
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS168_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:    37        11 - 47          4.94     7.38
  LCS_AVERAGE:     75.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        37 - 49          1.52    10.60
  LCS_AVERAGE:     21.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        37 - 45          0.65    10.59
  LCS_AVERAGE:     12.48

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      6    9   37     3    5    6    7   10   12   13   16   21   24   28   31   32   32   36   38   41   42   43   44 
LCS_GDT     Q      12     Q      12      6    9   37     3    4    6    7   10   13   16   21   24   27   29   31   33   36   37   38   41   42   43   45 
LCS_GDT     I      13     I      13      6    9   37     3    5    6    8   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     N      14     N      14      6    9   37     3    5    7    7   11   15   20   22   24   28   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     I      15     I      15      6    9   37     3    5    7    9   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     E      16     E      16      6    9   37     3    5    7    9   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     I      17     I      17      5    9   37     3    4    7   12   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     A      18     A      18      5    9   37     3    4    8   10   13   16   20   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     Y      19     Y      19      4    9   37     3    4    5    6    9   12   13   19   24   27   29   31   35   36   37   38   41   42   43   45 
LCS_GDT     A      20     A      20      4    7   37     3    4    5    6    7    8   11   16   18   20   22   26   32   32   33   34   37   42   42   45 
LCS_GDT     F      21     F      21      3    7   37     3    3    5    6    8   11   13   16   18   27   29   31   32   32   37   38   41   42   43   45 
LCS_GDT     P      22     P      22      4    7   37     0    3    5    6    8   10   13   16   17   25   28   31   32   32   33   38   41   42   43   45 
LCS_GDT     E      23     E      23      4    7   37     1    3    5    6   11   15   20   22   24   27   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     R      24     R      24      6   11   37     4    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     Y      25     Y      25      6   11   37     4    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     Y      26     Y      26      6   11   37     3    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     L      27     L      27      6   11   37     3    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     K      28     K      28      6   11   37     3    7    9   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     S      29     S      29      6   11   37     4    5   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     F      30     F      30      4   11   37     3    4    9   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     Q      31     Q      31      6   11   37     4    5   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     V      32     V      32      6   11   37     4    5   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     D      33     D      33      6   11   37     4    5   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     E      34     E      34      6   11   37     4    5    7    8   12   16   20   22   24   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     G      35     G      35      6   11   37     4    5    7    7   13   16   20   22   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     I      36     I      36      6   10   37     3    5    7    9   13   16   20   22   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     T      37     T      37      9   13   37     3    7    9   12   14   16   17   21   22   27   29   31   32   32   35   38   40   42   43   45 
LCS_GDT     V      38     V      38      9   13   37     7    8    9   12   14   16   17   19   22   27   29   31   32   32   34   38   40   42   43   45 
LCS_GDT     Q      39     Q      39      9   13   37     7    8    9   12   14   16   17   21   24   26   29   32   35   36   37   38   41   42   43   45 
LCS_GDT     T      40     T      40      9   13   37     7    8    9   12   14   16   20   22   24   27   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     A      41     A      41      9   13   37     7    8    9   12   14   16   20   22   24   27   29   32   35   36   37   38   41   42   43   45 
LCS_GDT     I      42     I      42      9   13   37     7    8    9   12   14   16   20   22   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     T      43     T      43      9   13   37     7    8    9   12   14   17   20   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     Q      44     Q      44      9   13   37     7    8    9   12   14   16   17   22   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     S      45     S      45      9   13   37     6    8    9   12   14   16   17   21   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     G      46     G      46      4   13   37     4    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     I      47     I      47      3   13   37     3    4    7   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     L      48     L      48      4   13   28     4    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     S      49     S      49      4   13   28     3    7   11   13   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     Q      50     Q      50      4    4   28     3    4    4    4    7    8    8   10   18   21   24   28   29   32   34   38   41   42   43   45 
LCS_GDT     F      51     F      51      4    5   26     3    4    4    6    7   12   16   18   19   22   23   26   28   31   34   37   39   42   43   45 
LCS_GDT     P      52     P      52      4    5   26     3    4    4   10   13   15   17   19   20   22   24   28   28   32   34   37   39   42   43   45 
LCS_GDT     E      53     E      53      4    5   26     3    4    4    6   10   12   16   21   22   26   27   30   33   36   37   38   41   42   43   45 
LCS_GDT     I      54     I      54      4    5   26     3    4    4    7   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     D      55     D      55      4    5   23     3    3    5   12   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_GDT     L      56     L      56      3    3   23     3    3    8   12   19   21   21   23   26   29   30   32   35   36   37   38   41   42   43   45 
LCS_AVERAGE  LCS_A:  36.53  (  12.48   21.36   75.76 )

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     11     13     19     21     21     23     26     29     30     32     35     36     37     38     41     42     43     45 
GDT PERCENT_CA  15.22  17.39  23.91  28.26  41.30  45.65  45.65  50.00  56.52  63.04  65.22  69.57  76.09  78.26  80.43  82.61  89.13  91.30  93.48  97.83
GDT RMS_LOCAL    0.32   0.39   1.17   1.28   1.84   1.98   1.98   2.39   3.09   3.32   3.42   3.74   4.20   4.34   4.50   4.73   5.20   5.37   5.53   5.88
GDT RMS_ALL_CA  10.85  10.92   7.23   7.26   6.80   6.72   6.72   6.51   6.37   6.44   6.46   6.32   6.24   6.21   6.15   6.20   6.05   6.03   6.03   6.00

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          9.037
LGA    Q      12      Q      12          7.151
LGA    I      13      I      13          3.247
LGA    N      14      N      14          5.339
LGA    I      15      I      15          1.838
LGA    E      16      E      16          1.833
LGA    I      17      I      17          1.153
LGA    A      18      A      18          3.803
LGA    Y      19      Y      19          8.507
LGA    A      20      A      20         11.843
LGA    F      21      F      21          9.912
LGA    P      22      P      22         10.513
LGA    E      23      E      23          6.098
LGA    R      24      R      24          2.231
LGA    Y      25      Y      25          2.149
LGA    Y      26      Y      26          2.077
LGA    L      27      L      27          1.319
LGA    K      28      K      28          2.279
LGA    S      29      S      29          2.063
LGA    F      30      F      30          2.664
LGA    Q      31      Q      31          2.576
LGA    V      32      V      32          1.802
LGA    D      33      D      33          2.044
LGA    E      34      E      34          5.501
LGA    G      35      G      35          6.406
LGA    I      36      I      36          6.584
LGA    T      37      T      37         11.619
LGA    V      38      V      38         11.385
LGA    Q      39      Q      39          8.493
LGA    T      40      T      40          7.351
LGA    A      41      A      41          7.917
LGA    I      42      I      42          5.294
LGA    T      43      T      43          3.370
LGA    Q      44      Q      44          4.922
LGA    S      45      S      45          4.734
LGA    G      46      G      46          2.421
LGA    I      47      I      47          3.198
LGA    L      48      L      48          3.281
LGA    S      49      S      49          3.689
LGA    Q      50      Q      50          9.495
LGA    F      51      F      51         10.522
LGA    P      52      P      52         11.106
LGA    E      53      E      53          8.283
LGA    I      54      I      54          2.701
LGA    D      55      D      55          3.878
LGA    L      56      L      56          2.590

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   46   46    4.0     23    2.39    44.565    41.734     0.923

LGA_LOCAL      RMSD =  2.391  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.283  Number of atoms =   46 
Std_ALL_ATOMS  RMSD =  5.983  (standard rmsd on all 46 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.767166 * X  +  -0.465463 * Y  +  -0.441361 * Z  +  21.724617
  Y_new =  -0.539676 * X  +  -0.840272 * Y  +  -0.051897 * Z  +  11.780495
  Z_new =  -0.346707 * X  +   0.278006 * Y  +  -0.895828 * Z  +   5.642416 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.840683   -0.300910  [ DEG:   162.7591    -17.2409 ]
  Theta =   0.354058    2.787534  [ DEG:    20.2861    159.7139 ]
  Phi   =  -0.613048    2.528544  [ DEG:   -35.1251    144.8749 ]
 
# 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_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363TS168_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   2.39  41.734     5.98
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS168_3-D1
PFRMAT TS
TARGET T0363
MODEL 3
PARENT N/A
ATOM     11  CA  ASN    11       8.926   4.071  13.734  1.00 25.00           C
ATOM     12  CA  GLN    12      12.605   4.942  13.021  1.00 25.00           C
ATOM     13  CA  ILE    13      15.006   6.905  10.866  1.00 25.00           C
ATOM     14  CA  ASN    14      18.218   9.029  11.117  1.00 25.00           C
ATOM     15  CA  ILE    15      19.617  11.139   8.235  1.00 25.00           C
ATOM     16  CA  GLU    16      21.176  13.846   6.165  1.00 25.00           C
ATOM     17  CA  ILE    17      24.494  14.842   4.493  1.00 25.00           C
ATOM     18  CA  ALA    18      26.426  16.005   1.430  1.00 25.00           C
ATOM     19  CA  TYR    19      28.334  13.220  -0.325  1.00 25.00           C
ATOM     20  CA  ALA    20      27.885  13.318  -4.044  1.00 25.00           C
ATOM     21  CA  PHE    21      26.688  16.323  -6.010  1.00 25.00           C
ATOM     22  CA  PRO    22      27.032  19.081  -8.645  1.00 25.00           C
ATOM     23  CA  GLU    23      29.635  21.551  -9.958  1.00 25.00           C
ATOM     24  CA  ARG    24      30.751  24.596  -7.861  1.00 25.00           C
ATOM     25  CA  TYR    25      27.965  23.889  -5.357  1.00 25.00           C
ATOM     26  CA  TYR    26      27.115  20.658  -3.537  1.00 25.00           C
ATOM     27  CA  LEU    27      24.138  18.916  -1.981  1.00 25.00           C
ATOM     28  CA  LYS    28      23.015  15.327  -2.645  1.00 25.00           C
ATOM     29  CA  SER    29      22.526  12.968   0.279  1.00 25.00           C
ATOM     30  CA  PHE    30      20.453  10.579   2.423  1.00 25.00           C
ATOM     31  CA  GLN    31      21.130   7.638   4.816  1.00 25.00           C
ATOM     32  CA  VAL    32      21.589   5.780   8.143  1.00 25.00           C
ATOM     33  CA  ASP    33      21.954   3.750  11.352  1.00 25.00           C
ATOM     34  CA  GLU    34      25.398   3.861  13.052  1.00 25.00           C
ATOM     35  CA  GLY    35      26.137   0.162  12.553  1.00 25.00           C
ATOM     36  CA  ILE    36      26.679   1.270   8.948  1.00 25.00           C
ATOM     37  CA  THR    37      24.306   1.760   6.052  1.00 25.00           C
ATOM     38  CA  VAL    38      25.442   5.007   4.525  1.00 25.00           C
ATOM     39  CA  GLN    39      28.079   5.879   7.161  1.00 25.00           C
ATOM     40  CA  THR    40      30.535   3.419   5.556  1.00 25.00           C
ATOM     41  CA  ALA    41      29.885   4.976   2.117  1.00 25.00           C
ATOM     42  CA  ILE    42      30.495   8.471   3.557  1.00 25.00           C
ATOM     43  CA  THR    43      33.773   7.276   5.136  1.00 25.00           C
ATOM     44  CA  GLN    44      34.865   5.770   1.788  1.00 25.00           C
ATOM     45  CA  SER    45      34.048   9.064   0.013  1.00 25.00           C
ATOM     46  CA  GLY    46      33.007  12.426   1.419  1.00 25.00           C
ATOM     47  CA  ILE    47      31.216  14.707   3.830  1.00 25.00           C
ATOM     48  CA  LEU    48      34.582  16.411   4.565  1.00 25.00           C
ATOM     49  CA  SER    49      37.364  14.246   3.070  1.00 25.00           C
ATOM     50  CA  GLN    50      37.902  12.551   6.462  1.00 25.00           C
ATOM     51  CA  PHE    51      35.021  13.366   8.863  1.00 25.00           C
ATOM     52  CA  PRO    52      37.497  14.014  11.678  1.00 25.00           C
ATOM     53  CA  GLU    53      39.849  16.105   9.492  1.00 25.00           C
ATOM     54  CA  ILE    54      37.941  18.855   7.672  1.00 25.00           C
ATOM     55  CA  ASP    55      35.191  20.571   9.609  1.00 25.00           C
ATOM     56  CA  LEU    56      33.940  17.755  11.922  1.00 25.00           C
TER
END
