
#######################################################
#                                                     #
#                        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 T0349TS393_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS393_2-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:    27         7 - 48          4.96    18.01
  LCS_AVERAGE:     43.71

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        48 - 65          1.85    14.35
  LONGEST_CONTINUOUS_SEGMENT:    18        49 - 66          1.89    14.25
  LCS_AVERAGE:     22.22

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         9 - 22          0.76    17.71
  LCS_AVERAGE:     14.56

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      5    6   15     3    4    5    5    5    5    6    7    8    9   11   14   14   14   18   20   22   24   26   28 
LCS_GDT     R       2     R       2      5    6   15     3    4    5    5    5    5    6    7    8    9   11   14   17   19   21   23   25   27   29   31 
LCS_GDT     E       3     E       3      5    6   15     3    4    5    5    5    5    6    7    8   11   16   18   20   20   21   23   27   28   29   31 
LCS_GDT     L       4     L       4      5    6   15     3    4    5    5    5    5    6    6    6    9   10   14   14   14   21   24   26   28   29   31 
LCS_GDT     L       5     L       5      5    6   25     3    4    5    5    5    5    6    8   11   12   15   19   21   22   26   28   29   29   31   31 
LCS_GDT     R       6     R       6      3    6   25     0    3    3    4    4    6    8   11   13   16   17   20   22   25   27   28   29   29   31   31 
LCS_GDT     T       7     T       7      3    4   27     3    3    4    4    5    7   10   12   14   19   21   24   25   26   27   28   29   30   31   32 
LCS_GDT     N       8     N       8      3   15   27     3    3    4    4    6    7   13   16   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     D       9     D       9     14   15   27    10   12   13   14   14   15   16   17   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     A      10     A      10     14   15   27    11   12   13   14   14   15   16   17   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     V      11     V      11     14   15   27    11   12   13   14   14   15   16   17   19   20   22   24   25   26   28   29   29   30   32   33 
LCS_GDT     L      12     L      12     14   15   27    11   12   13   14   14   15   16   17   19   20   22   25   26   27   28   29   29   31   32   33 
LCS_GDT     L      13     L      13     14   15   27    11   12   13   14   14   15   16   17   19   21   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     S      14     S      14     14   15   27    11   12   13   14   14   15   16   18   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     A      15     A      15     14   15   27    11   12   13   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     V      16     V      16     14   15   27    11   12   13   14   15   17   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     G      17     G      17     14   15   27    11   12   13   14   14   15   16   17   19   20   22   24   25   26   27   29   30   31   32   34 
LCS_GDT     A      18     A      18     14   15   27    11   12   13   14   14   15   16   17   19   20   22   24   25   26   27   29   30   31   32   34 
LCS_GDT     L      19     L      19     14   15   27    11   12   13   14   14   15   16   17   19   20   22   24   25   26   27   28   29   30   32   34 
LCS_GDT     L      20     L      20     14   15   27    11   12   13   14   14   15   16   16   18   18   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     D      21     D      21     14   15   27     3   12   13   14   14   15   16   17   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     G      22     G      22     14   15   27     3    4   11   14   14   15   16   17   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     A      23     A      23      3   15   27     3    5   12   14   14   15   16   17   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     D      24     D      24      5    7   27     3    4    5    7    8   10   12   14   18   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     I      25     I      25      5    7   27     3    4    5    7    9   10   13   16   19   20   22   24   25   26   27   28   29   30   31   32 
LCS_GDT     G      26     G      26      5    7   27     3    4    5    7    9   11   13   17   19   20   22   24   25   26   27   28   29   29   31   32 
LCS_GDT     H      27     H      27      5    7   27     3    4    5    7    9   11   13   17   19   20   22   24   25   26   27   28   29   29   32   34 
LCS_GDT     L      28     L      28      5    7   27     3    4    5    7    9   11   13   17   19   20   22   24   25   26   27   29   30   31   32   34 
LCS_GDT     V      29     V      29      5    6   27     3    4   12   12   13   17   19   20   22   22   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     P      45     P      45      4    7   27     0    4    5    5    7    7    8    9    9   10   14   16   19   23   27   28   29   31   32   34 
LCS_GDT     R      46     R      46      4    7   27     3    4    5    5    7    7    8   10   14   19   22   24   25   26   28   29   30   31   32   34 
LCS_GDT     R      47     R      47      4    7   27     3    4    5    7    9   10   16   18   21   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     V      48     V      48      4   18   27     3    4    5    6    7   10   17   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     L      49     L      49      4   18   25     3    4    5   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     V      50     V      50      4   18   25     3    4    7   13   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     H      51     H      51      5   18   25     3    5   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     E      52     E      52      5   18   25     3    9   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     D      53     D      53      5   18   25     3    4    6   11   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     D      54     D      54     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     L      55     L      55     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     A      56     A      56     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     G      57     G      57     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     A      58     A      58     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     R      59     R      59     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     R      60     R      60     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     L      61     L      61     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     L      62     L      62     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     T      63     T      63     12   18   25     9   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     D      64     D      64     12   18   25     5   11   12   14   18   18   19   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     A      65     A      65     12   18   25     4    8   12   14   18   18   19   21   21   23   24   25   26   27   27   28   30   31   32   34 
LCS_GDT     G      66     G      66      4   18   25     3    4    5   10   14   17   18   21   22   23   24   25   26   27   28   29   30   31   32   34 
LCS_GDT     L      67     L      67      4    7   25     2    4    5    7    9   10   12   16   18   20   21   25   26   27   28   29   30   31   32   34 
LCS_GDT     A      68     A      68      4    7   25     3    4    4    6    7    8    8    9   12   16   18   20   22   24   27   29   29   31   32   34 
LCS_GDT     H      69     H      69      4    7   21     3    4    4    6    7    8    8    9   10   13   16   19   21   21   23   24   27   30   30   32 
LCS_GDT     E      70     E      70      4    7   20     3    4    4    5    7    8    8    9   10   12   16   19   21   23   24   25   29   30   30   32 
LCS_GDT     L      71     L      71      4    5   20     3    4    5    6    7    7    8    9   10   11   16   18   21   23   26   27   29   30   30   32 
LCS_GDT     R      72     R      72      3    5   20     0    3    5    6    7    7    8    9   10   11   14   17   21   23   25   27   29   30   30   32 
LCS_AVERAGE  LCS_A:  26.83  (  14.56   22.22   43.71 )

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     14     18     18     19     21     22     23     24     25     26     27     28     29     30     31     32     34 
GDT PERCENT_CA  19.30  21.05  22.81  24.56  31.58  31.58  33.33  36.84  38.60  40.35  42.11  43.86  45.61  47.37  49.12  50.88  52.63  54.39  56.14  59.65
GDT RMS_LOCAL    0.30   0.35   0.48   0.76   1.53   1.53   1.69   2.18   2.70   2.77   2.95   3.22   3.46   3.83   4.31   4.72   4.80   5.17   5.53   6.10
GDT RMS_ALL_CA  17.73  17.75  17.80  17.71  14.39  14.39  14.34  14.16  14.03  13.96  13.99  13.96  14.00  13.99  14.02  14.00  13.83  13.84  13.87  13.74

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         24.012
LGA    R       2      R       2         22.707
LGA    E       3      E       3         20.241
LGA    L       4      L       4         19.407
LGA    L       5      L       5         17.032
LGA    R       6      R       6         17.730
LGA    T       7      T       7         18.762
LGA    N       8      N       8         15.826
LGA    D       9      D       9         15.210
LGA    A      10      A      10         14.249
LGA    V      11      V      11          9.961
LGA    L      12      L      12          7.046
LGA    L      13      L      13          6.963
LGA    S      14      S      14          6.039
LGA    A      15      A      15          1.495
LGA    V      16      V      16          3.953
LGA    G      17      G      17          9.360
LGA    A      18      A      18         10.217
LGA    L      19      L      19         12.426
LGA    L      20      L      20         15.358
LGA    D      21      D      21         19.065
LGA    G      22      G      22         21.770
LGA    A      23      A      23         23.982
LGA    D      24      D      24         25.050
LGA    I      25      I      25         22.560
LGA    G      26      G      26         23.090
LGA    H      27      H      27         16.293
LGA    L      28      L      28         12.642
LGA    V      29      V      29          6.113
LGA    P      45      P      45         13.978
LGA    R      46      R      46          9.978
LGA    R      47      R      47          5.430
LGA    V      48      V      48          3.838
LGA    L      49      L      49          1.823
LGA    V      50      V      50          2.978
LGA    H      51      H      51          2.707
LGA    E      52      E      52          0.882
LGA    D      53      D      53          2.368
LGA    D      54      D      54          2.359
LGA    L      55      L      55          2.395
LGA    A      56      A      56          1.960
LGA    G      57      G      57          1.858
LGA    A      58      A      58          1.663
LGA    R      59      R      59          0.802
LGA    R      60      R      60          0.963
LGA    L      61      L      61          1.451
LGA    L      62      L      62          1.313
LGA    T      63      T      63          0.522
LGA    D      64      D      64          1.612
LGA    A      65      A      65          3.626
LGA    G      66      G      66          3.453
LGA    L      67      L      67         10.033
LGA    A      68      A      68         14.294
LGA    H      69      H      69         20.858
LGA    E      70      E      70         26.289
LGA    L      71      L      71         23.461
LGA    R      72      R      72         28.868

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     21    2.18    33.333    31.363     0.921

LGA_LOCAL      RMSD =  2.181  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.976  Number of atoms =   57 
Std_ALL_ATOMS  RMSD = 12.199  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.496286 * X  +  -0.098560 * Y  +  -0.862547 * Z  +   1.087448
  Y_new =   0.231631 * X  +   0.972552 * Y  +   0.022144 * Z  +   5.610857
  Z_new =   0.836688 * X  +  -0.210782 * Y  +   0.505493 * Z  +   6.444779 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.395061    2.746531  [ DEG:   -22.6353    157.3647 ]
  Theta =  -0.991208   -2.150384  [ DEG:   -56.7921   -123.2079 ]
  Phi   =   0.436679   -2.704914  [ DEG:    25.0199   -154.9801 ]
 
# 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: T0349TS393_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_2-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   21   2.18  31.363    12.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_2-D1
PFRMAT TS
TARGET T0349
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1     -15.485  18.138   7.062  1.00 25.00           C
ATOM      2  CA  ARG     2     -12.661  15.636   6.517  1.00 25.00           C
ATOM      3  CA  GLU     3     -10.800  15.053   3.273  1.00 25.00           C
ATOM      4  CA  LEU     4     -12.218  11.520   2.859  1.00 25.00           C
ATOM      5  CA  LEU     5      -9.154  10.505   0.799  1.00 25.00           C
ATOM      6  CA  ARG     6      -6.837  11.924   3.498  1.00 25.00           C
ATOM      7  CA  THR     7      -8.745   9.980   6.191  1.00 25.00           C
ATOM      8  CA  ASN     8      -8.436   6.769   4.126  1.00 25.00           C
ATOM      9  CA  ASP     9      -4.675   7.362   3.721  1.00 25.00           C
ATOM     10  CA  ALA    10      -4.328   7.901   7.497  1.00 25.00           C
ATOM     11  CA  VAL    11      -6.248   4.654   8.161  1.00 25.00           C
ATOM     12  CA  LEU    12      -3.966   2.777   5.724  1.00 25.00           C
ATOM     13  CA  LEU    13      -0.876   4.209   7.476  1.00 25.00           C
ATOM     14  CA  SER    14      -2.269   3.122  10.874  1.00 25.00           C
ATOM     15  CA  ALA    15      -2.913  -0.398   9.513  1.00 25.00           C
ATOM     16  CA  VAL    16       0.666  -0.555   8.158  1.00 25.00           C
ATOM     17  CA  GLY    17       2.029   0.554  11.560  1.00 25.00           C
ATOM     18  CA  ALA    18      -0.061  -2.140  13.303  1.00 25.00           C
ATOM     19  CA  LEU    19       1.263  -4.780  10.865  1.00 25.00           C
ATOM     20  CA  LEU    20       4.856  -3.636  11.539  1.00 25.00           C
ATOM     21  CA  ASP    21       4.245  -3.859  15.314  1.00 25.00           C
ATOM     22  CA  GLY    22       4.351  -7.688  15.230  1.00 25.00           C
ATOM     23  CA  ALA    23       2.817  -9.585  12.289  1.00 25.00           C
ATOM     24  CA  ASP    24      -0.863  -9.170  13.384  1.00 25.00           C
ATOM     25  CA  ILE    25      -1.756  -8.655   9.713  1.00 25.00           C
ATOM     26  CA  GLY    26       0.668  -9.035   6.804  1.00 25.00           C
ATOM     27  CA  HIS    27       0.729  -6.139   4.370  1.00 25.00           C
ATOM     28  CA  LEU    28       0.185  -5.230   0.702  1.00 25.00           C
ATOM     29  CA  VAL    29      -0.515  -2.033  -1.206  1.00 25.00           C
ATOM     45  CA  PRO    45       5.307  -0.218   6.139  1.00 25.00           C
ATOM     46  CA  ARG    46       2.794   1.721   3.991  1.00 25.00           C
ATOM     47  CA  ARG    47       0.012   2.740   1.596  1.00 25.00           C
ATOM     48  CA  VAL    48       0.066   6.295   0.325  1.00 25.00           C
ATOM     49  CA  LEU    49       1.377   7.472  -3.102  1.00 25.00           C
ATOM     50  CA  VAL    50      -0.903  10.449  -3.711  1.00 25.00           C
ATOM     51  CA  HIS    51       2.177  12.267  -5.017  1.00 25.00           C
ATOM     52  CA  GLU    52       4.820  14.701  -3.619  1.00 25.00           C
ATOM     53  CA  ASP    53       4.342  16.496  -0.269  1.00 25.00           C
ATOM     54  CA  ASP    54       1.497  14.098   0.639  1.00 25.00           C
ATOM     55  CA  LEU    55       3.707  11.100  -0.252  1.00 25.00           C
ATOM     56  CA  ALA    56       6.529  12.504   1.924  1.00 25.00           C
ATOM     57  CA  GLY    57       4.083  12.977   4.832  1.00 25.00           C
ATOM     58  CA  ALA    58       2.856   9.374   4.421  1.00 25.00           C
ATOM     59  CA  ARG    59       6.472   8.114   4.429  1.00 25.00           C
ATOM     60  CA  ARG    60       7.189  10.120   7.613  1.00 25.00           C
ATOM     61  CA  LEU    61       4.068   8.647   9.272  1.00 25.00           C
ATOM     62  CA  LEU    62       5.179   5.117   8.287  1.00 25.00           C
ATOM     63  CA  THR    63       8.659   5.780   9.744  1.00 25.00           C
ATOM     64  CA  ASP    64       7.083   7.043  12.998  1.00 25.00           C
ATOM     65  CA  ALA    65       4.896   3.905  13.186  1.00 25.00           C
ATOM     66  CA  GLY    66       2.577   6.083  15.284  1.00 25.00           C
ATOM     67  CA  LEU    67      -0.294   8.551  15.338  1.00 25.00           C
ATOM     68  CA  ALA    68       0.542   8.699  19.031  1.00 25.00           C
ATOM     69  CA  HIS    69      -0.405   9.652  22.577  1.00 25.00           C
ATOM     70  CA  GLU    70      -1.956  12.963  23.540  1.00 25.00           C
ATOM     71  CA  LEU    71      -0.809  14.121  20.092  1.00 25.00           C
ATOM     72  CA  ARG    72       1.094  16.816  21.931  1.00 25.00           C
TER
END
