
#######################################################
#                                                     #
#                        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 T0381TS168_3-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS168_3-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:    33        17 - 49          4.76    14.49
  LCS_AVERAGE:     47.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        17 - 35          1.89    14.14
  LONGEST_CONTINUOUS_SEGMENT:    19        46 - 64          1.91    16.12
  LCS_AVERAGE:     25.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        17 - 30          0.64    14.46
  LCS_AVERAGE:     14.67

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   19   33     7   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     Q      18     Q      18     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     S      19     S      19     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     L      20     L      20     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     A      21     A      21     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     R      22     R      22     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     G      23     G      23     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     L      24     L      24     14   19   33    12   13   14   15   18   20   23   26   26   26   28   28   30   31   32   33   34   36   37   39 
LCS_GDT     A      25     A      25     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   32   33   34   36   38   40 
LCS_GDT     V      26     V      26     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   33   34   35   36   38   39   40 
LCS_GDT     I      27     I      27     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   31   33   35   35   37   39   40 
LCS_GDT     R      28     R      28     14   19   33    12   13   14   15   16   20   23   26   26   26   28   28   30   33   34   35   35   38   39   40 
LCS_GDT     C      29     C      29     14   19   33    12   13   14   15   16   20   23   26   26   26   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     F      30     F      30     14   19   33     3    5   13   15   16   20   23   26   26   26   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     D      31     D      31      5   19   33     3    5    5    9   16   20   23   26   26   26   29   30   31   34   35   35   36   38   39   42 
LCS_GDT     H      32     H      32      5   19   33     3    5    5    9   13   19   23   26   26   26   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     R      33     R      33      5   19   33     3    5    5    9   16   20   23   26   26   26   28   28   31   34   35   35   36   38   40   42 
LCS_GDT     N      34     N      34      4   19   33     3    3    5    8   16   20   23   26   26   26   28   29   31   34   35   35   36   38   40   42 
LCS_GDT     Q      35     Q      35      4   19   33     7   12   14   15   16   20   23   26   26   26   28   28   31   34   35   35   36   38   40   42 
LCS_GDT     R      36     R      36      4   11   33     3    3    5    7   11   12   18   26   26   26   28   28   30   31   33   35   35   38   40   42 
LCS_GDT     R      37     R      37      4   11   33     1    3    7    9   12   18   23   26   26   26   28   28   30   31   33   35   35   38   40   42 
LCS_GDT     T      38     T      38      9   11   33     3    4    8   10   14   20   23   26   26   26   28   28   30   31   33   33   35   36   38   40 
LCS_GDT     L      39     L      39      9   10   33     8    9    9   10   13   17   19   26   26   26   28   28   30   31   33   35   35   38   40   42 
LCS_GDT     S      40     S      40      9   10   33     8    9    9   10   13   17   19   20   22   24   26   28   30   31   33   35   36   38   40   42 
LCS_GDT     D      41     D      41      9   10   33     8    9    9   10   16   18   19   21   22   24   26   28   31   34   35   35   36   38   40   42 
LCS_GDT     V      42     V      42      9   10   33     8    9    9   10   15   18   19   21   23   25   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     A      43     A      43      9   10   33     8    9    9   10   13   17   19   21   22   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     R      44     R      44      9   10   33     8    9    9   10   13   17   19   20   22   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     A      45     A      45      9   10   33     8    9    9   10   13   17   19   20   22   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     T      46     T      46      9   19   33     8    9   11   14   15   17   20   22   23   24   26   29   31   33   34   35   36   38   40   42 
LCS_GDT     D      47     D      47      4   19   33     5   14   15   15   18   18   20   22   23   23   25   27   29   33   34   35   36   38   40   41 
LCS_GDT     L      48     L      48      4   19   33     5   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     T      49     T      49      4   19   33     5    5    9   13   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     R      50     R      50     13   19   26     6   13   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     A      51     A      51     13   19   26    11   14   15   15   18   20   23   26   26   26   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     T      52     T      52     13   19   26     9   14   15   15   18   20   23   26   26   26   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     A      53     A      53     13   19   26    11   14   15   15   18   18   23   26   26   26   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     R      54     R      54     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     R      55     R      55     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     F      56     F      56     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     L      57     L      57     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     L      58     L      58     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     T      59     T      59     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     L      60     L      60     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     V      61     V      61     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     E      62     E      62     13   19   26    11   14   15   15   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     L      63     L      63      3   19   26     3    3    5    6   18   18   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     G      64     G      64      3   19   26     3    3    5   10   15   17   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     Y      65     Y      65      4   10   26     3    4    6    9   13   17   20   22   23   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     V      66     V      66      4   10   26     3    3    6    7   13   17   19   20   22   23   28   30   31   34   35   35   36   38   40   42 
LCS_GDT     A      67     A      67      4   10   26     5    9    9   10   13   17   19   20   22   23   25   27   29   31   33   35   35   38   40   42 
LCS_GDT     T      68     T      68      4   10   23     3    4    6    8   10   14   17   19   22   23   27   27   29   31   33   33   35   36   38   40 
LCS_GDT     D      69     D      69      4   10   23     3    4    6    9   11   12   13   15   20   23   27   27   29   31   33   33   35   36   38   40 
LCS_GDT     G      70     G      70      4   10   23     3    4    7    9   11   12   13   15   16   18   27   27   29   30   33   33   34   36   38   40 
LCS_GDT     S      71     S      71      4   10   23     3    4    7    9   11   12   13   15   16   21   23   26   28   31   33   33   35   36   38   40 
LCS_GDT     A      72     A      72      4   10   23     3    4    7    9   11   17   19   20   22   23   27   27   29   31   33   33   35   36   38   40 
LCS_GDT     F      73     F      73      4   10   18     3    4    5    9   12   17   19   20   22   23   27   27   29   31   33   35   35   38   40   42 
LCS_GDT     W      74     W      74      4   10   18     3    4    7    9   11   12   13   17   20   23   27   27   31   34   35   35   36   38   40   42 
LCS_GDT     L      75     L      75      4   10   18     3    4    7    9   11   12   13   17   20   23   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     T      76     T      76      4   10   18     3    4    7    9   11   12   14   18   22   24   29   30   31   34   35   35   36   38   40   42 
LCS_GDT     P      77     P      77      3   10   18     0    3    5    9   11   12   16   18   22   24   29   30   31   34   35   35   36   38   40   42 
LCS_AVERAGE  LCS_A:  29.23  (  14.67   25.67   47.35 )

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     14     15     15     18     20     23     26     26     26     29     30     31     34     35     35     36     38     40     42 
GDT PERCENT_CA  19.67  22.95  24.59  24.59  29.51  32.79  37.70  42.62  42.62  42.62  47.54  49.18  50.82  55.74  57.38  57.38  59.02  62.30  65.57  68.85
GDT RMS_LOCAL    0.23   0.45   0.59   0.59   1.47   2.17   2.41   2.62   2.62   2.62   3.78   3.86   4.00   4.62   4.70   4.70   4.87   5.34   5.85   6.10
GDT RMS_ALL_CA  14.26  17.09  17.09  17.09  17.23  13.38  13.30  13.28  13.28  13.28  12.71  12.69  12.73  12.32  12.32  12.32  12.30  12.33  12.17  12.16

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17          2.039
LGA    Q      18      Q      18          1.689
LGA    S      19      S      19          2.959
LGA    L      20      L      20          2.305
LGA    A      21      A      21          0.721
LGA    R      22      R      22          1.686
LGA    G      23      G      23          2.323
LGA    L      24      L      24          2.176
LGA    A      25      A      25          1.609
LGA    V      26      V      26          1.166
LGA    I      27      I      27          1.806
LGA    R      28      R      28          2.549
LGA    C      29      C      29          2.356
LGA    F      30      F      30          2.323
LGA    D      31      D      31          2.985
LGA    H      32      H      32          3.338
LGA    R      33      R      33          2.187
LGA    N      34      N      34          2.714
LGA    Q      35      Q      35          2.668
LGA    R      36      R      36          3.802
LGA    R      37      R      37          3.451
LGA    T      38      T      38          2.572
LGA    L      39      L      39          3.881
LGA    S      40      S      40          8.735
LGA    D      41      D      41          8.887
LGA    V      42      V      42          6.171
LGA    A      43      A      43          9.713
LGA    R      44      R      44         15.651
LGA    A      45      A      45         15.635
LGA    T      46      T      46         13.298
LGA    D      47      D      47         17.184
LGA    L      48      L      48         11.918
LGA    T      49      T      49         10.040
LGA    R      50      R      50          7.178
LGA    A      51      A      51          2.954
LGA    T      52      T      52          3.416
LGA    A      53      A      53          3.861
LGA    R      54      R      54          9.262
LGA    R      55      R      55         10.630
LGA    F      56      F      56          8.329
LGA    L      57      L      57         12.509
LGA    L      58      L      58         17.979
LGA    T      59      T      59         17.959
LGA    L      60      L      60         16.587
LGA    V      61      V      61         23.062
LGA    E      62      E      62         26.710
LGA    L      63      L      63         28.755
LGA    G      64      G      64         27.637
LGA    Y      65      Y      65         21.195
LGA    V      66      V      66         20.916
LGA    A      67      A      67         21.613
LGA    T      68      T      68         22.569
LGA    D      69      D      69         26.217
LGA    G      70      G      70         23.796
LGA    S      71      S      71         16.327
LGA    A      72      A      72         12.522
LGA    F      73      F      73         11.550
LGA    W      74      W      74         12.721
LGA    L      75      L      75         15.349
LGA    T      76      T      76         21.640
LGA    P      77      P      77         20.635

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   61   61    4.0     26    2.62    36.885    34.566     0.957

LGA_LOCAL      RMSD =  2.617  Number of atoms =   26  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.350  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 10.529  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.574192 * X  +  -0.060234 * Y  +   0.816502 * Z  +  22.071192
  Y_new =   0.316762 * X  +  -0.935967 * Y  +   0.153710 * Z  +  43.813156
  Z_new =   0.754961 * X  +   0.346896 * Y  +   0.556505 * Z  +  27.180328 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.557410   -2.584183  [ DEG:    31.9372   -148.0628 ]
  Theta =  -0.855594   -2.285999  [ DEG:   -49.0219   -130.9781 ]
  Phi   =   2.637472   -0.504121  [ DEG:   151.1160    -28.8840 ]
 
# 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: T0381TS168_3-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS168_3-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   26   2.62  34.566    10.53
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS168_3-D1
PFRMAT TS
TARGET T0381
MODEL 3
PARENT N/A
ATOM     17  CA  VAL    17       9.632  54.491  35.564  1.00 25.00           C
ATOM     18  CA  GLN    18       8.494  57.431  33.389  1.00 25.00           C
ATOM     19  CA  SER    19      11.704  57.175  31.318  1.00 25.00           C
ATOM     20  CA  LEU    20      11.139  53.415  30.862  1.00 25.00           C
ATOM     21  CA  ALA    21       7.535  54.068  29.741  1.00 25.00           C
ATOM     22  CA  ARG    22       8.764  56.691  27.237  1.00 25.00           C
ATOM     23  CA  GLY    23      11.353  54.217  25.877  1.00 25.00           C
ATOM     24  CA  LEU    24       8.637  51.543  25.504  1.00 25.00           C
ATOM     25  CA  ALA    25       6.402  54.036  23.643  1.00 25.00           C
ATOM     26  CA  VAL    26       9.306  54.935  21.313  1.00 25.00           C
ATOM     27  CA  ILE    27       9.942  51.220  20.632  1.00 25.00           C
ATOM     28  CA  ARG    28       6.229  50.701  19.850  1.00 25.00           C
ATOM     29  CA  CYS    29       6.294  53.687  17.451  1.00 25.00           C
ATOM     30  CA  PHE    30       9.395  52.259  15.718  1.00 25.00           C
ATOM     31  CA  ASP    31       7.665  48.860  15.367  1.00 25.00           C
ATOM     32  CA  HIS    32       8.416  46.429  12.559  1.00 25.00           C
ATOM     33  CA  ARG    33       5.981  46.946   9.661  1.00 25.00           C
ATOM     34  CA  ASN    34       7.352  50.239   8.209  1.00 25.00           C
ATOM     35  CA  GLN    35       8.844  53.771   8.420  1.00 25.00           C
ATOM     36  CA  ARG    36       6.561  55.982   6.312  1.00 25.00           C
ATOM     37  CA  ARG    37       3.796  56.368   8.954  1.00 25.00           C
ATOM     38  CA  THR    38       4.856  60.016   8.762  1.00 25.00           C
ATOM     39  CA  LEU    39       6.050  59.452  12.337  1.00 25.00           C
ATOM     40  CA  SER    40       9.357  60.758  10.915  1.00 25.00           C
ATOM     41  CA  ASP    41       8.456  64.313  12.015  1.00 25.00           C
ATOM     42  CA  VAL    42       7.621  63.041  15.529  1.00 25.00           C
ATOM     43  CA  ALA    43      10.973  61.195  15.684  1.00 25.00           C
ATOM     44  CA  ARG    44      12.803  64.377  14.590  1.00 25.00           C
ATOM     45  CA  ALA    45      10.976  66.386  17.290  1.00 25.00           C
ATOM     46  CA  THR    46      11.940  63.775  19.920  1.00 25.00           C
ATOM     47  CA  ASP    47      13.083  66.377  22.406  1.00 25.00           C
ATOM     48  CA  LEU    48       9.711  68.038  22.571  1.00 25.00           C
ATOM     49  CA  THR    49       8.324  67.956  26.096  1.00 25.00           C
ATOM     50  CA  ARG    50       5.197  69.394  24.554  1.00 25.00           C
ATOM     51  CA  ALA    51       1.753  68.431  23.187  1.00 25.00           C
ATOM     52  CA  THR    52       3.294  65.458  21.330  1.00 25.00           C
ATOM     53  CA  ALA    53       5.067  64.343  24.536  1.00 25.00           C
ATOM     54  CA  ARG    54       1.773  64.592  26.474  1.00 25.00           C
ATOM     55  CA  ARG    55       0.006  62.510  23.790  1.00 25.00           C
ATOM     56  CA  PHE    56       2.776  59.872  23.978  1.00 25.00           C
ATOM     57  CA  LEU    57       2.445  59.760  27.791  1.00 25.00           C
ATOM     58  CA  LEU    58      -1.347  59.325  27.473  1.00 25.00           C
ATOM     59  CA  THR    59      -0.835  56.478  24.964  1.00 25.00           C
ATOM     60  CA  LEU    60       1.642  54.790  27.348  1.00 25.00           C
ATOM     61  CA  VAL    61      -0.867  55.113  30.223  1.00 25.00           C
ATOM     62  CA  GLU    62      -3.610  53.578  28.035  1.00 25.00           C
ATOM     63  CA  LEU    63      -5.225  50.177  28.809  1.00 25.00           C
ATOM     64  CA  GLY    64      -3.228  48.406  26.051  1.00 25.00           C
ATOM     65  CA  TYR    65      -1.340  50.667  23.644  1.00 25.00           C
ATOM     66  CA  VAL    66      -3.365  53.292  21.721  1.00 25.00           C
ATOM     67  CA  ALA    67      -3.355  54.658  18.163  1.00 25.00           C
ATOM     68  CA  THR    68      -6.047  54.928  15.529  1.00 25.00           C
ATOM     69  CA  ASP    69      -9.447  55.745  13.911  1.00 25.00           C
ATOM     70  CA  GLY    70      -8.968  56.196  10.171  1.00 25.00           C
ATOM     71  CA  SER    71      -5.356  57.261   9.603  1.00 25.00           C
ATOM     72  CA  ALA    72      -1.794  55.905  10.182  1.00 25.00           C
ATOM     73  CA  PHE    73       0.808  54.907  12.780  1.00 25.00           C
ATOM     74  CA  TRP    74       1.170  52.384  15.581  1.00 25.00           C
ATOM     75  CA  LEU    75       0.770  48.665  16.185  1.00 25.00           C
ATOM     76  CA  THR    76      -1.220  47.454  19.178  1.00 25.00           C
ATOM     77  CA  PRO    77       1.878  47.077  21.312  1.00 25.00           C
TER
END
