
#######################################################
#                                                     #
#                        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_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381TS168_2-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:    54        24 - 77          4.95     6.14
  LCS_AVERAGE:     84.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        48 - 67          2.00     8.67
  LONGEST_CONTINUOUS_SEGMENT:    20        49 - 68          1.85     8.90
  LCS_AVERAGE:     27.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        17 - 30          0.64    15.98
  LONGEST_CONTINUOUS_SEGMENT:    14        50 - 63          0.68     9.91
  LONGEST_CONTINUOUS_SEGMENT:    14        51 - 64          0.96     9.62
  LCS_AVERAGE:     16.02

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   17   33     6   13   13   14   16   16   18   19   22   29   34   36   39   41   44   48   51   53   54   54 
LCS_GDT     Q      18     Q      18     14   17   33    12   13   13   14   16   16   21   30   38   41   44   46   48   50   52   52   53   55   56   57 
LCS_GDT     S      19     S      19     14   17   33    12   13   13   14   16   16   24   29   36   41   44   46   48   50   52   52   53   54   56   56 
LCS_GDT     L      20     L      20     14   17   33    12   13   13   14   16   16   18   21   25   33   35   36   40   43   48   51   51   53   54   54 
LCS_GDT     A      21     A      21     14   17   33    12   13   13   14   16   16   18   23   29   33   36   46   48   49   52   52   53   55   56   57 
LCS_GDT     R      22     R      22     14   17   33    12   13   13   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     G      23     G      23     14   17   33    12   13   13   14   16   18   21   29   32   41   44   46   48   50   52   52   53   55   56   57 
LCS_GDT     L      24     L      24     14   17   54    12   13   13   14   16   16   18   24   29   38   44   46   48   50   52   52   53   55   56   57 
LCS_GDT     A      25     A      25     14   17   54    12   13   13   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     V      26     V      26     14   17   54    12   13   13   14   16   23   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     I      27     I      27     14   17   54    12   13   13   14   16   16   24   29   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     R      28     R      28     14   17   54    12   13   13   14   16   24   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     C      29     C      29     14   17   54    12   13   13   14   17   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     F      30     F      30     14   17   54     3    6   13   14   18   24   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     D      31     D      31      4   17   54     3    3    5   13   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     H      32     H      32      4   17   54     3    3    4   12   16   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     R      33     R      33      3   17   54     3    3    6   10   19   26   29   33   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     N      34     N      34      3    7   54     1    3    3    5   13   16   24   30   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     Q      35     Q      35      3   10   54     0    3    5   10   13   17   28   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     R      36     R      36      3   12   54     1    3    8   11   12   16   18   27   33   36   41   46   48   51   52   53   54   55   56   57 
LCS_GDT     R      37     R      37      3   12   54     1    3    8   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     T      38     T      38      9   12   54     3    4    8   11   13   20   25   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      39     L      39      9   12   54     8    8    9   11   13   20   25   33   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     S      40     S      40      9   12   54     8    8    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     D      41     D      41      9   12   54     8    8    9   11   12   19   27   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     V      42     V      42      9   12   54     8    8    9   11   12   20   27   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     A      43     A      43      9   12   54     8    8    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     R      44     R      44      9   12   54     8    8    9   11   15   23   28   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     A      45     A      45      9   12   54     8    8    9   11   12   15   24   27   37   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     T      46     T      46      9   12   54     8    8    9   11   12   19   28   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     D      47     D      47      4   12   54     2    4    8   12   17   18   28   32   37   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      48     L      48      4   20   54     3    4    5   10   16   20   23   29   36   40   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     T      49     T      49      4   20   54     3    4   13   15   18   20   23   26   30   33   38   42   47   51   52   53   54   55   56   57 
LCS_GDT     R      50     R      50     14   20   54     6   12   14   16   17   20   21   23   26   28   30   34   38   42   45   49   54   54   56   56 
LCS_GDT     A      51     A      51     14   20   54     9   13   15   16   18   20   22   26   28   32   35   38   43   45   50   53   54   54   56   57 
LCS_GDT     T      52     T      52     14   20   54     9   13   15   16   18   20   22   26   28   32   35   38   43   45   52   53   54   54   56   57 
LCS_GDT     A      53     A      53     14   20   54     9   13   15   16   18   20   23   26   28   33   36   42   47   51   52   53   54   55   56   57 
LCS_GDT     R      54     R      54     14   20   54     9   13   15   16   18   20   23   26   30   33   38   42   48   51   52   53   54   55   56   57 
LCS_GDT     R      55     R      55     14   20   54     9   13   15   16   18   20   23   26   30   35   40   46   48   51   52   53   54   55   56   57 
LCS_GDT     F      56     F      56     14   20   54     9   13   15   16   18   21   23   27   32   38   42   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      57     L      57     14   20   54     9   13   15   16   18   21   23   27   35   40   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      58     L      58     14   20   54     9   13   15   16   18   21   23   29   36   40   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     T      59     T      59     14   20   54     9   13   15   16   18   21   25   32   37   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      60     L      60     14   20   54     9   13   15   16   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     V      61     V      61     14   20   54     9   13   15   16   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     E      62     E      62     14   20   54     9   13   15   16   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      63     L      63     14   20   54     4   13   15   16   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     G      64     G      64     14   20   54     4    5   10   15   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     Y      65     Y      65      4   20   54     3    4   15   16   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     V      66     V      66      4   20   54     3    8   15   16   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     A      67     A      67      4   20   54     3    4    8   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     T      68     T      68      5   20   54     3    4    8   13   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     D      69     D      69      5   17   54     3    4    8   13   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     G      70     G      70      7   17   54     3    6    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     S      71     S      71      7   17   54     3    6    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     A      72     A      72      7   17   54     3    6    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     F      73     F      73      7   17   54     3    5    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     W      74     W      74      7   17   54     3    6    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     L      75     L      75      7   17   54     3    5    9   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     T      76     T      76      7   17   54     3    6   10   14   19   26   29   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_GDT     P      77     P      77      3   14   54     3    3    4   10   13   19   26   35   38   41   44   46   48   51   52   53   54   55   56   57 
LCS_AVERAGE  LCS_A:  42.67  (  16.02   27.41   84.57 )

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     15     16     19     26     29     35     38     41     44     46     48     51     52     53     54     55     56     57 
GDT PERCENT_CA  19.67  21.31  24.59  26.23  31.15  42.62  47.54  57.38  62.30  67.21  72.13  75.41  78.69  83.61  85.25  86.89  88.52  90.16  91.80  93.44
GDT RMS_LOCAL    0.23   0.32   0.76   0.85   1.89   2.21   2.37   2.81   2.98   3.19   3.45   3.60   3.77   4.30   4.16   4.65   4.85   4.73   4.83   5.10
GDT RMS_ALL_CA  15.93  16.02   9.46   9.71   6.20   6.25   6.26   6.16   6.30   6.09   5.97   6.46   6.42   5.95   6.13   6.06   6.14   5.89   5.91   5.92

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17         11.055
LGA    Q      18      Q      18          5.448
LGA    S      19      S      19          5.879
LGA    L      20      L      20          9.491
LGA    A      21      A      21          7.248
LGA    R      22      R      22          1.881
LGA    G      23      G      23          5.831
LGA    L      24      L      24          6.402
LGA    A      25      A      25          3.348
LGA    V      26      V      26          3.026
LGA    I      27      I      27          4.558
LGA    R      28      R      28          3.925
LGA    C      29      C      29          3.975
LGA    F      30      F      30          2.404
LGA    D      31      D      31          2.717
LGA    H      32      H      32          3.844
LGA    R      33      R      33          4.382
LGA    N      34      N      34          5.171
LGA    Q      35      Q      35          3.658
LGA    R      36      R      36          6.402
LGA    R      37      R      37          1.906
LGA    T      38      T      38          3.849
LGA    L      39      L      39          4.352
LGA    S      40      S      40          1.867
LGA    D      41      D      41          3.723
LGA    V      42      V      42          3.449
LGA    A      43      A      43          0.813
LGA    R      44      R      44          3.241
LGA    A      45      A      45          4.910
LGA    T      46      T      46          3.731
LGA    D      47      D      47          5.298
LGA    L      48      L      48          7.745
LGA    T      49      T      49         13.105
LGA    R      50      R      50         16.913
LGA    A      51      A      51         15.958
LGA    T      52      T      52         14.677
LGA    A      53      A      53         11.929
LGA    R      54      R      54         11.120
LGA    R      55      R      55         10.490
LGA    F      56      F      56          8.571
LGA    L      57      L      57          6.893
LGA    L      58      L      58          6.950
LGA    T      59      T      59          6.283
LGA    L      60      L      60          3.578
LGA    V      61      V      61          2.894
LGA    E      62      E      62          3.043
LGA    L      63      L      63          3.792
LGA    G      64      G      64          3.132
LGA    Y      65      Y      65          2.486
LGA    V      66      V      66          1.000
LGA    A      67      A      67          1.317
LGA    T      68      T      68          2.334
LGA    D      69      D      69          3.810
LGA    G      70      G      70          2.131
LGA    S      71      S      71          2.227
LGA    A      72      A      72          1.795
LGA    F      73      F      73          0.504
LGA    W      74      W      74          1.018
LGA    L      75      L      75          1.941
LGA    T      76      T      76          1.023
LGA    P      77      P      77          3.583

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   61   61    4.0     35    2.81    47.951    44.421     1.204

LGA_LOCAL      RMSD =  2.806  Number of atoms =   35  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.324  Number of atoms =   61 
Std_ALL_ATOMS  RMSD =  5.885  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.856928 * X  +  -0.096810 * Y  +  -0.506263 * Z  +  12.686847
  Y_new =   0.270179 * X  +  -0.920820 * Y  +  -0.281236 * Z  +  40.974876
  Z_new =  -0.438951 * X  +  -0.377781 * Y  +   0.815232 * Z  +  32.825100 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.433943    2.707649  [ DEG:   -24.8631    155.1369 ]
  Theta =   0.454431    2.687162  [ DEG:    26.0370    153.9630 ]
  Phi   =   2.836170   -0.305423  [ DEG:   162.5006    -17.4994 ]
 
# 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_2-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS168_2-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   35   2.81  44.421     5.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS168_2-D1
PFRMAT TS
TARGET T0381
MODEL 2
PARENT N/A
ATOM     17  CA  VAL    17       9.717  64.281  27.653  1.00 25.00           C
ATOM     18  CA  GLN    18       8.491  60.947  29.086  1.00 25.00           C
ATOM     19  CA  SER    19       5.588  60.913  26.589  1.00 25.00           C
ATOM     20  CA  LEU    20       8.021  61.607  23.714  1.00 25.00           C
ATOM     21  CA  ALA    21      10.278  58.750  24.901  1.00 25.00           C
ATOM     22  CA  ARG    22       7.260  56.397  25.054  1.00 25.00           C
ATOM     23  CA  GLY    23       6.249  57.421  21.505  1.00 25.00           C
ATOM     24  CA  LEU    24       9.817  56.767  20.275  1.00 25.00           C
ATOM     25  CA  ALA    25       9.787  53.321  21.942  1.00 25.00           C
ATOM     26  CA  VAL    26       6.429  52.521  20.284  1.00 25.00           C
ATOM     27  CA  ILE    27       7.824  53.596  16.883  1.00 25.00           C
ATOM     28  CA  ARG    28      10.896  51.371  17.414  1.00 25.00           C
ATOM     29  CA  CYS    29       8.632  48.418  18.321  1.00 25.00           C
ATOM     30  CA  PHE    30       6.545  49.017  15.167  1.00 25.00           C
ATOM     31  CA  ASP    31       9.732  49.112  13.045  1.00 25.00           C
ATOM     32  CA  HIS    32      10.750  45.947  11.081  1.00 25.00           C
ATOM     33  CA  ARG    33       8.398  47.184   8.347  1.00 25.00           C
ATOM     34  CA  ASN    34       6.044  48.193   5.532  1.00 25.00           C
ATOM     35  CA  GLN    35       5.682  51.485   7.362  1.00 25.00           C
ATOM     36  CA  ARG    36       2.802  53.404   8.975  1.00 25.00           C
ATOM     37  CA  ARG    37       5.176  56.173  10.000  1.00 25.00           C
ATOM     38  CA  THR    38       2.451  58.850  10.098  1.00 25.00           C
ATOM     39  CA  LEU    39       3.651  58.720  13.756  1.00 25.00           C
ATOM     40  CA  SER    40       0.550  60.894  14.322  1.00 25.00           C
ATOM     41  CA  ASP    41      -1.490  57.787  15.246  1.00 25.00           C
ATOM     42  CA  VAL    42       1.235  56.702  17.708  1.00 25.00           C
ATOM     43  CA  ALA    43       1.244  60.194  19.278  1.00 25.00           C
ATOM     44  CA  ARG    44      -2.569  60.077  19.621  1.00 25.00           C
ATOM     45  CA  ALA    45      -2.338  56.633  21.281  1.00 25.00           C
ATOM     46  CA  THR    46       0.309  57.957  23.712  1.00 25.00           C
ATOM     47  CA  ASP    47       0.496  58.756  27.462  1.00 25.00           C
ATOM     48  CA  LEU    48       2.997  58.855  30.340  1.00 25.00           C
ATOM     49  CA  THR    49       5.379  60.043  33.112  1.00 25.00           C
ATOM     50  CA  ARG    50       9.114  60.278  33.796  1.00 25.00           C
ATOM     51  CA  ALA    51      12.524  61.950  34.284  1.00 25.00           C
ATOM     52  CA  THR    52      14.276  58.585  33.764  1.00 25.00           C
ATOM     53  CA  ALA    53      12.258  58.002  30.562  1.00 25.00           C
ATOM     54  CA  ARG    54      13.209  61.490  29.299  1.00 25.00           C
ATOM     55  CA  ARG    55      16.898  60.781  30.044  1.00 25.00           C
ATOM     56  CA  PHE    56      16.668  57.459  28.153  1.00 25.00           C
ATOM     57  CA  LEU    57      15.060  59.241  25.169  1.00 25.00           C
ATOM     58  CA  LEU    58      17.851  61.864  25.201  1.00 25.00           C
ATOM     59  CA  THR    59      20.491  59.091  25.278  1.00 25.00           C
ATOM     60  CA  LEU    60      18.785  57.350  22.324  1.00 25.00           C
ATOM     61  CA  VAL    61      18.739  60.647  20.377  1.00 25.00           C
ATOM     62  CA  GLU    62      22.462  61.163  21.112  1.00 25.00           C
ATOM     63  CA  LEU    63      24.473  57.925  21.091  1.00 25.00           C
ATOM     64  CA  GLY    64      23.867  55.831  18.009  1.00 25.00           C
ATOM     65  CA  TYR    65      20.321  56.348  16.858  1.00 25.00           C
ATOM     66  CA  VAL    66      16.791  57.720  16.714  1.00 25.00           C
ATOM     67  CA  ALA    67      16.414  59.790  13.585  1.00 25.00           C
ATOM     68  CA  THR    68      15.734  63.378  12.385  1.00 25.00           C
ATOM     69  CA  ASP    69      17.028  65.944   9.842  1.00 25.00           C
ATOM     70  CA  GLY    70      13.891  65.991   7.691  1.00 25.00           C
ATOM     71  CA  SER    71      10.781  63.787   7.299  1.00 25.00           C
ATOM     72  CA  ALA    72      11.346  60.347   8.839  1.00 25.00           C
ATOM     73  CA  PHE    73      11.407  58.693  12.232  1.00 25.00           C
ATOM     74  CA  TRP    74      13.481  55.661  11.069  1.00 25.00           C
ATOM     75  CA  LEU    75      16.303  53.500  12.407  1.00 25.00           C
ATOM     76  CA  THR    76      19.424  52.202  14.160  1.00 25.00           C
ATOM     77  CA  PRO    77      18.932  49.877  17.194  1.00 25.00           C
TER
END
