
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS393_4-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:    29         7 - 50          4.95    10.93
  LCS_AVERAGE:     45.24

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        49 - 66          1.96     9.85
  LONGEST_CONTINUOUS_SEGMENT:    18        50 - 67          1.74    10.19
  LCS_AVERAGE:     22.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13         9 - 21          0.48    18.06
  LCS_AVERAGE:     13.97

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      4    5   15     3    4    4    5    5    6    7    8    9   10   13   15   16   16   17   19   20   21   22   28 
LCS_GDT     R       2     R       2      4    5   15     3    4    4    5    5    6    7    8    9   10   12   15   16   16   18   20   21   24   26   28 
LCS_GDT     E       3     E       3      4    5   15     3    4    4    5    5    6    7    8    9   10   13   14   18   19   22   22   26   28   34   36 
LCS_GDT     L       4     L       4      4    5   15     3    4    4    5    5    5    5    6    9   10   13   14   18   19   22   22   26   32   37   40 
LCS_GDT     L       5     L       5      3    5   25     3    3    3    5    5    6    7    8    9   10   13   13   16   37   40   44   46   47   47   48 
LCS_GDT     R       6     R       6      3    4   28     0    3    3    4    4    5    8   14   18   21   29   34   39   43   45   46   47   48   48   48 
LCS_GDT     T       7     T       7      3    4   29    10   12   12   14   17   20   22   24   27   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     N       8     N       8      3   16   29     3    3    5    5    9   12   18   22   28   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     D       9     D       9     13   16   29    10   12   14   14   14   15   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      10     A      10     13   16   29    11   12   14   14   14   17   20   24   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     V      11     V      11     13   16   29    11   12   14   14   14   15   19   24   26   30   32   36   38   43   45   46   47   48   48   48 
LCS_GDT     L      12     L      12     13   16   29    11   12   14   14   14   15   19   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      13     L      13     13   16   29    11   12   14   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     S      14     S      14     13   16   29    11   12   14   14   14   16   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      15     A      15     13   16   29    11   12   14   14   14   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     V      16     V      16     13   16   29    11   12   14   14   16   19   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     G      17     G      17     13   16   29    11   12   14   14   14   15   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      18     A      18     13   16   29    11   12   14   14   14   16   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      19     L      19     13   16   29    11   12   14   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      20     L      20     13   16   29    11   12   14   14   14   15   15   20   28   32   34   36   39   43   45   46   47   48   48   48 
LCS_GDT     D      21     D      21     13   16   29     8   12   14   14   14   15   19   24   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     G      22     G      22      3   16   29     3    3    4    7   13   15   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      23     A      23      3   16   29     3    6   14   14   14   15   16   23   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     D      24     D      24      4   16   29     3    4    4    7   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     I      25     I      25      4    7   29     3    4    4    7   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     G      26     G      26      4    7   29     3    4    4    7   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     H      27     H      27      4    7   29     3    4    4    7   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      28     L      28      4    7   29     3    4    4    7   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     V      29     V      29      4    7   29     3    4    4    7   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     P      45     P      45      4    6   29     0    4    4    5    5    7    8   10   11   14   16   19   23   24   29   30   34   37   41   45 
LCS_GDT     R      46     R      46      5    6   29     2    4    6    6    6    7   11   12   15   19   22   26   31   37   42   46   46   48   48   48 
LCS_GDT     R      47     R      47      5    6   29     3    4    6    6    8   12   16   19   24   27   32   35   40   43   45   46   47   48   48   48 
LCS_GDT     V      48     V      48      5    6   29     3    4    6    6   12   14   20   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      49     L      49      5   18   29     3    4    6    8   13   19   22   24   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     V      50     V      50      6   18   29     2    6    7   10   16   18   22   24   27   30   31   34   38   43   45   46   47   48   48   48 
LCS_GDT     H      51     H      51      6   18   24     3    6   12   14   16   20   22   24   27   30   31   33   36   43   45   46   47   48   48   48 
LCS_GDT     E      52     E      52      6   18   24     3   10   12   14   16   20   22   24   27   30   31   35   40   43   45   46   47   48   48   48 
LCS_GDT     D      53     D      53      6   18   24     3    6    6   10   16   19   22   24   27   30   31   35   40   43   45   46   47   48   48   48 
LCS_GDT     D      54     D      54     12   18   24    10   12   12   14   17   20   22   24   27   30   31   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      55     L      55     12   18   24     9   12   12   14   17   20   22   24   27   30   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      56     A      56     12   18   24    10   12   12   14   17   20   22   24   27   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     G      57     G      57     12   18   24    10   12   12   14   17   20   22   24   27   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      58     A      58     12   18   24    10   12   12   14   17   20   22   24   28   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     R      59     R      59     12   18   24    10   12   12   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     R      60     R      60     12   18   24    10   12   12   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      61     L      61     12   18   24    10   12   12   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      62     L      62     12   18   24    10   12   12   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     T      63     T      63     12   18   24    10   12   12   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     D      64     D      64     12   18   24     5   12   12   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      65     A      65     12   18   24     4   10   12   14   17   20   22   24   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     G      66     G      66     12   18   24     4    4    8   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     L      67     L      67      4   18   24     3    4    7   14   17   20   22   25   30   32   34   36   40   43   45   46   47   48   48   48 
LCS_GDT     A      68     A      68      4    7   24     3    4    4    5    6    7   12   21   23   27   30   35   39   43   45   46   47   48   48   48 
LCS_GDT     H      69     H      69      4    7   24     3    3    4    5    6    7    8   11   13   20   23   26   31   37   41   45   47   48   48   48 
LCS_GDT     E      70     E      70      4    7   24     3    3    4    5    6    7    7    8    9   11   13   15   19   21   24   26   33   33   38   40 
LCS_GDT     L      71     L      71      4    7   22     3    3    4    5    6    6    7    8    8   11   13   15   19   21   23   26   33   33   44   47 
LCS_GDT     R      72     R      72      3    7   14     0    3    4    5    6    6    7    8    8   11   12   14   16   18   18   18   20   24   25   28 
LCS_AVERAGE  LCS_A:  27.34  (  13.97   22.81   45.24 )

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     14     14     17     20     22     25     30     32     34     36     40     43     45     46     47     48     48     48 
GDT PERCENT_CA  19.30  21.05  24.56  24.56  29.82  35.09  38.60  43.86  52.63  56.14  59.65  63.16  70.18  75.44  78.95  80.70  82.46  84.21  84.21  84.21
GDT RMS_LOCAL    0.30   0.35   0.71   0.71   1.52   1.94   2.11   2.95   3.28   3.44   3.68   3.87   4.46   4.67   4.88   4.95   5.23   5.40   5.40   5.40
GDT RMS_ALL_CA  18.09  18.01  18.03  18.03   9.21   9.36   9.37  11.38  11.15  11.07  10.84  10.46   9.74   9.76   9.38   9.44   9.26   9.23   9.23   9.23

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         34.437
LGA    R       2      R       2         29.050
LGA    E       3      E       3         22.905
LGA    L       4      L       4         17.728
LGA    L       5      L       5         12.427
LGA    R       6      R       6         11.090
LGA    T       7      T       7          7.623
LGA    N       8      N       8          6.014
LGA    D       9      D       9          1.833
LGA    A      10      A      10          4.490
LGA    V      11      V      11          5.968
LGA    L      12      L      12          3.783
LGA    L      13      L      13          1.336
LGA    S      14      S      14          3.652
LGA    A      15      A      15          3.815
LGA    V      16      V      16          3.496
LGA    G      17      G      17          3.358
LGA    A      18      A      18          2.516
LGA    L      19      L      19          3.238
LGA    L      20      L      20          5.341
LGA    D      21      D      21          4.665
LGA    G      22      G      22          3.174
LGA    A      23      A      23          4.378
LGA    D      24      D      24          3.288
LGA    I      25      I      25          3.546
LGA    G      26      G      26          3.652
LGA    H      27      H      27          3.268
LGA    L      28      L      28          3.002
LGA    V      29      V      29          2.355
LGA    P      45      P      45         16.798
LGA    R      46      R      46         12.121
LGA    R      47      R      47          7.530
LGA    V      48      V      48          2.280
LGA    L      49      L      49          4.267
LGA    V      50      V      50         10.103
LGA    H      51      H      51         12.200
LGA    E      52      E      52         11.556
LGA    D      53      D      53         11.641
LGA    D      54      D      54          9.789
LGA    L      55      L      55          8.418
LGA    A      56      A      56          6.730
LGA    G      57      G      57          6.425
LGA    A      58      A      58          5.561
LGA    R      59      R      59          3.735
LGA    R      60      R      60          2.812
LGA    L      61      L      61          3.652
LGA    L      62      L      62          1.504
LGA    T      63      T      63          1.331
LGA    D      64      D      64          3.974
LGA    A      65      A      65          4.008
LGA    G      66      G      66          1.087
LGA    L      67      L      67          3.417
LGA    A      68      A      68         10.022
LGA    H      69      H      69         15.820
LGA    E      70      E      70         20.883
LGA    L      71      L      71         20.158
LGA    R      72      R      72         27.408

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     25    2.95    42.544    38.596     0.818

LGA_LOCAL      RMSD =  2.955  Number of atoms =   25  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.976  Number of atoms =   57 
Std_ALL_ATOMS  RMSD =  8.585  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.194939 * X  +  -0.012217 * Y  +   0.980739 * Z  +   2.389538
  Y_new =   0.903806 * X  +   0.386148 * Y  +   0.184457 * Z  +   1.340722
  Z_new =  -0.380964 * X  +   0.922356 * Y  +  -0.064233 * Z  +   6.102601 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.640325   -1.501268  [ DEG:    93.9837    -86.0163 ]
  Theta =   0.390838    2.750754  [ DEG:    22.3934    157.6066 ]
  Phi   =   1.783229   -1.358364  [ DEG:   102.1715    -77.8285 ]
 
# 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_4-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_4-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   25   2.95  38.596     8.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_4-D1
PFRMAT TS
TARGET T0349
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1       1.268 -18.355  11.982  1.00 25.00           C
ATOM      2  CA  ARG     2      -0.427 -16.288   9.289  1.00 25.00           C
ATOM      3  CA  GLU     3       1.935 -15.554   6.402  1.00 25.00           C
ATOM      4  CA  LEU     4       4.357 -12.790   5.320  1.00 25.00           C
ATOM      5  CA  LEU     5       1.832 -11.567   2.714  1.00 25.00           C
ATOM      6  CA  ARG     6      -0.925 -11.518   5.371  1.00 25.00           C
ATOM      7  CA  THR     7       1.343  -9.523   7.724  1.00 25.00           C
ATOM      8  CA  ASN     8       2.099  -7.027   4.918  1.00 25.00           C
ATOM      9  CA  ASP     9      -1.645  -6.653   4.209  1.00 25.00           C
ATOM     10  CA  ALA    10      -2.314  -6.041   7.930  1.00 25.00           C
ATOM     11  CA  VAL    11       0.449  -3.392   8.017  1.00 25.00           C
ATOM     12  CA  LEU    12      -1.056  -1.686   4.935  1.00 25.00           C
ATOM     13  CA  LEU    13      -4.510  -1.692   6.588  1.00 25.00           C
ATOM     14  CA  SER    14      -3.019  -0.158   9.764  1.00 25.00           C
ATOM     15  CA  ALA    15      -1.296   2.552   7.677  1.00 25.00           C
ATOM     16  CA  VAL    16      -4.598   3.313   5.895  1.00 25.00           C
ATOM     17  CA  GLY    17      -6.388   3.576   9.270  1.00 25.00           C
ATOM     18  CA  ALA    18      -3.678   5.960  10.550  1.00 25.00           C
ATOM     19  CA  LEU    19      -4.043   8.106   7.399  1.00 25.00           C
ATOM     20  CA  LEU    20      -7.840   8.214   7.883  1.00 25.00           C
ATOM     21  CA  ASP    21      -7.369   9.267  11.536  1.00 25.00           C
ATOM     22  CA  GLY    22      -8.473  12.864  10.910  1.00 25.00           C
ATOM     23  CA  ALA    23      -7.333  13.826   7.429  1.00 25.00           C
ATOM     24  CA  ASP    24      -4.601  15.816   9.172  1.00 25.00           C
ATOM     25  CA  ILE    25      -2.188  13.378   7.608  1.00 25.00           C
ATOM     26  CA  GLY    26      -3.271  12.435   4.105  1.00 25.00           C
ATOM     27  CA  HIS    27      -4.930   9.384   2.628  1.00 25.00           C
ATOM     28  CA  LEU    28      -2.995   8.282  -0.499  1.00 25.00           C
ATOM     29  CA  VAL    29      -3.961   4.899  -2.086  1.00 25.00           C
ATOM     45  CA  PRO    45       7.869   0.682   7.454  1.00 25.00           C
ATOM     46  CA  ARG    46       4.131   0.065   6.793  1.00 25.00           C
ATOM     47  CA  ARG    47       3.993   1.444   3.223  1.00 25.00           C
ATOM     48  CA  VAL    48       2.108   2.739   0.130  1.00 25.00           C
ATOM     49  CA  LEU    49       3.898   2.834  -3.192  1.00 25.00           C
ATOM     50  CA  VAL    50       5.450   2.353  -6.693  1.00 25.00           C
ATOM     51  CA  HIS    51       8.527   4.610  -7.074  1.00 25.00           C
ATOM     52  CA  GLU    52      11.640   5.889  -5.426  1.00 25.00           C
ATOM     53  CA  ASP    53      10.611   9.327  -4.091  1.00 25.00           C
ATOM     54  CA  ASP    54       6.999   8.117  -3.689  1.00 25.00           C
ATOM     55  CA  LEU    55       8.223   5.015  -1.806  1.00 25.00           C
ATOM     56  CA  ALA    56      10.349   7.219   0.493  1.00 25.00           C
ATOM     57  CA  GLY    57       7.327   9.472   1.169  1.00 25.00           C
ATOM     58  CA  ALA    58       5.191   6.402   1.991  1.00 25.00           C
ATOM     59  CA  ARG    59       7.895   5.131   4.387  1.00 25.00           C
ATOM     60  CA  ARG    60       8.032   8.559   6.089  1.00 25.00           C
ATOM     61  CA  LEU    61       4.220   8.555   6.459  1.00 25.00           C
ATOM     62  CA  LEU    62       4.347   5.045   7.984  1.00 25.00           C
ATOM     63  CA  THR    63       7.055   6.184  10.442  1.00 25.00           C
ATOM     64  CA  ASP    64       4.927   9.215  11.419  1.00 25.00           C
ATOM     65  CA  ALA    65       1.898   6.940  11.979  1.00 25.00           C
ATOM     66  CA  GLY    66       3.478   3.725  13.380  1.00 25.00           C
ATOM     67  CA  LEU    67       4.211   0.429  15.129  1.00 25.00           C
ATOM     68  CA  ALA    68       4.740   1.437  18.759  1.00 25.00           C
ATOM     69  CA  HIS    69       4.209   2.754  22.226  1.00 25.00           C
ATOM     70  CA  GLU    70       5.366   0.411  24.966  1.00 25.00           C
ATOM     71  CA  LEU    71       4.378  -2.353  22.504  1.00 25.00           C
ATOM     72  CA  ARG    72       3.053  -4.208  25.571  1.00 25.00           C
TER
END
