673  1.00 25.00           C
ATOM     13  CA  ILE    13      15.379  10.982  13.120  1.00 25.00           C
ATOM     14  CA  ASN    14      17.530  13.584  11.369  1.00 25.00           C
ATOM     15  CA  ILE    15      19.134  11.671   8.547  1.00 25.00           C
ATOM     16  CA  GLU    16      20.207  14.382   6.131  1.00 25.00           C
ATOM     17  CA  ILE    17      22.859  13.737   3.523  1.00 25.00           C
ATOM     18  CA  ALA    18      24.627  14.915   0.327  1.00 25.00           C
ATOM     19  CA  TYR    19      27.759  16.245  -1.495  1.00 25.00           C
ATOM     20  CA  ALA    20      25.549  15.276  -4.486  1.00 25.00           C
ATOM     21  CA  PHE    21      24.018  18.754  -4.988  1.00 25.00           C
ATOM     22  CA  PRO    22      22.416  21.332  -7.245  1.00 25.00           C
ATOM     23  CA  GLU    23      23.452  23.849  -9.911  1.00 25.00           C
ATOM     24  CA  ARG    24      27.025  22.586 -10.459  1.00 25.00           C
ATOM     25  CA  TYR    25      28.444  23.589  -7.081  1.00 25.00           C
ATOM     26  CA  TYR    26      26.605  23.042  -3.754  1.00 25.00           C
ATOM     27  CA  LEU    27      25.828  20.975  -0.640  1.00 25.00           C
ATOM     28  CA  LYS    28      26.226  19.403   2.798  1.00 25.00           C
ATOM     29  CA  SER    29      25.245  17.779   6.040  1.00 25.00           C
ATOM     30  CA  PHE    30      25.173  14.248   7.349  1.00 25.00           C
ATOM     31  CA  GLN    31      25.161  14.831  11.110  1.00 25.00           C
ATOM     32  CA  VAL    32      22.709  12.449  12.781  1.00 25.00           C
ATOM     33  CA  ASP    33      21.748   9.438  14.809  1.00 25.00           C
ATOM     34  CA  GLU    34      24.671   7.826  16.720  1.00 25.00           C
ATOM     35  CA  GLY    35      26.066   4.658  15.080  1.00 25.00           C
ATOM     36  CA  ILE    36      24.391   4.537  11.619  1.00 25.00           C
ATOM     37  CA  THR    37      21.814   6.959  10.293  1.00 25.00           C
ATOM     38  CA  VAL    38      24.126   8.918   7.902  1.00 25.00           C
ATOM     39  CA  GLN    39      26.336   9.475  10.979  1.00 25.00           C
ATOM     40  CA  THR    40      28.613   6.591   9.896  1.00 25.00           C
ATOM     41  CA  ALA    41      28.872   8.086   6.379  1.00 25.00           C
ATOM     42  CA  ILE    42      29.767  11.499   7.869  1.00 25.00           C
ATOM     43  CA  THR    43      32.458   9.868  10.053  1.00 25.00           C
ATOM     44  CA  GLN    44      33.889   8.069   6.989  1.00 25.00           C
ATOM     45  CA  SER    45      33.962  11.373   5.053  1.00 25.00           C
ATOM     46  CA  GLY    46      32.187   9.668   2.112  1.00 25.00           C
ATOM     47  CA  ILE    47      31.622  12.072  -0.707  1.00 25.00           C
ATOM     48  CA  LEU    48      35.352  13.016  -0.769  1.00 25.00           C
ATOM     49  CA  SER    49      37.317  10.365   1.176  1.00 25.00           C
ATOM     50  CA  GLN    50      38.883  13.095   3.359  1.00 25.00           C
ATOM     51  CA  PHE    51      37.338  16.564   3.160  1.00 25.00           C
ATOM     52  CA  PRO    52      39.610  18.565   0.856  1.00 25.00           C
ATOM     53  CA  GLU    53      39.849  21.131   3.575  1.00 25.00           C
ATOM     54  CA  ILE    54      39.568  21.665   7.312  1.00 25.00           C
ATOM     55  CA  ASP    55      39.685  18.346   9.222  1.00 25.00           C
ATOM     56  CA  LEU    56      36.218  19.253  10.548  1.00 25.00           C
TER
END
