
#######################################################
#                                                     #
#                        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   61 (   61),  selected   61 , name T0381TS393_5-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS393_5-D1.T0381_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:    34        17 - 50          4.89    14.73
  LCS_AVERAGE:     49.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        46 - 64          1.99    15.09
  LCS_AVERAGE:     24.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        49 - 63          0.92    15.69
  LCS_AVERAGE:     16.21

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:   61
LCS_GDT     V      17     V      17     14   18   34     6   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   37   39   40 
LCS_GDT     Q      18     Q      18     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   37   39   40 
LCS_GDT     S      19     S      19     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   37   39   40 
LCS_GDT     L      20     L      20     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   37   39   40 
LCS_GDT     A      21     A      21     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   37   39   40 
LCS_GDT     R      22     R      22     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   37   39   40 
LCS_GDT     G      23     G      23     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   32   34   35   37   39   40 
LCS_GDT     L      24     L      24     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   32   34   35   37   39   40 
LCS_GDT     A      25     A      25     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   32   34   35   37   39   40 
LCS_GDT     V      26     V      26     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   32   34   35   37   39   41 
LCS_GDT     I      27     I      27     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   32   33   35   35   36   40 
LCS_GDT     R      28     R      28     14   18   34    12   13   14   15   16   18   22   23   24   26   27   29   30   31   33   34   35   35   39   41 
LCS_GDT     C      29     C      29     14   18   34    12   13   14   15   16   18   22   23   24   26   27   30   31   32   33   35   36   37   39   42 
LCS_GDT     F      30     F      30     14   18   34     3    6   14   15   16   18   22   23   24   26   27   30   31   32   33   35   36   37   39   42 
LCS_GDT     D      31     D      31      4   18   34     3    4    5   11   16   18   22   23   24   26   27   30   31   32   33   35   36   37   39   42 
LCS_GDT     H      32     H      32      3   18   34     3    3    5    9   14   18   22   23   24   26   27   30   31   32   33   35   36   37   39   42 
LCS_GDT     R      33     R      33      3   18   34     3    4    5   10   16   18   22   23   24   26   27   29   30   31   32   35   36   37   39   42 
LCS_GDT     N      34     N      34      4   18   34     3    3    4    5    8   17   22   23   24   26   27   29   30   31   35   35   36   38   39   42 
LCS_GDT     Q      35     Q      35      4    7   34     1    3    4    5   13   18   22   23   24   26   27   29   32   33   35   35   36   38   39   42 
LCS_GDT     R      36     R      36      4    7   34     0    3    4    5    8   10   14   21   24   25   27   29   32   33   35   35   36   38   38   41 
LCS_GDT     R      37     R      37      4    7   34     3    3    5    7   10   17   22   22   24   26   27   29   32   33   35   35   36   38   39   42 
LCS_GDT     T      38     T      38      9   10   34     3    3    8   14   16   18   22   23   24   26   27   29   30   32   34   35   36   38   39   40 
LCS_GDT     L      39     L      39      9   10   34     8   10   12   14   16   18   22   23   24   26   27   29   32   33   35   35   36   38   39   42 
LCS_GDT     S      40     S      40      9   10   34     8   10   12   14   16   18   20   23   24   26   27   29   32   33   35   35   36   38   39   42 
LCS_GDT     D      41     D      41      9   10   34     8   10   12   14   16   18   20   22   24   26   27   29   32   33   35   35   36   38   39   42 
LCS_GDT     V      42     V      42      9   10   34     8   10   12   14   16   18   20   23   24   26   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     A      43     A      43      9   10   34     8    9   12   15   16   18   20   22   24   26   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     R      44     R      44      9   10   34     8   10   12   14   16   18   20   22   24   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     A      45     A      45      9   10   34     8   10   12   14   16   18   20   22   24   25   27   29   31   32   35   35   36   38   39   42 
LCS_GDT     T      46     T      46      9   19   34     8    8   11   15   16   18   20   22   24   24   26   30   31   32   33   35   36   38   39   42 
LCS_GDT     D      47     D      47      9   19   34     3    4   12   15   16   18   20   22   24   24   26   28   31   32   33   35   36   38   39   42 
LCS_GDT     L      48     L      48      5   19   34     3    4    6    7   11   17   18   19   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     T      49     T      49     15   19   34     3   10   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     R      50     R      50     15   19   34     3   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     A      51     A      51     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     T      52     T      52     15   19   28     9   13   14   15   16   17   18   21   24   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     A      53     A      53     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     R      54     R      54     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     R      55     R      55     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     F      56     F      56     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     L      57     L      57     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     L      58     L      58     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     T      59     T      59     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     L      60     L      60     15   19   28     9   13   14   15   16   18   20   21   24   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     V      61     V      61     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     E      62     E      62     15   19   28     9   13   14   15   16   17   18   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     L      63     L      63     15   19   28     3    3    4   14   16   16   19   21   24   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     G      64     G      64      3   19   28     3    5    8   14   16   18   20   22   24   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     Y      65     Y      65      4   10   28     1    5    9   12   15   18   20   22   24   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     V      66     V      66      4   10   28     3   10   12   14   16   18   20   22   24   24   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     A      67     A      67      4   10   28     3    4    8   14   16   18   20   21   24   24   25   27   30   33   35   35   36   38   39   42 
LCS_GDT     T      68     T      68      4   10   23     3    4    4    6   10   12   18   18   19   23   24   26   28   30   33   34   35   37   39   40 
LCS_GDT     D      69     D      69      4   10   23     3    4    4    8   10   12   13   15   19   22   23   26   28   30   33   34   35   37   39   40 
LCS_GDT     G      70     G      70      4   10   23     4    4    5    8   10   12   13   15   16   22   24   26   28   30   33   34   35   37   39   40 
LCS_GDT     S      71     S      71      4   10   23     4    4    5    8   10   12   18   18   22   24   25   27   28   30   33   34   35   37   39   40 
LCS_GDT     A      72     A      72      5   10   22     4    5   12   14   16   18   20   22   24   24   25   28   29   30   33   34   35   37   39   40 
LCS_GDT     F      73     F      73      5   10   19     4   10   12   14   16   18   20   22   24   24   25   29   32   33   35   35   36   38   39   42 
LCS_GDT     W      74     W      74      5    9   19     3    5    8   10   15   16   18   22   23   24   27   29   32   33   35   35   36   38   39   42 
LCS_GDT     L      75     L      75      5    9   19     3    5    6   10   15   16   17   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     T      76     T      76      5    9   19     3    5    6   10   15   16   17   21   23   25   27   30   32   33   35   35   36   38   39   42 
LCS_GDT     P      77     P      77      5    9   19     0    3    6    7    9   15   17   21   23   25   27   30   31   32   33   35   36   37   39   42 
LCS_AVERAGE  LCS_A:  30.06  (  16.21   24.51   49.48 )

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     12     13     14     15     16     18     22     23     24     26     27     30     32     33     35     35     36     38     39     42 
GDT PERCENT_CA  19.67  21.31  22.95  24.59  26.23  29.51  36.07  37.70  39.34  42.62  44.26  49.18  52.46  54.10  57.38  57.38  59.02  62.30  63.93  68.85
GDT RMS_LOCAL    0.23   0.32   0.68   0.94   1.10   1.71   2.63   2.66   2.62   3.00   3.24   3.72   4.45   4.65   4.91   4.85   4.94   5.43   5.42   6.09
GDT RMS_ALL_CA  15.98  15.96  15.70  15.76  16.01  11.35  14.26  14.64  11.37  14.66  14.41  12.65  12.11  12.16  12.10  12.11  12.22  11.87  11.75  12.11

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17          1.842
LGA    Q      18      Q      18          1.172
LGA    S      19      S      19          2.717
LGA    L      20      L      20          2.445
LGA    A      21      A      21          1.237
LGA    R      22      R      22          1.838
LGA    G      23      G      23          2.652
LGA    L      24      L      24          2.281
LGA    A      25      A      25          1.607
LGA    V      26      V      26          1.905
LGA    I      27      I      27          2.025
LGA    R      28      R      28          2.014
LGA    C      29      C      29          2.531
LGA    F      30      F      30          2.828
LGA    D      31      D      31          2.912
LGA    H      32      H      32          3.952
LGA    R      33      R      33          2.666
LGA    N      34      N      34          3.310
LGA    Q      35      Q      35          3.491
LGA    R      36      R      36          5.758
LGA    R      37      R      37          4.397
LGA    T      38      T      38          3.138
LGA    L      39      L      39          3.668
LGA    S      40      S      40          3.921
LGA    D      41      D      41          4.822
LGA    V      42      V      42          3.926
LGA    A      43      A      43          5.882
LGA    R      44      R      44         10.403
LGA    A      45      A      45         11.426
LGA    T      46      T      46         10.264
LGA    D      47      D      47         13.558
LGA    L      48      L      48          8.436
LGA    T      49      T      49          5.852
LGA    R      50      R      50         10.702
LGA    A      51      A      51         11.938
LGA    T      52      T      52          8.716
LGA    A      53      A      53          8.525
LGA    R      54      R      54         15.928
LGA    R      55      R      55         17.430
LGA    F      56      F      56         13.824
LGA    L      57      L      57         16.713
LGA    L      58      L      58         23.398
LGA    T      59      T      59         22.900
LGA    L      60      L      60         19.790
LGA    V      61      V      61         25.963
LGA    E      62      E      62         30.498
LGA    L      63      L      63         29.704
LGA    G      64      G      64         28.525
LGA    Y      65      Y      65         23.157
LGA    V      66      V      66         20.675
LGA    A      67      A      67         24.387
LGA    T      68      T      68         24.671
LGA    D      69      D      69         28.439
LGA    G      70      G      70         25.419
LGA    S      71      S      71         18.415
LGA    A      72      A      72         13.487
LGA    F      73      F      73         13.973
LGA    W      74      W      74         14.237
LGA    L      75      L      75         14.677
LGA    T      76      T      76         20.025
LGA    P      77      P      77         20.368

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   61   61    4.0     23    2.66    35.246    32.968     0.835

LGA_LOCAL      RMSD =  2.656  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.421  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 10.631  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.219060 * X  +   0.000112 * Y  +   0.975711 * Z  +  21.470350
  Y_new =   0.973450 * X  +   0.068020 * Y  +  -0.218560 * Z  +  43.246277
  Z_new =  -0.066393 * X  +   0.997684 * Y  +   0.014792 * Z  +  29.252819 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.555972   -1.585621  [ DEG:    89.1506    -90.8494 ]
  Theta =   0.066442    3.075151  [ DEG:     3.8068    176.1932 ]
  Phi   =   1.349449   -1.792143  [ DEG:    77.3177   -102.6823 ]
 
# 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: T0381TS393_5-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS393_5-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   61   61   4.0   23   2.66  32.968    10.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS393_5-D1
PFRMAT TS
TARGET T0381
MODEL 5
PARENT N/A
ATOM     17  CA  VAL    17       8.500  54.969  35.422  1.00 25.00           C
ATOM     18  CA  GLN    18       7.955  57.864  32.975  1.00 25.00           C
ATOM     19  CA  SER    19      11.364  57.182  31.369  1.00 25.00           C
ATOM     20  CA  LEU    20      10.487  53.470  31.023  1.00 25.00           C
ATOM     21  CA  ALA    21       7.142  54.387  29.398  1.00 25.00           C
ATOM     22  CA  ARG    22       8.941  56.726  26.957  1.00 25.00           C
ATOM     23  CA  GLY    23      11.421  53.943  26.079  1.00 25.00           C
ATOM     24  CA  LEU    24       8.521  51.517  25.474  1.00 25.00           C
ATOM     25  CA  ALA    25       6.809  54.089  23.211  1.00 25.00           C
ATOM     26  CA  VAL    26      10.064  54.568  21.251  1.00 25.00           C
ATOM     27  CA  ILE    27      10.407  50.775  20.843  1.00 25.00           C
ATOM     28  CA  ARG    28       6.793  50.559  19.594  1.00 25.00           C
ATOM     29  CA  CYS    29       7.466  53.373  17.084  1.00 25.00           C
ATOM     30  CA  PHE    30      10.606  51.558  15.855  1.00 25.00           C
ATOM     31  CA  ASP    31       8.602  48.321  15.440  1.00 25.00           C
ATOM     32  CA  HIS    32       9.575  47.811  11.740  1.00 25.00           C
ATOM     33  CA  ARG    33       6.334  46.774   9.971  1.00 25.00           C
ATOM     34  CA  ASN    34       6.879  49.401   7.355  1.00 25.00           C
ATOM     35  CA  GLN    35       6.939  53.231   6.997  1.00 25.00           C
ATOM     36  CA  ARG    36       4.009  55.535   6.242  1.00 25.00           C
ATOM     37  CA  ARG    37       2.999  54.781   9.831  1.00 25.00           C
ATOM     38  CA  THR    38       3.724  58.389  10.533  1.00 25.00           C
ATOM     39  CA  LEU    39       5.063  59.027  14.016  1.00 25.00           C
ATOM     40  CA  SER    40       5.248  62.759  13.175  1.00 25.00           C
ATOM     41  CA  ASP    41       1.951  63.365  15.027  1.00 25.00           C
ATOM     42  CA  VAL    42       3.282  61.461  18.071  1.00 25.00           C
ATOM     43  CA  ALA    43       6.488  63.555  18.009  1.00 25.00           C
ATOM     44  CA  ARG    44       4.414  66.770  17.833  1.00 25.00           C
ATOM     45  CA  ALA    45       2.300  65.598  20.803  1.00 25.00           C
ATOM     46  CA  THR    46       5.479  64.828  22.795  1.00 25.00           C
ATOM     47  CA  ASP    47       6.038  68.374  24.133  1.00 25.00           C
ATOM     48  CA  LEU    48       2.303  68.415  24.943  1.00 25.00           C
ATOM     49  CA  THR    49      -0.685  66.701  26.688  1.00 25.00           C
ATOM     50  CA  ARG    50      -0.910  63.708  29.039  1.00 25.00           C
ATOM     51  CA  ALA    51      -4.287  62.148  28.125  1.00 25.00           C
ATOM     52  CA  THR    52      -2.795  60.760  24.883  1.00 25.00           C
ATOM     53  CA  ALA    53       0.147  59.283  26.839  1.00 25.00           C
ATOM     54  CA  ARG    54      -2.281  57.665  29.319  1.00 25.00           C
ATOM     55  CA  ARG    55      -4.296  56.185  26.418  1.00 25.00           C
ATOM     56  CA  PHE    56      -1.083  54.798  24.862  1.00 25.00           C
ATOM     57  CA  LEU    57      -0.099  53.241  28.220  1.00 25.00           C
ATOM     58  CA  LEU    58      -3.570  51.649  28.526  1.00 25.00           C
ATOM     59  CA  THR    59      -3.263  50.240  24.979  1.00 25.00           C
ATOM     60  CA  LEU    60       0.186  48.803  25.821  1.00 25.00           C
ATOM     61  CA  VAL    61      -1.234  47.192  28.993  1.00 25.00           C
ATOM     62  CA  GLU    62      -4.104  45.670  26.966  1.00 25.00           C
ATOM     63  CA  LEU    63      -2.723  42.198  26.243  1.00 25.00           C
ATOM     64  CA  GLY    64      -2.432  42.987  22.555  1.00 25.00           C
ATOM     65  CA  TYR    65      -2.491  46.114  20.364  1.00 25.00           C
ATOM     66  CA  VAL    66      -2.552  49.887  20.020  1.00 25.00           C
ATOM     67  CA  ALA    67      -5.197  50.275  17.290  1.00 25.00           C
ATOM     68  CA  THR    68      -7.444  53.388  16.990  1.00 25.00           C
ATOM     69  CA  ASP    69     -10.412  52.461  14.738  1.00 25.00           C
ATOM     70  CA  GLY    70      -8.185  51.828  11.708  1.00 25.00           C
ATOM     71  CA  SER    71      -5.392  53.405   9.592  1.00 25.00           C
ATOM     72  CA  ALA    72      -2.545  55.454  11.064  1.00 25.00           C
ATOM     73  CA  PHE    73      -1.102  53.514  14.011  1.00 25.00           C
ATOM     74  CA  TRP    74       0.211  50.432  15.750  1.00 25.00           C
ATOM     75  CA  LEU    75       2.131  47.655  17.414  1.00 25.00           C
ATOM     76  CA  THR    76       1.460  43.927  17.280  1.00 25.00           C
ATOM     77  CA  PRO    77       2.941  43.096  20.647  1.00 25.00           C
TER
END
