
#######################################################
#                                                     #
#                        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   65 (   65),  selected   65 , name T0324TS168_1-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS168_1-D2.T0324_D2.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        49 - 81          4.94     7.51
  LCS_AVERAGE:     48.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        60 - 78          1.48     6.62
  LONGEST_CONTINUOUS_SEGMENT:    19        61 - 79          1.83     6.71
  LONGEST_CONTINUOUS_SEGMENT:    19        62 - 80          1.92     7.08
  LCS_AVERAGE:     21.68

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        62 - 78          0.82     6.67
  LCS_AVERAGE:     17.94

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:   65
LCS_GDT     S      17     S      17      3   15   21     0    6    8   11   14   14   19   26   30   34   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Q      18     Q      18     14   15   21     9   13   15   22   24   26   28   30   33   36   38   43   45   50   53   55   58   61   62   63 
LCS_GDT     P      19     P      19     14   15   21    10   13   14   14   18   21   28   30   33   36   38   43   45   47   50   54   58   61   62   63 
LCS_GDT     A      20     A      20     14   15   21    10   13   14   14   17   22   25   29   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Y      21     Y      21     14   15   21    10   13   14   14   19   24   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     T      22     T      22     14   15   21    10   13   14   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     T      23     T      23     14   15   30    10   13   14   15   19   22   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     V      24     V      24     14   15   32    10   13   14   14   15   18   25   28   31   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     M      25     M      25     14   15   32    10   13   14   14   14   17   19   27   31   35   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     R      26     R      26     14   15   32    10   13   14   20   23   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     E      27     E      27     14   15   32    10   13   14   16   19   24   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     V      28     V      28     14   15   32    10   13   14   14   14   14   15   23   25   33   37   43   46   50   53   55   58   61   62   63 
LCS_GDT     L      29     L      29     14   15   32     9   13   14   14   14   14   16   21   25   32   36   43   46   50   51   55   58   61   62   63 
LCS_GDT     A      30     A      30     14   15   32     9   13   16   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     T      31     T      31     14   15   32     4   10   14   14   14   17   26   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Y      32     Y      32      4    6   32     3    7   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     G      33     G      33      4    6   32     3    4    6   19   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     K      34     K      34      4    6   32     3    4    6   19   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     P      35     P      35      4    6   32     3    4    5    8   14   23   27   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     F      36     F      36      3    6   32     3    3    5    8    9   11   15   18   25   31   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     S      37     S      37      3    9   32     0    3    5    8   10   13   17   19   22   30   38   41   44   49   53   55   58   61   62   63 
LCS_GDT     P      38     P      38      8    9   32     7    8    9    9   10   11   15   19   20   23   27   36   42   44   48   53   58   59   61   63 
LCS_GDT     A      39     A      39      8    9   32     7    8    9    9   11   13   17   19   25   32   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     Q      40     Q      40      8    9   32     7    8    9    9    9   11   15   19   25   32   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     A      41     A      41      8    9   32     7    8    9    9   10   13   15   19   24   31   38   41   46   50   53   55   58   61   62   63 
LCS_GDT     Q      42     Q      42      8    9   32     7    8    9    9   11   13   17   19   25   31   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     K      43     K      43      8    9   32     7    8    9    9    9   10   21   23   26   34   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     T      44     T      44      8    9   32     7    8    9    9    9   11   21   23   28   34   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     F      45     F      45      8   13   32     4    8    9    9    9   11   15   19   26   32   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     P      46     P      46     12   13   32     3    5   11   12   12   13   13   14   16   22   24   35   43   46   50   55   58   61   62   63 
LCS_GDT     M      47     M      47     12   13   32     4   10   11   12   12   17   17   23   27   34   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     A      48     A      48     12   13   32     3   10   11   12   12   13   15   23   27   32   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     A      49     A      49     12   13   33     8   10   11   12   12   17   22   27   30   34   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     E      50     E      50     12   13   33     8   10   11   12   13   17   20   27   28   34   37   41   45   49   53   55   58   61   62   63 
LCS_GDT     Q      51     Q      51     12   13   33     8   10   15   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     A      52     A      52     12   13   33     8   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     M      53     M      53     12   13   33     8   10   11   12   12   13   13   14   30   34   38   40   43   49   53   55   58   61   62   63 
LCS_GDT     T      54     T      54     12   13   33     8   10   11   12   12   13   13   23   30   34   38   40   42   45   52   55   58   61   62   63 
LCS_GDT     E      55     E      55     12   13   33     8   10   11   12   12   13   22   25   29   34   38   40   42   45   52   55   58   61   62   63 
LCS_GDT     L      56     L      56     12   13   33     8   10   11   12   12   13   15   22   27   29   32   36   40   43   45   48   48   51   59   63 
LCS_GDT     G      57     G      57     12   13   33     3    4    9   12   12   13   13   16   20   24   25   27   31   36   39   42   43   46   48   52 
LCS_GDT     I      58     I      58      5    6   33     3    4    5    7   11   17   19   22   27   29   35   39   42   45   52   55   58   61   62   63 
LCS_GDT     A      59     A      59      5    6   33     3    4    5    7   11   17   22   23   28   34   38   41   44   49   53   55   58   61   62   63 
LCS_GDT     A      60     A      60      5   19   33     4    4    7   14   19   22   24   30   33   36   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     S      61     S      61     14   19   33     4    4    7   11   17   22   24   30   33   36   38   42   46   50   53   55   58   61   62   63 
LCS_GDT     E      62     E      62     17   19   33     9   14   17   18   23   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     F      63     F      63     17   19   33    12   14   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     D      64     D      64     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     H      65     H      65     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     F      66     F      66     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Q      67     Q      67     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     A      68     A      68     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Q      69     Q      69     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Y      70     Y      70     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     E      71     E      71     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     D      72     D      72     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     V      73     V      73     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     M      74     M      74     17   19   33    12   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     A      75     A      75     17   19   33    11   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     S      76     S      76     17   19   33     4   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     H      77     H      77     17   19   33     4   15   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     Y      78     Y      78     17   19   33     3   13   17   22   24   26   28   30   33   36   38   43   46   50   53   55   58   61   62   63 
LCS_GDT     D      79     D      79      4   19   33     3    4    4    8   10   18   23   28   32   35   37   43   45   47   50   53   57   61   62   63 
LCS_GDT     Q      80     Q      80      4   19   33     3    4    4    8   11   17   21   28   30   35   37   42   45   47   50   52   56   59   62   63 
LCS_GDT     I      81     I      81      3    9   33     0    3    3    3    4   13   16   22   26   32   36   41   43   47   51   55   58   61   62   63 
LCS_AVERAGE  LCS_A:  29.34  (  17.94   21.68   48.40 )

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     15     17     22     24     26     28     30     33     36     38     43     46     50     53     55     58     61     62     63 
GDT PERCENT_CA  18.46  23.08  26.15  33.85  36.92  40.00  43.08  46.15  50.77  55.38  58.46  66.15  70.77  76.92  81.54  84.62  89.23  93.85  95.38  96.92
GDT RMS_LOCAL    0.26   0.75   0.86   1.34   1.50   1.63   1.86   2.08   2.45   2.76   3.42   3.78   4.37   6.39   4.90   5.27   5.37   5.63   5.72   5.88
GDT RMS_ALL_CA   6.68   6.82   6.86   7.06   6.96   6.96   7.04   7.14   6.97   6.88   6.64   7.01   6.73   6.73   6.42   6.34   6.31   6.28   6.28   6.26

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17          7.976
LGA    Q      18      Q      18          3.344
LGA    P      19      P      19          3.848
LGA    A      20      A      20          4.715
LGA    Y      21      Y      21          4.300
LGA    T      22      T      22          3.337
LGA    T      23      T      23          3.573
LGA    V      24      V      24          5.014
LGA    M      25      M      25          5.517
LGA    R      26      R      26          3.479
LGA    E      27      E      27          2.825
LGA    V      28      V      28          6.466
LGA    L      29      L      29          6.810
LGA    A      30      A      30          2.685
LGA    T      31      T      31          3.979
LGA    Y      32      Y      32          1.466
LGA    G      33      G      33          2.285
LGA    K      34      K      34          2.242
LGA    P      35      P      35          4.631
LGA    F      36      F      36          9.050
LGA    S      37      S      37         12.496
LGA    P      38      P      38         15.440
LGA    A      39      A      39         12.616
LGA    Q      40      Q      40          9.948
LGA    A      41      A      41         11.099
LGA    Q      42      Q      42         12.611
LGA    K      43      K      43         10.431
LGA    T      44      T      44          8.643
LGA    F      45      F      45         10.690
LGA    P      46      P      46         11.894
LGA    M      47      M      47          8.561
LGA    A      48      A      48         10.510
LGA    A      49      A      49          7.817
LGA    E      50      E      50          8.774
LGA    Q      51      Q      51          2.816
LGA    A      52      A      52          1.165
LGA    M      53      M      53          7.353
LGA    T      54      T      54          8.583
LGA    E      55      E      55          8.575
LGA    L      56      L      56         11.861
LGA    G      57      G      57         15.856
LGA    I      58      I      58         11.114
LGA    A      59      A      59          9.644
LGA    A      60      A      60          5.737
LGA    S      61      S      61          5.686
LGA    E      62      E      62          2.767
LGA    F      63      F      63          1.486
LGA    D      64      D      64          0.626
LGA    H      65      H      65          1.432
LGA    F      66      F      66          1.247
LGA    Q      67      Q      67          0.263
LGA    A      68      A      68          0.777
LGA    Q      69      Q      69          0.788
LGA    Y      70      Y      70          0.247
LGA    E      71      E      71          0.651
LGA    D      72      D      72          0.905
LGA    V      73      V      73          0.612
LGA    M      74      M      74          0.647
LGA    A      75      A      75          0.628
LGA    S      76      S      76          1.074
LGA    H      77      H      77          1.153
LGA    Y      78      Y      78          1.502
LGA    D      79      D      79          5.698
LGA    Q      80      Q      80          6.811
LGA    I      81      I      81          8.331

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     30    2.08    46.923    40.731     1.376

LGA_LOCAL      RMSD =  2.081  Number of atoms =   30  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.025  Number of atoms =   65 
Std_ALL_ATOMS  RMSD =  6.241  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.001267 * X  +  -0.999038 * Y  +  -0.043840 * Z  +  26.476591
  Y_new =  -0.908149 * X  +  -0.019502 * Y  +   0.418193 * Z  +  21.772522
  Z_new =  -0.418646 * X  +   0.039283 * Y  +  -0.907300 * Z  +   0.413421 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.098323   -0.043270  [ DEG:   177.5208     -2.4792 ]
  Theta =   0.431954    2.709639  [ DEG:    24.7491    155.2509 ]
  Phi   =  -1.569402    1.572191  [ DEG:   -89.9201     90.0799 ]
 
# 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: T0324TS168_1-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_1-D2.T0324_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   65   65   4.0   30   2.08  40.731     6.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_1-D2
PFRMAT TS
TARGET T0324
MODEL 1
PARENT N/A
ATOM     17  CA  SER    17      28.598  21.708   5.413  1.00 25.00           C
ATOM     18  CA  GLN    18      27.300  20.637   8.822  1.00 25.00           C
ATOM     19  CA  PRO    19      26.426  17.478  10.803  1.00 25.00           C
ATOM     20  CA  ALA    20      22.743  18.521  10.890  1.00 25.00           C
ATOM     21  CA  TYR    21      22.796  19.116   7.106  1.00 25.00           C
ATOM     22  CA  THR    22      24.361  15.663   6.562  1.00 25.00           C
ATOM     23  CA  THR    23      21.665  14.066   8.763  1.00 25.00           C
ATOM     24  CA  VAL    24      18.936  15.871   6.771  1.00 25.00           C
ATOM     25  CA  MET    25      20.481  14.640   3.491  1.00 25.00           C
ATOM     26  CA  ARG    26      20.573  11.060   4.850  1.00 25.00           C
ATOM     27  CA  GLU    27      16.897  11.332   5.887  1.00 25.00           C
ATOM     28  CA  VAL    28      15.982  12.615   2.397  1.00 25.00           C
ATOM     29  CA  LEU    29      17.876   9.695   0.799  1.00 25.00           C
ATOM     30  CA  ALA    30      16.034   7.224   3.074  1.00 25.00           C
ATOM     31  CA  THR    31      12.680   8.800   2.108  1.00 25.00           C
ATOM     32  CA  TYR    32       9.550   8.516   4.271  1.00 25.00           C
ATOM     33  CA  GLY    33       6.809   8.834   1.678  1.00 25.00           C
ATOM     34  CA  LYS    34       8.244  12.341   1.353  1.00 25.00           C
ATOM     35  CA  PRO    35       9.594  13.443  -1.989  1.00 25.00           C
ATOM     36  CA  PHE    36       7.725  16.711  -2.396  1.00 25.00           C
ATOM     37  CA  SER    37       4.692  15.015  -0.920  1.00 25.00           C
ATOM     38  CA  PRO    38       3.746  18.180   1.037  1.00 25.00           C
ATOM     39  CA  ALA    39       4.676  21.446  -0.731  1.00 25.00           C
ATOM     40  CA  GLN    40       4.932  23.232   2.647  1.00 25.00           C
ATOM     41  CA  ALA    41       7.179  20.433   3.983  1.00 25.00           C
ATOM     42  CA  GLN    42       9.408  20.708   0.880  1.00 25.00           C
ATOM     43  CA  LYS    43       9.652  24.500   1.361  1.00 25.00           C
ATOM     44  CA  THR    44      10.606  23.996   5.037  1.00 25.00           C
ATOM     45  CA  PHE    45      13.295  21.467   4.019  1.00 25.00           C
ATOM     46  CA  PRO    46      13.243  18.921   6.918  1.00 25.00           C
ATOM     47  CA  MET    47      11.322  20.103  10.029  1.00 25.00           C
ATOM     48  CA  ALA    48      12.599  23.670  10.611  1.00 25.00           C
ATOM     49  CA  ALA    49      14.955  21.957  13.023  1.00 25.00           C
ATOM     50  CA  GLU    50      14.167  23.339  16.507  1.00 25.00           C
ATOM     51  CA  GLN    51      10.698  21.721  16.392  1.00 25.00           C
ATOM     52  CA  ALA    52      12.264  18.379  15.368  1.00 25.00           C
ATOM     53  CA  MET    53      14.762  18.636  18.260  1.00 25.00           C
ATOM     54  CA  THR    54      11.901  19.367  20.699  1.00 25.00           C
ATOM     55  CA  GLU    55       9.970  16.335  19.380  1.00 25.00           C
ATOM     56  CA  LEU    56      13.074  14.135  19.819  1.00 25.00           C
ATOM     57  CA  GLY    57      12.535  12.721  23.315  1.00 25.00           C
ATOM     58  CA  ILE    58       9.179  11.932  21.650  1.00 25.00           C
ATOM     59  CA  ALA    59       5.970   9.902  21.520  1.00 25.00           C
ATOM     60  CA  ALA    60       5.312   6.564  19.737  1.00 25.00           C
ATOM     61  CA  SER    61       7.285   3.307  19.329  1.00 25.00           C
ATOM     62  CA  GLU    62       7.769   4.039  15.601  1.00 25.00           C
ATOM     63  CA  PHE    63       8.997   7.571  16.427  1.00 25.00           C
ATOM     64  CA  ASP    64      11.456   6.142  18.993  1.00 25.00           C
ATOM     65  CA  HIS    65      12.742   3.635  16.399  1.00 25.00           C
ATOM     66  CA  PHE    66      13.206   6.462  13.859  1.00 25.00           C
ATOM     67  CA  GLN    67      15.128   8.516  16.459  1.00 25.00           C
ATOM     68  CA  ALA    68      17.365   5.504  17.220  1.00 25.00           C
ATOM     69  CA  GLN    69      18.035   5.025  13.480  1.00 25.00           C
ATOM     70  CA  TYR    70      18.934   8.733  13.142  1.00 25.00           C
ATOM     71  CA  GLU    71      21.321   8.453  16.123  1.00 25.00           C
ATOM     72  CA  ASP    72      22.962   5.371  14.551  1.00 25.00           C
ATOM     73  CA  VAL    73      23.374   7.250  11.239  1.00 25.00           C
ATOM     74  CA  MET    74      24.959  10.208  13.087  1.00 25.00           C
ATOM     75  CA  ALA    75      27.366   7.830  14.880  1.00 25.00           C
ATOM     76  CA  SER    76      28.314   6.227  11.533  1.00 25.00           C
ATOM     77  CA  HIS    77      28.947   9.689  10.026  1.00 25.00           C
ATOM     78  CA  TYR    78      31.147  10.619  13.020  1.00 25.00           C
ATOM     79  CA  ASP    79      33.120   7.362  12.611  1.00 25.00           C
ATOM     80  CA  GLN    80      35.465   9.367  10.363  1.00 25.00           C
ATOM     81  CA  ILE    81      33.853  10.781   7.225  1.00 25.00           C
TER
END
