
#######################################################
#                                                     #
#                        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_4-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS168_4-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:    44        30 - 73          4.98     6.54
  LCS_AVERAGE:     64.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        60 - 78          1.48     6.48
  LONGEST_CONTINUOUS_SEGMENT:    19        61 - 79          1.83     6.37
  LONGEST_CONTINUOUS_SEGMENT:    19        62 - 80          1.92     6.54
  LCS_AVERAGE:     25.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        62 - 78          0.82     6.28
  LCS_AVERAGE:     19.22

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   32     3    3    4    5    5   12   15   20   28   35   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     Q      18     Q      18     14   15   32     9   13   14   19   23   25   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     P      19     P      19     14   15   34    10   13   14   14   19   22   26   29   32   34   39   43   48   53   58   59   62   64   64   65 
LCS_GDT     A      20     A      20     14   15   37    10   13   14   14   18   19   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     Y      21     Y      21     14   15   37    10   13   14   14   14   20   24   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     T      22     T      22     14   15   37    10   13   14   19   23   25   27   29   32   36   41   46   51   55   58   59   62   64   64   65 
LCS_GDT     T      23     T      23     14   15   38    10   13   14   14   14   22   26   28   31   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     V      24     V      24     14   15   39    10   13   14   14   14   19   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     M      25     M      25     14   15   39    10   13   14   14   14   15   20   26   31   35   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     R      26     R      26     14   15   39    10   13   14   19   23   25   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     E      27     E      27     14   15   39    10   13   14   15   18   22   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     V      28     V      28     14   15   39    10   13   14   14   17   18   20   26   31   36   39   44   52   55   57   59   62   64   64   65 
LCS_GDT     L      29     L      29     14   15   39     9   13   14   14   14   14   15   15   19   22   36   41   48   51   55   58   62   64   64   65 
LCS_GDT     A      30     A      30     14   15   44     9   13   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     T      31     T      31     14   17   44     4   10   14   14   17   20   23   30   32   36   41   46   52   55   57   59   62   64   64   65 
LCS_GDT     Y      32     Y      32      5   17   44     3    4    9   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     G      33     G      33      5   17   44     3    4   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     K      34     K      34      5   17   44     3    3    6   14   19   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     P      35     P      35     11   17   44     3    4   10   14   17   18   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     F      36     F      36     12   17   44     9   10   12   14   17   18   21   27   31   36   40   46   52   55   58   59   62   64   64   65 
LCS_GDT     S      37     S      37     12   17   44     9   10   12   14   17   18   21   27   31   36   39   46   52   55   58   59   62   64   64   65 
LCS_GDT     P      38     P      38     12   17   44     9   10   12   14   17   18   21   26   31   36   39   45   52   54   57   59   62   64   64   65 
LCS_GDT     A      39     A      39     12   17   44     9   10   12   14   17   18   22   30   32   36   40   46   52   55   58   59   62   64   64   65 
LCS_GDT     Q      40     Q      40     12   17   44     9   10   12   14   17   18   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      41     A      41     12   17   44     9   10   12   14   17   18   21   30   32   36   40   46   52   55   58   59   62   64   64   65 
LCS_GDT     Q      42     Q      42     12   17   44     9   10   12   14   17   18   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     K      43     K      43     12   17   44     9   10   12   14   17   19   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     T      44     T      44     12   17   44     9   10   12   14   17   20   24   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     F      45     F      45     12   17   44     4   10   12   14   17   18   23   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     P      46     P      46     12   17   44     7   10   12   18   18   20   24   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     M      47     M      47     12   17   44     3    9   11   14   17   18   24   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      48     A      48     11   15   44     3   10   11   12   15   18   19   26   31   36   40   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      49     A      49     11   15   44     8   10   11   12   13   17   20   26   30   35   39   46   52   55   58   59   62   64   64   65 
LCS_GDT     E      50     E      50     11   15   44     8   10   11   12   13   15   18   22   27   29   36   42   49   54   58   59   62   64   64   65 
LCS_GDT     Q      51     Q      51     11   15   44     8   10   11   14   17   21   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      52     A      52     11   15   44     8   12   16   19   23   25   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     M      53     M      53     11   15   44     8   10   11   12   13   15   17   26   30   34   38   45   52   55   58   59   62   64   64   65 
LCS_GDT     T      54     T      54     11   15   44     8   10   11   12   13   15   17   26   30   34   38   42   49   55   58   59   62   64   64   65 
LCS_GDT     E      55     E      55     11   15   44     8   10   11   12   18   22   22   27   30   34   38   45   52   55   58   59   62   64   64   65 
LCS_GDT     L      56     L      56     11   15   44     8   10   11   12   13   15   20   26   27   33   37   40   43   54   58   59   62   64   64   65 
LCS_GDT     G      57     G      57     11   15   44     8   10   11   12   13   15   17   19   23   25   30   34   35   40   44   48   56   62   64   65 
LCS_GDT     I      58     I      58      5    6   44     3    4    5    7   15   17   20   26   28   32   38   42   49   55   58   59   62   64   64   65 
LCS_GDT     A      59     A      59      5    6   44     3    4    5    5    8   14   19   23   28   33   39   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      60     A      60      5   19   44     4    4    6   13   18   22   26   28   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     S      61     S      61     14   19   44     4    4    6   13   18   22   26   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     E      62     E      62     17   19   44     9   14   17   19   22   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     F      63     F      63     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     D      64     D      64     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     H      65     H      65     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     F      66     F      66     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     Q      67     Q      67     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      68     A      68     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     Q      69     Q      69     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     Y      70     Y      70     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     E      71     E      71     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     D      72     D      72     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     V      73     V      73     17   19   44    11   14   17   19   23   25   27   30   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     M      74     M      74     17   19   43    11   14   17   19   23   25   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     A      75     A      75     17   19   43    10   14   17   19   23   25   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     S      76     S      76     17   19   43     4   14   17   19   23   25   27   29   32   36   41   46   52   55   58   59   62   64   64   65 
LCS_GDT     H      77     H      77     17   19   43     7   14   17   19   23   25   27   29   32   36   41   46   51   55   58   59   62   64   64   65 
LCS_GDT     Y      78     Y      78     17   19   41     4   13   17   19   23   25   27   29   32   36   41   46   49   54   58   59   62   64   64   65 
LCS_GDT     D      79     D      79      5   19   36     4    4    5    9   10   18   26   28   32   34   37   42   48   50   55   59   61   64   64   65 
LCS_GDT     Q      80     Q      80      5   19   36     4    4    6    9   16   20   26   28   32   33   37   42   48   50   55   59   61   64   64   65 
LCS_GDT     I      81     I      81      5   16   36     0    3    6    9   16   21   26   28   32   34   39   42   48   51   58   59   62   64   64   65 
LCS_AVERAGE  LCS_A:  36.50  (  19.22   25.47   64.80 )

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     14     17     19     23     25     27     30     32     36     41     46     52     55     58     59     62     64     64     65 
GDT PERCENT_CA  16.92  21.54  26.15  29.23  35.38  38.46  41.54  46.15  49.23  55.38  63.08  70.77  80.00  84.62  89.23  90.77  95.38  98.46  98.46 100.00
GDT RMS_LOCAL    0.17   0.41   0.72   0.99   1.53   1.64   1.94   2.88   2.51   3.13   3.54   3.91   4.60   4.81   5.06   5.04   5.27   5.45   5.45   5.61
GDT RMS_ALL_CA   6.28   6.35   6.18   6.22   6.40   6.34   6.33   6.80   6.66   6.00   6.03   5.93   5.89   5.73   5.62   5.69   5.64   5.62   5.62   5.61

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17          8.720
LGA    Q      18      Q      18          8.400
LGA    P      19      P      19          8.866
LGA    A      20      A      20          3.600
LGA    Y      21      Y      21          3.953
LGA    T      22      T      22          7.806
LGA    T      23      T      23          6.168
LGA    V      24      V      24          2.008
LGA    M      25      M      25          5.572
LGA    R      26      R      26          6.275
LGA    E      27      E      27          3.264
LGA    V      28      V      28          4.742
LGA    L      29      L      29          6.475
LGA    A      30      A      30          3.662
LGA    T      31      T      31          3.769
LGA    Y      32      Y      32          3.884
LGA    G      33      G      33          3.394
LGA    K      34      K      34          2.139
LGA    P      35      P      35          3.373
LGA    F      36      F      36          5.066
LGA    S      37      S      37          5.753
LGA    P      38      P      38          5.807
LGA    A      39      A      39          3.882
LGA    Q      40      Q      40          3.102
LGA    A      41      A      41          3.700
LGA    Q      42      Q      42          2.684
LGA    K      43      K      43          0.390
LGA    T      44      T      44          2.182
LGA    F      45      F      45          3.982
LGA    P      46      P      46          4.731
LGA    M      47      M      47          4.783
LGA    A      48      A      48          7.612
LGA    A      49      A      49          9.218
LGA    E      50      E      50         12.103
LGA    Q      51      Q      51          9.191
LGA    A      52      A      52          6.920
LGA    M      53      M      53         11.014
LGA    T      54      T      54         13.085
LGA    E      55      E      55         10.780
LGA    L      56      L      56         12.196
LGA    G      57      G      57         16.042
LGA    I      58      I      58         12.271
LGA    A      59      A      59         11.902
LGA    A      60      A      60          5.439
LGA    S      61      S      61          3.920
LGA    E      62      E      62          1.902
LGA    F      63      F      63          1.615
LGA    D      64      D      64          1.849
LGA    H      65      H      65          2.029
LGA    F      66      F      66          1.995
LGA    Q      67      Q      67          2.441
LGA    A      68      A      68          2.667
LGA    Q      69      Q      69          2.567
LGA    Y      70      Y      70          2.919
LGA    E      71      E      71          3.626
LGA    D      72      D      72          3.480
LGA    V      73      V      73          3.413
LGA    M      74      M      74          4.868
LGA    A      75      A      75          5.620
LGA    S      76      S      76          6.292
LGA    H      77      H      77          6.481
LGA    Y      78      Y      78          8.603
LGA    D      79      D      79         13.205
LGA    Q      80      Q      80         13.926
LGA    I      81      I      81         12.679

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     30    2.88    46.923    42.116     1.007

LGA_LOCAL      RMSD =  2.878  Number of atoms =   30  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.987  Number of atoms =   65 
Std_ALL_ATOMS  RMSD =  5.609  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.383915 * X  +  -0.753499 * Y  +   0.533712 * Z  +  31.182074
  Y_new =  -0.916458 * X  +   0.381523 * Y  +  -0.120598 * Z  +  16.331608
  Z_new =  -0.112753 * X  +  -0.535424 * Y  +  -0.837023 * Z  +   2.940561 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.572509    0.569084  [ DEG:  -147.3939     32.6061 ]
  Theta =   0.112994    3.028599  [ DEG:     6.4741    173.5259 ]
  Phi   =  -1.967498    1.174094  [ DEG:  -112.7294     67.2706 ]
 
# 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_4-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_4-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   2.88  42.116     5.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_4-D2
PFRMAT TS
TARGET T0324
MODEL 4
PARENT N/A
ATOM     17  CA  SER    17      30.699  13.182   8.411  1.00 25.00           C
ATOM     18  CA  GLN    18      30.355  15.041  11.758  1.00 25.00           C
ATOM     19  CA  PRO    19      27.574  13.593  13.956  1.00 25.00           C
ATOM     20  CA  ALA    20      25.068  16.076  12.464  1.00 25.00           C
ATOM     21  CA  TYR    21      26.167  15.098   8.928  1.00 25.00           C
ATOM     22  CA  THR    22      25.740  11.392   9.793  1.00 25.00           C
ATOM     23  CA  THR    23      22.236  12.093  11.174  1.00 25.00           C
ATOM     24  CA  VAL    24      21.329  13.991   7.975  1.00 25.00           C
ATOM     25  CA  MET    25      22.596  11.067   5.850  1.00 25.00           C
ATOM     26  CA  ARG    26      20.511   8.620   7.933  1.00 25.00           C
ATOM     27  CA  GLU    27      17.417  10.831   7.479  1.00 25.00           C
ATOM     28  CA  VAL    28      18.024  10.945   3.699  1.00 25.00           C
ATOM     29  CA  LEU    29      18.356   7.131   3.611  1.00 25.00           C
ATOM     30  CA  ALA    30      15.082   6.777   5.567  1.00 25.00           C
ATOM     31  CA  THR    31      13.336   9.151   3.120  1.00 25.00           C
ATOM     32  CA  TYR    32      11.919  10.814   6.270  1.00 25.00           C
ATOM     33  CA  GLY    33       9.069  11.678   3.937  1.00 25.00           C
ATOM     34  CA  LYS    34      11.282  14.282   2.251  1.00 25.00           C
ATOM     35  CA  PRO    35      10.750  17.182  -0.190  1.00 25.00           C
ATOM     36  CA  PHE    36      10.214  19.333   2.895  1.00 25.00           C
ATOM     37  CA  SER    37      10.238  22.964   1.646  1.00 25.00           C
ATOM     38  CA  PRO    38      13.184  25.389   1.508  1.00 25.00           C
ATOM     39  CA  ALA    39      12.265  27.318   4.686  1.00 25.00           C
ATOM     40  CA  GLN    40      11.481  24.030   6.484  1.00 25.00           C
ATOM     41  CA  ALA    41      14.849  22.588   5.370  1.00 25.00           C
ATOM     42  CA  GLN    42      16.641  25.723   6.646  1.00 25.00           C
ATOM     43  CA  LYS    43      14.828  25.420  10.007  1.00 25.00           C
ATOM     44  CA  THR    44      15.844  21.735  10.251  1.00 25.00           C
ATOM     45  CA  PHE    45      19.482  22.662   9.495  1.00 25.00           C
ATOM     46  CA  PRO    46      20.726  21.874  12.999  1.00 25.00           C
ATOM     47  CA  MET    47      18.179  24.160  14.547  1.00 25.00           C
ATOM     48  CA  ALA    48      19.890  24.253  17.902  1.00 25.00           C
ATOM     49  CA  ALA    49      21.719  21.006  18.669  1.00 25.00           C
ATOM     50  CA  GLU    50      20.866  20.703  22.390  1.00 25.00           C
ATOM     51  CA  GLN    51      17.377  22.138  21.731  1.00 25.00           C
ATOM     52  CA  ALA    52      16.859  19.635  18.878  1.00 25.00           C
ATOM     53  CA  MET    53      17.946  16.764  21.168  1.00 25.00           C
ATOM     54  CA  THR    54      15.503  17.959  23.866  1.00 25.00           C
ATOM     55  CA  GLU    55      12.683  18.108  21.279  1.00 25.00           C
ATOM     56  CA  LEU    56      13.522  14.556  20.120  1.00 25.00           C
ATOM     57  CA  GLY    57      12.542  13.698  23.695  1.00 25.00           C
ATOM     58  CA  ILE    58       8.912  14.013  22.785  1.00 25.00           C
ATOM     59  CA  ALA    59       7.015  10.757  23.554  1.00 25.00           C
ATOM     60  CA  ALA    60       4.716   8.985  21.053  1.00 25.00           C
ATOM     61  CA  SER    61       5.383   5.417  19.831  1.00 25.00           C
ATOM     62  CA  GLU    62       6.596   6.771  16.461  1.00 25.00           C
ATOM     63  CA  PHE    63       8.919   9.230  18.257  1.00 25.00           C
ATOM     64  CA  ASP    64      10.310   6.382  20.407  1.00 25.00           C
ATOM     65  CA  HIS    65      10.914   4.274  17.269  1.00 25.00           C
ATOM     66  CA  PHE    66      12.724   7.214  15.612  1.00 25.00           C
ATOM     67  CA  GLN    67      14.903   7.662  18.730  1.00 25.00           C
ATOM     68  CA  ALA    68      15.747   3.926  18.707  1.00 25.00           C
ATOM     69  CA  GLN    69      16.686   4.136  15.001  1.00 25.00           C
ATOM     70  CA  TYR    70      18.926   7.159  15.714  1.00 25.00           C
ATOM     71  CA  GLU    71      20.619   5.260  18.577  1.00 25.00           C
ATOM     72  CA  ASP    72      21.202   2.257  16.273  1.00 25.00           C
ATOM     73  CA  VAL    73      22.718   4.560  13.614  1.00 25.00           C
ATOM     74  CA  MET    74      25.019   6.124  16.245  1.00 25.00           C
ATOM     75  CA  ALA    75      26.115   2.638  17.394  1.00 25.00           C
ATOM     76  CA  SER    76      26.843   1.646  13.768  1.00 25.00           C
ATOM     77  CA  HIS    77      28.905   4.836  13.282  1.00 25.00           C
ATOM     78  CA  TYR    78      30.871   4.082  16.481  1.00 25.00           C
ATOM     79  CA  ASP    79      31.537   0.514  15.259  1.00 25.00           C
ATOM     80  CA  GLN    80      33.699   1.646  12.285  1.00 25.00           C
ATOM     81  CA  ILE    81      35.360   4.994  12.821  1.00 25.00           C
TER
END
