
#######################################################
#                                                     #
#                        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_5-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS168_5-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:    38        36 - 73          4.99     7.57
  LCS_AVERAGE:     53.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        60 - 78          1.48     6.41
  LONGEST_CONTINUOUS_SEGMENT:    19        61 - 79          1.83     6.79
  LCS_AVERAGE:     20.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        62 - 78          0.82     6.81
  LCS_AVERAGE:     16.31

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      0   16   21     0    4    8   12   15   15   15   20   27   33   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     Q      18     Q      18     14   16   21     9   13   14   18   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     P      19     P      19     14   16   21    10   13   14   14   15   22   24   27   30   33   36   41   47   51   53   57   59   61   62   64 
LCS_GDT     A      20     A      20     14   16   29    10   13   14   14   15   18   21   25   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     Y      21     Y      21     14   16   29    10   13   14   14   15   15   23   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     T      22     T      22     14   16   29    10   13   14   14   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     T      23     T      23     14   16   29    10   13   14   14   17   22   24   27   30   33   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     V      24     V      24     14   16   31    10   13   14   14   15   15   20   25   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     M      25     M      25     14   16   31    10   13   14   14   15   15   20   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     R      26     R      26     14   16   31    10   13   14   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     E      27     E      27     14   16   31    10   13   14   14   16   19   24   27   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     V      28     V      28     14   16   31    10   13   14   14   15   15   15   21   28   32   38   42   48   51   55   57   59   61   62   64 
LCS_GDT     L      29     L      29     14   16   31     9   13   14   14   15   15   16   27   31   33   39   44   48   51   55   57   59   61   62   64 
LCS_GDT     A      30     A      30     14   16   31     9   13   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     T      31     T      31     14   16   31     4   10   14   14   15   15   17   24   29   32   38   42   48   51   55   57   59   61   62   64 
LCS_GDT     Y      32     Y      32      3   16   31     3    3    5    6   13   18   22   26   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     G      33     G      33      3    5   31     3    3    5    6    9   18   23   25   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     K      34     K      34      5    5   31     3    4    6    6   10   18   22   26   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     P      35     P      35      5    5   31     3    4    6    6    7    9   20   25   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     F      36     F      36      5    5   38     3    4    6    6    7    9   15   22   29   33   37   46   48   51   55   57   59   61   62   64 
LCS_GDT     S      37     S      37      5    5   38     3    4    6    7    9   10   13   20   23   28   32   39   46   51   55   57   59   61   62   64 
LCS_GDT     P      38     P      38      8    9   38     7    8    8    8    9    9   12   20   21   23   31   36   42   47   52   56   59   61   62   64 
LCS_GDT     A      39     A      39      8    9   38     7    8    8    8   17   19   19   24   29   33   39   46   48   51   55   57   59   61   62   64 
LCS_GDT     Q      40     Q      40      8    9   38     7    8    8    8    8    9   10   23   30   33   37   46   48   51   55   57   59   61   62   64 
LCS_GDT     A      41     A      41      8    9   38     7    8    8    8    8    9   14   21   28   32   36   42   46   51   55   57   59   61   62   64 
LCS_GDT     Q      42     Q      42      8    9   38     7    8    8   12   16   19   20   24   28   29   35   42   46   51   55   57   59   61   62   64 
LCS_GDT     K      43     K      43      8    9   38     7    8    8    8   17   19   23   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     T      44     T      44      8    9   38     7    8    8    8    8    9   10   24   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     F      45     F      45      8    9   38     4    8   10   14   17   19   21   26   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     P      46     P      46      4    9   38     3   11   13   14   17   19   23   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     M      47     M      47      4    5   38     3    4    6    9   14   19   20   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     A      48     A      48      4    9   38     3    4    6    6    7   15   23   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     A      49     A      49      8    9   38     8    8    8    8    8    9   10   20   26   31   36   46   48   51   55   57   59   61   62   64 
LCS_GDT     E      50     E      50      8    9   38     8    8    8    8    8    9   10   14   24   30   33   37   45   50   55   57   59   61   62   64 
LCS_GDT     Q      51     Q      51      8    9   38     8    8    8    8    8    9   22   25   30   33   36   39   46   51   55   57   59   61   62   64 
LCS_GDT     A      52     A      52      8    9   38     8    8    8    9   19   22   24   27   30   33   39   46   48   51   55   57   59   61   62   64 
LCS_GDT     M      53     M      53      8    9   38     8    8    8    8    8   20   24   27   30   33   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     T      54     T      54      8    9   38     8    8    8    8    8    9   10   14   16   20   27   38   39   50   53   57   59   61   62   64 
LCS_GDT     E      55     E      55      8    9   38     8    8    8    8    8    9   15   22   29   32   35   38   39   41   45   55   59   61   62   64 
LCS_GDT     L      56     L      56      8    9   38     8    8    8    8    8    9   22   24   30   33   36   38   42   50   55   57   59   61   62   64 
LCS_GDT     G      57     G      57      3    9   38     3    3    4    8   15   17   22   24   30   33   36   38   42   47   51   55   59   61   62   64 
LCS_GDT     I      58     I      58      3    5   38     3    3    4    4    6    9   15   16   21   24   27   32   37   40   49   55   57   61   62   64 
LCS_GDT     A      59     A      59      3    5   38     0    3    5    6    7   15   20   24   30   33   36   39   46   51   55   57   59   61   62   64 
LCS_GDT     A      60     A      60      4   19   38     4    4    7   12   19   22   24   27   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     S      61     S      61     14   19   38     4    4    7   11   17   22   24   27   30   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     E      62     E      62     17   19   38     9   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     F      63     F      63     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     D      64     D      64     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     H      65     H      65     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     F      66     F      66     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     Q      67     Q      67     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     A      68     A      68     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     Q      69     Q      69     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     Y      70     Y      70     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     E      71     E      71     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     D      72     D      72     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     V      73     V      73     17   19   38    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     M      74     M      74     17   19   36    12   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     A      75     A      75     17   19   36    10   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     S      76     S      76     17   19   36     4   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     H      77     H      77     17   19   36     4   14   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     Y      78     Y      78     17   19   35     3   13   18   19   21   22   24   27   31   34   41   46   48   51   55   57   59   61   62   64 
LCS_GDT     D      79     D      79      4   19   34     3    4    5    6   12   14   20   24   30   33   35   40   45   50   52   54   57   61   62   64 
LCS_GDT     Q      80     Q      80      4    8   34     3    4    5    6    7   11   14   18   20   28   29   33   34   39   45   51   55   60   62   64 
LCS_GDT     I      81     I      81      3    5   34     3    3    5    6    6    8   11   14   20   21   22   31   32   37   46   49   55   61   62   64 
LCS_AVERAGE  LCS_A:  30.18  (  16.31   20.36   53.87 )

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     18     19     21     22     24     27     31     34     41     46     48     51     55     57     59     61     62     64 
GDT PERCENT_CA  18.46  21.54  27.69  29.23  32.31  33.85  36.92  41.54  47.69  52.31  63.08  70.77  73.85  78.46  84.62  87.69  90.77  93.85  95.38  98.46
GDT RMS_LOCAL    0.26   0.41   0.93   1.02   1.23   1.69   1.87   2.22   2.83   3.36   3.83   4.18   4.27   4.48   4.94   5.11   5.40   5.59   5.69   5.91
GDT RMS_ALL_CA   6.74   6.72   6.49   6.51   6.64   6.77   6.72   6.85   7.15   6.74   6.46   6.34   6.50   6.44   6.24   6.19   6.17   6.11   6.14   6.06

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17          8.348
LGA    Q      18      Q      18          4.624
LGA    P      19      P      19          2.991
LGA    A      20      A      20          5.680
LGA    Y      21      Y      21          6.394
LGA    T      22      T      22          3.856
LGA    T      23      T      23          3.129
LGA    V      24      V      24          6.536
LGA    M      25      M      25          7.091
LGA    R      26      R      26          3.208
LGA    E      27      E      27          3.729
LGA    V      28      V      28          8.447
LGA    L      29      L      29          7.915
LGA    A      30      A      30          2.101
LGA    T      31      T      31          6.786
LGA    Y      32      Y      32          6.134
LGA    G      33      G      33          4.923
LGA    K      34      K      34          7.608
LGA    P      35      P      35          7.636
LGA    F      36      F      36          8.572
LGA    S      37      S      37         11.115
LGA    P      38      P      38         13.166
LGA    A      39      A      39         11.299
LGA    Q      40      Q      40          9.981
LGA    A      41      A      41         10.496
LGA    Q      42      Q      42         11.866
LGA    K      43      K      43         12.003
LGA    T      44      T      44         10.570
LGA    F      45      F      45          9.985
LGA    P      46      P      46         10.074
LGA    M      47      M      47         11.055
LGA    A      48      A      48         10.363
LGA    A      49      A      49          9.643
LGA    E      50      E      50         10.172
LGA    Q      51      Q      51          5.940
LGA    A      52      A      52          2.229
LGA    M      53      M      53          3.943
LGA    T      54      T      54          7.529
LGA    E      55      E      55          7.297
LGA    L      56      L      56          5.459
LGA    G      57      G      57          7.348
LGA    I      58      I      58          9.490
LGA    A      59      A      59          6.598
LGA    A      60      A      60          2.131
LGA    S      61      S      61          2.848
LGA    E      62      E      62          1.807
LGA    F      63      F      63          2.974
LGA    D      64      D      64          2.307
LGA    H      65      H      65          0.502
LGA    F      66      F      66          1.590
LGA    Q      67      Q      67          2.149
LGA    A      68      A      68          1.499
LGA    Q      69      Q      69          0.174
LGA    Y      70      Y      70          1.230
LGA    E      71      E      71          1.661
LGA    D      72      D      72          1.302
LGA    V      73      V      73          0.491
LGA    M      74      M      74          0.600
LGA    A      75      A      75          1.382
LGA    S      76      S      76          2.084
LGA    H      77      H      77          1.722
LGA    Y      78      Y      78          1.759
LGA    D      79      D      79          6.755
LGA    Q      80      Q      80         10.711
LGA    I      81      I      81         11.091

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     27    2.22    45.000    39.131     1.164

LGA_LOCAL      RMSD =  2.220  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.944  Number of atoms =   65 
Std_ALL_ATOMS  RMSD =  6.047  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.382063 * X  +  -0.704509 * Y  +   0.598076 * Z  +  29.572880
  Y_new =  -0.302496 * X  +   0.706859 * Y  +   0.639411 * Z  +  20.644638
  Z_new =  -0.873226 * X  +   0.063380 * Y  +  -0.483176 * Z  +   0.575591 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.011164   -0.130428  [ DEG:   172.5270     -7.4730 ]
  Theta =   1.061785    2.079808  [ DEG:    60.8358    119.1642 ]
  Phi   =  -2.471906    0.669686  [ DEG:  -141.6298     38.3702 ]
 
# 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_5-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0324TS168_5-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   27   2.22  39.131     6.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS168_5-D2
PFRMAT TS
TARGET T0324
MODEL 5
PARENT N/A
ATOM     17  CA  SER    17      30.478  18.262   5.450  1.00 25.00           C
ATOM     18  CA  GLN    18      27.971  19.173   8.242  1.00 25.00           C
ATOM     19  CA  PRO    19      24.561  18.581   9.881  1.00 25.00           C
ATOM     20  CA  ALA    20      22.797  19.797   6.707  1.00 25.00           C
ATOM     21  CA  TYR    21      24.946  17.445   4.581  1.00 25.00           C
ATOM     22  CA  THR    22      24.089  14.524   6.906  1.00 25.00           C
ATOM     23  CA  THR    23      20.364  15.369   6.635  1.00 25.00           C
ATOM     24  CA  VAL    24      20.639  15.474   2.817  1.00 25.00           C
ATOM     25  CA  MET    25      22.395  12.071   2.825  1.00 25.00           C
ATOM     26  CA  ARG    26      19.635  10.625   5.052  1.00 25.00           C
ATOM     27  CA  GLU    27      16.963  12.009   2.682  1.00 25.00           C
ATOM     28  CA  VAL    28      18.777  10.452  -0.311  1.00 25.00           C
ATOM     29  CA  LEU    29      18.944   7.087   1.510  1.00 25.00           C
ATOM     30  CA  ALA    30      15.198   7.291   2.281  1.00 25.00           C
ATOM     31  CA  THR    31      14.458   8.062  -1.395  1.00 25.00           C
ATOM     32  CA  TYR    32      10.776   8.017  -0.406  1.00 25.00           C
ATOM     33  CA  GLY    33       8.418   9.722  -2.858  1.00 25.00           C
ATOM     34  CA  LYS    34      11.626  10.626  -4.646  1.00 25.00           C
ATOM     35  CA  PRO    35      10.038  13.836  -5.975  1.00 25.00           C
ATOM     36  CA  PHE    36       8.999  15.852  -2.939  1.00 25.00           C
ATOM     37  CA  SER    37       5.604  17.356  -2.038  1.00 25.00           C
ATOM     38  CA  PRO    38       6.366  21.120  -2.342  1.00 25.00           C
ATOM     39  CA  ALA    39       9.641  21.062  -4.327  1.00 25.00           C
ATOM     40  CA  GLN    40      10.637  24.442  -2.826  1.00 25.00           C
ATOM     41  CA  ALA    41       9.870  23.135   0.691  1.00 25.00           C
ATOM     42  CA  GLN    42      11.995  20.018   0.022  1.00 25.00           C
ATOM     43  CA  LYS    43      14.878  22.218  -1.210  1.00 25.00           C
ATOM     44  CA  THR    44      14.607  24.379   1.940  1.00 25.00           C
ATOM     45  CA  PHE    45      14.672  21.238   4.131  1.00 25.00           C
ATOM     46  CA  PRO    46      13.927  23.035   7.441  1.00 25.00           C
ATOM     47  CA  MET    47      10.235  23.970   7.641  1.00 25.00           C
ATOM     48  CA  ALA    48      10.998  24.036  11.407  1.00 25.00           C
ATOM     49  CA  ALA    49      14.650  23.921  12.465  1.00 25.00           C
ATOM     50  CA  GLU    50      16.748  20.782  13.109  1.00 25.00           C
ATOM     51  CA  GLN    51      15.317  20.522  16.651  1.00 25.00           C
ATOM     52  CA  ALA    52      11.762  20.863  15.267  1.00 25.00           C
ATOM     53  CA  MET    53      12.475  18.117  12.694  1.00 25.00           C
ATOM     54  CA  THR    54      13.828  15.842  15.462  1.00 25.00           C
ATOM     55  CA  GLU    55      10.693  16.490  17.563  1.00 25.00           C
ATOM     56  CA  LEU    56       8.474  15.652  14.556  1.00 25.00           C
ATOM     57  CA  GLY    57       5.605  16.610  16.873  1.00 25.00           C
ATOM     58  CA  ILE    58       6.255  14.712  20.072  1.00 25.00           C
ATOM     59  CA  ALA    59       4.507  11.792  18.466  1.00 25.00           C
ATOM     60  CA  ALA    60       4.279   8.575  16.476  1.00 25.00           C
ATOM     61  CA  SER    61       6.077   5.246  17.072  1.00 25.00           C
ATOM     62  CA  GLU    62       7.228   5.186  13.420  1.00 25.00           C
ATOM     63  CA  PHE    63       8.526   8.775  13.744  1.00 25.00           C
ATOM     64  CA  ASP    64      10.419   7.828  16.935  1.00 25.00           C
ATOM     65  CA  HIS    65      11.960   4.808  15.154  1.00 25.00           C
ATOM     66  CA  PHE    66      13.027   7.044  12.233  1.00 25.00           C
ATOM     67  CA  GLN    67      14.611   9.527  14.680  1.00 25.00           C
ATOM     68  CA  ALA    68      16.490   6.668  16.404  1.00 25.00           C
ATOM     69  CA  GLN    69      17.748   5.417  13.009  1.00 25.00           C
ATOM     70  CA  TYR    70      18.928   8.949  12.117  1.00 25.00           C
ATOM     71  CA  GLU    71      20.755   9.214  15.472  1.00 25.00           C
ATOM     72  CA  ASP    72      22.436   5.829  14.851  1.00 25.00           C
ATOM     73  CA  VAL    73      23.520   6.980  11.363  1.00 25.00           C
ATOM     74  CA  MET    74      24.959  10.205  12.847  1.00 25.00           C
ATOM     75  CA  ALA    75      26.870   8.173  15.471  1.00 25.00           C
ATOM     76  CA  SER    76      28.264   5.894  12.727  1.00 25.00           C
ATOM     77  CA  HIS    77      29.364   8.957  10.708  1.00 25.00           C
ATOM     78  CA  TYR    78      31.084  10.412  13.805  1.00 25.00           C
ATOM     79  CA  ASP    79      32.882   7.083  14.400  1.00 25.00           C
ATOM     80  CA  GLN    80      33.729   4.805  11.519  1.00 25.00           C
ATOM     81  CA  ILE    81      33.007   6.825   8.330  1.00 25.00           C
TER
END
