
#######################################################
#                                                     #
#                        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   57 (   57),  selected   57 , name T0349TS168_1-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS168_1-D1.T0349_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:    25         8 - 47          4.85    17.16
  LONGEST_CONTINUOUS_SEGMENT:    25        29 - 68          4.90    11.73
  LCS_AVERAGE:     42.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        50 - 68          1.89    11.17
  LCS_AVERAGE:     21.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13         9 - 21          0.48    19.35
  LONGEST_CONTINUOUS_SEGMENT:    13        54 - 66          0.97    10.81
  LCS_AVERAGE:     14.59

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:   57
LCS_GDT     M       1     M       1      3    5   15     3    4    4    4    5    6    6    7    9   10   11   13   14   14   15   16   17   19   22   24 
LCS_GDT     R       2     R       2      3    5   15     3    4    4    4    5    6    6    7    9   10   11   13   14   14   20   23   28   29   33   34 
LCS_GDT     E       3     E       3      3    5   15     3    4    4    4    5    6    7    9   10   13   18   25   27   30   30   33   36   37   38   41 
LCS_GDT     L       4     L       4      3    5   15     3    3    3    4    5    6    6    6   10   12   15   26   31   32   34   35   37   39   42   44 
LCS_GDT     L       5     L       5      3    5   24     3    3    3    4   11   13   20   20   23   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     R       6     R       6      3    4   24    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     T       7     T       7      3    4   24     3    3    3    4    5    7   11   13   16   25   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     N       8     N       8      3   14   25     3    3    3    4    9   12   14   16   18   19   21   23   26   28   31   35   37   40   42   44 
LCS_GDT     D       9     D       9     13   14   25    10   12   13   13   13   13   14   16   17   19   21   23   26   30   34   35   37   40   42   44 
LCS_GDT     A      10     A      10     13   14   25    11   12   13   13   13   13   14   16   18   19   21   23   26   28   31   35   37   40   42   44 
LCS_GDT     V      11     V      11     13   14   25    11   12   13   13   13   13   14   16   18   19   21   22   24   28   29   32   34   35   39   41 
LCS_GDT     L      12     L      12     13   14   25    11   12   13   13   13   13   14   16   18   19   21   23   27   30   34   35   37   40   42   44 
LCS_GDT     L      13     L      13     13   14   25    11   12   13   13   13   17   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     S      14     S      14     13   14   25    11   12   13   13   13   13   14   16   18   23   25   29   31   32   34   35   37   40   42   44 
LCS_GDT     A      15     A      15     13   14   25    11   12   13   13   13   13   14   16   23   25   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     V      16     V      16     13   14   25    11   12   13   13   14   16   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     G      17     G      17     13   14   25    11   12   13   13   13   13   15   20   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     A      18     A      18     13   14   25    11   12   13   13   13   14   17   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     L      19     L      19     13   14   25    11   12   13   13   13   15   18   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     L      20     L      20     13   14   25    11   12   13   13   13   13   14   16   18   19   23   25   27   31   34   35   37   40   42   44 
LCS_GDT     D      21     D      21     13   14   25     8   12   13   13   13   13   13   15   17   20   23   25   27   31   34   35   37   40   42   44 
LCS_GDT     G      22     G      22      4   14   25     3    4    5    6   12   13   14   16   18   20   23   25   27   31   34   35   37   40   42   44 
LCS_GDT     A      23     A      23      4    7   25     3    4    5    6    9   12   14   16   18   19   21   22   25   28   30   34   36   37   41   44 
LCS_GDT     D      24     D      24      4    7   25     3    4    5    6    9   12   13   16   18   19   21   22   24   28   30   32   33   34   37   40 
LCS_GDT     I      25     I      25      5    7   25     3    4    6    6    7   10   11   13   16   18   19   21   24   26   27   28   32   32   35   36 
LCS_GDT     G      26     G      26      5    7   25     3    4    5    6    9   10   12   14   16   19   21   21   23   26   27   28   32   33   35   36 
LCS_GDT     H      27     H      27      5    7   25     3    4    5    6    9   12   14   16   18   19   21   22   25   28   30   34   36   37   41   44 
LCS_GDT     L      28     L      28      5    7   25     3    4    5    6    9   10   14   15   18   19   21   22   26   28   30   35   37   40   42   44 
LCS_GDT     V      29     V      29      5    6   25     3    4    5    6    8   13   15   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     P      45     P      45      3    4   25     3    3    3    4    5    5    6    6    8    9   12   15   17   18   19   19   21   22   25   33 
LCS_GDT     R      46     R      46      3    6   25     3    3    4    6    9   10   12   13   18   21   21   25   26   28   30   33   34   38   40   41 
LCS_GDT     R      47     R      47      3    6   25     3    3    3    6    9   14   15   18   19   21   23   25   27   29   32   35   37   39   42   44 
LCS_GDT     V      48     V      48      3    6   25     3    3    3    6    7   14   14   18   19   21   23   25   26   29   32   35   37   39   42   44 
LCS_GDT     L      49     L      49      3   10   25     3    3    3    6   10   14   17   19   19   22   26   29   31   32   34   35   37   40   42   44 
LCS_GDT     V      50     V      50      6   19   25     3    5    7   12   16   18   20   22   24   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     H      51     H      51      6   19   25     3    8   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     E      52     E      52      6   19   25     3   10   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     D      53     D      53      6   19   25     3    4    6   12   15   17   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     D      54     D      54     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     L      55     L      55     13   19   25     9   12   12   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     A      56     A      56     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     G      57     G      57     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     A      58     A      58     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     R      59     R      59     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     R      60     R      60     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     L      61     L      61     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     L      62     L      62     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     T      63     T      63     13   19   25    10   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     D      64     D      64     13   19   25     6   12   13   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     A      65     A      65     13   19   25     4   10   12   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     G      66     G      66     13   19   25     3    4    9   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     L      67     L      67     11   19   25     3    6   11   15   16   18   20   22   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     A      68     A      68      5   19   25     3    5    6    6    7   12   18   20   25   26   27   29   31   32   34   35   37   40   42   44 
LCS_GDT     H      69     H      69      5    7   24     3    5    6    7   10   14   16   18   19   19   22   27   29   31   33   35   37   40   41   43 
LCS_GDT     E      70     E      70      5    7   23     3    5    6    6    7   10   10   11   12   13   14   16   18   21   23   26   28   32   33   35 
LCS_GDT     L      71     L      71      5    7   23     3    5    6    6    7   10   10   11   12   13   14   16   18   21   21   24   26   29   33   36 
LCS_GDT     R      72     R      72      5    7   17     3    5    6    6    7   10   10   11   12   13   14   16   18   21   21   22   23   24   25   26 
LCS_AVERAGE  LCS_A:  26.21  (  14.59   21.91   42.14 )

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     11     12     13     15     16     18     20     22     25     26     27     29     31     32     34     35     37     40     42     44 
GDT PERCENT_CA  19.30  21.05  22.81  26.32  28.07  31.58  35.09  38.60  43.86  45.61  47.37  50.88  54.39  56.14  59.65  61.40  64.91  70.18  73.68  77.19
GDT RMS_LOCAL    0.30   0.35   0.48   1.09   1.24   1.61   2.00   2.42   2.98   3.03   3.16   3.53   3.80   3.94   4.28   4.78   4.99   5.56   5.80   6.26
GDT RMS_ALL_CA  19.35  19.29  19.35  10.53  11.47  10.61  10.54  10.13   9.78   9.93   9.85   9.89   9.89   9.93  10.07   9.82   9.86   9.83  10.01   9.95

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         23.154
LGA    R       2      R       2         16.663
LGA    E       3      E       3          9.768
LGA    L       4      L       4          6.226
LGA    L       5      L       5          4.828
LGA    R       6      R       6          1.596
LGA    T       7      T       7          7.005
LGA    N       8      N       8         11.037
LGA    D       9      D       9          8.653
LGA    A      10      A      10         10.234
LGA    V      11      V      11         12.192
LGA    L      12      L      12          7.953
LGA    L      13      L      13          3.977
LGA    S      14      S      14          7.920
LGA    A      15      A      15          6.132
LGA    V      16      V      16          3.920
LGA    G      17      G      17          6.884
LGA    A      18      A      18          6.103
LGA    L      19      L      19          3.963
LGA    L      20      L      20          9.804
LGA    D      21      D      21         11.562
LGA    G      22      G      22         12.324
LGA    A      23      A      23         15.145
LGA    D      24      D      24         20.234
LGA    I      25      I      25         18.197
LGA    G      26      G      26         18.639
LGA    H      27      H      27         13.871
LGA    L      28      L      28         12.038
LGA    V      29      V      29          6.189
LGA    P      45      P      45         20.511
LGA    R      46      R      46         13.989
LGA    R      47      R      47         12.744
LGA    V      48      V      48         10.538
LGA    L      49      L      49          7.234
LGA    V      50      V      50          3.568
LGA    H      51      H      51          2.438
LGA    E      52      E      52          1.884
LGA    D      53      D      53          2.833
LGA    D      54      D      54          1.656
LGA    L      55      L      55          1.568
LGA    A      56      A      56          1.347
LGA    G      57      G      57          1.371
LGA    A      58      A      58          0.948
LGA    R      59      R      59          0.309
LGA    R      60      R      60          0.932
LGA    L      61      L      61          1.021
LGA    L      62      L      62          0.290
LGA    T      63      T      63          0.820
LGA    D      64      D      64          1.927
LGA    A      65      A      65          2.585
LGA    G      66      G      66          3.397
LGA    L      67      L      67          3.977
LGA    A      68      A      68          4.933
LGA    H      69      H      69          9.166
LGA    E      70      E      70         14.870
LGA    L      71      L      71         13.955
LGA    R      72      R      72         19.652

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     22    2.42    36.842    33.603     0.872

LGA_LOCAL      RMSD =  2.424  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.066  Number of atoms =   57 
Std_ALL_ATOMS  RMSD =  9.553  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.818985 * X  +  -0.443798 * Y  +   0.363740 * Z  +   1.283254
  Y_new =   0.436182 * X  +  -0.893366 * Y  +  -0.107900 * Z  +   5.099793
  Z_new =   0.372839 * X  +   0.070289 * Y  +   0.925230 * Z  +   6.200858 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.075823   -3.065769  [ DEG:     4.3444   -175.6556 ]
  Theta =  -0.382066   -2.759526  [ DEG:   -21.8908   -158.1092 ]
  Phi   =   2.652215   -0.489377  [ DEG:   151.9608    -28.0392 ]
 
# 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: T0349TS168_1-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS168_1-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   57   57   4.0   22   2.42  33.603     9.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS168_1-D1
PFRMAT TS
TARGET T0349
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1       8.569 -11.603  -3.211  1.00 25.00           C
ATOM      2  CA  ARG     2       6.592  -8.345  -3.451  1.00 25.00           C
ATOM      3  CA  GLU     3       7.784  -4.711  -3.336  1.00 25.00           C
ATOM      4  CA  LEU     4       7.178  -0.954  -3.768  1.00 25.00           C
ATOM      5  CA  LEU     5       3.392  -1.536  -3.727  1.00 25.00           C
ATOM      6  CA  ARG     6       3.723  -3.623  -0.532  1.00 25.00           C
ATOM      7  CA  THR     7       5.803  -0.849   1.094  1.00 25.00           C
ATOM      8  CA  ASN     8       3.160   1.742   0.113  1.00 25.00           C
ATOM      9  CA  ASP     9       0.407  -0.464   1.604  1.00 25.00           C
ATOM     10  CA  ALA    10       2.416  -0.822   4.845  1.00 25.00           C
ATOM     11  CA  VAL    11       2.880   2.977   5.006  1.00 25.00           C
ATOM     12  CA  LEU    12      -0.882   3.483   4.486  1.00 25.00           C
ATOM     13  CA  LEU    13      -1.630   0.976   7.284  1.00 25.00           C
ATOM     14  CA  SER    14       0.800   2.809   9.608  1.00 25.00           C
ATOM     15  CA  ALA    15      -0.886   6.146   8.781  1.00 25.00           C
ATOM     16  CA  VAL    16      -4.321   4.622   9.520  1.00 25.00           C
ATOM     17  CA  GLY    17      -3.033   3.281  12.868  1.00 25.00           C
ATOM     18  CA  ALA    18      -1.635   6.738  13.743  1.00 25.00           C
ATOM     19  CA  LEU    19      -5.000   8.346  12.869  1.00 25.00           C
ATOM     20  CA  LEU    20      -6.819   5.799  15.075  1.00 25.00           C
ATOM     21  CA  ASP    21      -4.414   6.543  17.960  1.00 25.00           C
ATOM     22  CA  GLY    22      -4.395   3.499  20.287  1.00 25.00           C
ATOM     23  CA  ALA    23      -7.311   1.887  18.477  1.00 25.00           C
ATOM     24  CA  ASP    24      -5.742  -1.557  18.747  1.00 25.00           C
ATOM     25  CA  ILE    25      -4.009  -0.985  15.449  1.00 25.00           C
ATOM     26  CA  GLY    26      -6.906  -0.707  13.017  1.00 25.00           C
ATOM     27  CA  HIS    27      -8.460   1.449  10.224  1.00 25.00           C
ATOM     28  CA  LEU    28     -10.103   1.842   6.782  1.00 25.00           C
ATOM     29  CA  VAL    29      -7.894   1.716   3.733  1.00 25.00           C
ATOM     45  CA  PRO    45      -6.812  11.114   5.643  1.00 25.00           C
ATOM     46  CA  ARG    46      -7.463   9.033   2.459  1.00 25.00           C
ATOM     47  CA  ARG    47      -8.254   9.174  -1.299  1.00 25.00           C
ATOM     48  CA  VAL    48      -5.368  11.569  -2.087  1.00 25.00           C
ATOM     49  CA  LEU    49      -2.525  11.821  -4.569  1.00 25.00           C
ATOM     50  CA  VAL    50       0.898  10.168  -4.833  1.00 25.00           C
ATOM     51  CA  HIS    51       2.368  13.671  -4.367  1.00 25.00           C
ATOM     52  CA  GLU    52       5.744  15.167  -3.471  1.00 25.00           C
ATOM     53  CA  ASP    53       5.071  17.096  -0.232  1.00 25.00           C
ATOM     54  CA  ASP    54       2.073  14.835   0.522  1.00 25.00           C
ATOM     55  CA  LEU    55       4.232  11.730  -0.087  1.00 25.00           C
ATOM     56  CA  ALA    56       6.923  13.110   2.261  1.00 25.00           C
ATOM     57  CA  GLY    57       4.275  13.775   4.946  1.00 25.00           C
ATOM     58  CA  ALA    58       2.948  10.204   4.556  1.00 25.00           C
ATOM     59  CA  ARG    59       6.501   8.819   4.898  1.00 25.00           C
ATOM     60  CA  ARG    60       7.039  10.911   8.060  1.00 25.00           C
ATOM     61  CA  LEU    61       3.743   9.609   9.511  1.00 25.00           C
ATOM     62  CA  LEU    62       4.794   6.010   8.736  1.00 25.00           C
ATOM     63  CA  THR    63       8.170   6.601  10.445  1.00 25.00           C
ATOM     64  CA  ASP    64       6.390   8.036  13.518  1.00 25.00           C
ATOM     65  CA  ALA    65       4.077   4.985  13.632  1.00 25.00           C
ATOM     66  CA  GLY    66       6.311   2.222  12.176  1.00 25.00           C
ATOM     67  CA  LEU    67       9.052   0.688  10.006  1.00 25.00           C
ATOM     68  CA  ALA    68      11.960  -0.465  12.162  1.00 25.00           C
ATOM     69  CA  HIS    69      14.931   0.278  14.340  1.00 25.00           C
ATOM     70  CA  GLU    70      14.578  -1.960  17.349  1.00 25.00           C
ATOM     71  CA  LEU    71      12.402  -4.347  15.336  1.00 25.00           C
ATOM     72  CA  ARG    72      13.260  -7.727  16.858  1.00 25.00           C
TER
END
