
#######################################################
#                                                     #
#                        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 T0324TS393_3-D2
# Molecule2: number of CA atoms   65 (  494),  selected   65 , name T0324_D2.pdb
# PARAMETERS: T0324TS393_3-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:    41        36 - 76          4.93     7.54
  LCS_AVERAGE:     57.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        59 - 78          1.99    10.90
  LCS_AVERAGE:     25.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        62 - 78          0.82     8.01
  LCS_AVERAGE:     18.11

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   20     0    1   10   14   15   16   16   24   27   30   35   40   44   49   54   55   58   60   61   63 
LCS_GDT     Q      18     Q      18     14   16   20     9   13   14   14   20   23   25   28   30   33   36   40   42   44   51   55   58   60   61   63 
LCS_GDT     P      19     P      19     14   16   20    10   13   14   14   19   21   24   28   30   33   36   40   41   44   46   50   55   60   61   63 
LCS_GDT     A      20     A      20     14   16   20    10   13   14   16   19   22   24   27   29   33   36   40   44   49   54   55   58   60   61   63 
LCS_GDT     Y      21     Y      21     14   16   20    10   13   14   14   15   16   24   26   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     T      22     T      22     14   16   26    10   13   14   14   20   23   25   28   30   33   36   40   42   45   52   55   58   60   61   63 
LCS_GDT     T      23     T      23     14   16   33    10   13   14   15   20   22   24   28   30   33   36   40   43   49   54   55   58   60   61   63 
LCS_GDT     V      24     V      24     14   16   33    10   13   14   14   15   17   20   26   27   31   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     M      25     M      25     14   16   33    10   13   14   14   15   16   19   23   27   32   36   40   44   49   54   55   58   60   61   63 
LCS_GDT     R      26     R      26     14   16   33    10   13   14   14   21   23   25   28   30   33   36   40   44   49   54   55   58   60   61   63 
LCS_GDT     E      27     E      27     14   16   33    10   13   15   18   20   22   24   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     V      28     V      28     14   16   33    10   13   14   14   15   16   17   19   21   27   32   37   42   47   54   55   57   60   61   63 
LCS_GDT     L      29     L      29     14   16   33     9   13   14   14   15   16   18   23   27   29   35   40   44   47   54   55   58   60   61   63 
LCS_GDT     A      30     A      30     14   16   33     9   13   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     T      31     T      31     14   16   33     4   10   14   14   15   16   19   23   30   32   36   39   42   45   47   50   56   59   61   63 
LCS_GDT     Y      32     Y      32      3   16   33     3    3    3   12   20   23   25   28   30   33   37   40   44   47   54   55   58   60   61   63 
LCS_GDT     G      33     G      33      3   16   33     3    5   15   20   21   23   25   27   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     K      34     K      34      3   16   33     3    3    7   15   15   16   20   25   27   30   37   40   44   47   54   55   58   60   61   63 
LCS_GDT     P      35     P      35     11   16   40     3    6   12   15   15   16   20   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     F      36     F      36     11   16   41     3    5   13   15   15   16   20   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     S      37     S      37     11   16   41     3    4   13   15   15   16   20   24   27   29   35   40   44   49   54   55   58   60   61   63 
LCS_GDT     P      38     P      38     11   16   41     7    8   13   15   15   16   18   21   25   29   34   38   42   47   54   55   57   59   61   63 
LCS_GDT     A      39     A      39     11   16   41     7    8   13   15   15   16   20   24   27   29   34   39   44   49   54   55   58   60   61   63 
LCS_GDT     Q      40     Q      40     11   16   41     7    8   13   15   15   16   20   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     A      41     A      41     11   16   41     7    8   13   15   15   16   20   24   27   29   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     Q      42     Q      42     11   16   41     7    8   13   15   15   16   20   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     K      43     K      43     11   16   41     7    8   13   15   15   16   20   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     T      44     T      44     11   16   41     7    8   13   15   15   16   18   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     F      45     F      45     11   16   41     4    8   13   15   15   16   18   24   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     P      46     P      46     10   16   41     3    5   13   15   15   16   17   21   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     M      47     M      47     10   16   41     3    8   13   15   15   16   19   25   27   30   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     A      48     A      48      9   16   41     3    5   13   15   15   16   18   23   27   30   35   40   44   49   54   55   58   60   61   63 
LCS_GDT     A      49     A      49      9   13   41     8    8   10   11   11   13   17   22   26   31   35   39   44   49   54   55   58   60   61   63 
LCS_GDT     E      50     E      50      9   13   41     8    8   10   11   11   12   19   22   26   31   34   39   43   48   54   55   58   60   61   63 
LCS_GDT     Q      51     Q      51      9   13   41     8    8   10   13   17   23   25   26   28   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     A      52     A      52      9   13   41     8   12   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     M      53     M      53      9   13   41     8    8   10   13   15   19   22   26   30   32   36   40   41   49   54   55   58   60   61   63 
LCS_GDT     T      54     T      54      9   13   41     8    9   13   17   18   20   23   28   30   33   36   40   44   49   54   55   58   60   61   63 
LCS_GDT     E      55     E      55      9   13   41     8    8   10   11   20   22   24   27   30   33   36   40   44   49   54   55   58   60   61   63 
LCS_GDT     L      56     L      56      9   13   41     8    8   10   11   11   21   24   26   27   31   34   38   40   43   45   47   52   58   61   63 
LCS_GDT     G      57     G      57      9   13   41     3    5   10   11   11   12   22   26   27   27   29   33   38   42   42   44   46   57   60   63 
LCS_GDT     I      58     I      58      5   18   41     3    5    5   13   18   20   24   26   27   31   34   38   42   49   54   55   58   60   61   63 
LCS_GDT     A      59     A      59      5   20   41     3    5    5    6    8   14   22   26   27   30   34   38   44   49   54   55   58   60   61   63 
LCS_GDT     A      60     A      60      5   20   41     4    5    6   15   18   22   24   27   28   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     S      61     S      61     14   20   41     4    4    6   12   17   22   24   27   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     E      62     E      62     17   20   41     9   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     F      63     F      63     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     D      64     D      64     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     H      65     H      65     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     F      66     F      66     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     Q      67     Q      67     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     A      68     A      68     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     Q      69     Q      69     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     Y      70     Y      70     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     E      71     E      71     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     D      72     D      72     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     V      73     V      73     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     M      74     M      74     17   20   41    11   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     A      75     A      75     17   20   41    10   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     S      76     S      76     17   20   41     4   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     H      77     H      77     17   20   40     4   14   18   20   21   23   25   28   30   33   37   40   44   49   54   55   58   60   61   63 
LCS_GDT     Y      78     Y      78     17   20   34     3   13   17   20   21   23   25   28   30   33   36   40   43   46   52   55   58   60   61   63 
LCS_GDT     D      79     D      79      4   19   34     3    3    4    6    9   18   24   28   30   33   36   40   42   44   51   54   58   60   61   63 
LCS_GDT     Q      80     Q      80      4   11   34     3    3    4    5    9   12   17   22   28   33   36   39   42   44   46   50   55   58   61   62 
LCS_GDT     I      81     I      81      3    6   34     3    3    3    4    6   12   17   22   28   33   36   40   42   44   51   55   58   60   61   63 
LCS_AVERAGE  LCS_A:  33.66  (  18.11   25.63   57.25 )

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     18     20     21     23     25     28     30     33     37     40     44     49     54     55     58     60     61     63 
GDT PERCENT_CA  16.92  21.54  27.69  30.77  32.31  35.38  38.46  43.08  46.15  50.77  56.92  61.54  67.69  75.38  83.08  84.62  89.23  92.31  93.85  96.92
GDT RMS_LOCAL    0.17   0.41   0.85   1.13   1.27   1.58   1.83   2.38   2.64   2.89   3.88   3.67   4.32   5.01   5.30   5.33   5.57   5.72   5.80   6.09
GDT RMS_ALL_CA   8.00   8.16   7.18   6.99   7.01   7.18   7.23   7.97   8.30   7.59   6.79   7.35   6.75   6.47   6.47   6.36   6.28   6.28   6.28   6.26

#      Molecule1      Molecule2       DISTANCE
LGA    S      17      S      17          8.842
LGA    Q      18      Q      18          3.993
LGA    P      19      P      19          3.368
LGA    A      20      A      20          5.421
LGA    Y      21      Y      21          5.519
LGA    T      22      T      22          3.421
LGA    T      23      T      23          3.562
LGA    V      24      V      24          6.031
LGA    M      25      M      25          6.286
LGA    R      26      R      26          3.173
LGA    E      27      E      27          3.499
LGA    V      28      V      28          7.471
LGA    L      29      L      29          7.163
LGA    A      30      A      30          2.053
LGA    T      31      T      31          5.074
LGA    Y      32      Y      32          3.132
LGA    G      33      G      33          5.321
LGA    K      34      K      34          8.649
LGA    P      35      P      35         10.665
LGA    F      36      F      36         11.658
LGA    S      37      S      37         15.358
LGA    P      38      P      38         18.140
LGA    A      39      A      39         17.189
LGA    Q      40      Q      40         14.410
LGA    A      41      A      41         15.004
LGA    Q      42      Q      42         16.418
LGA    K      43      K      43         13.911
LGA    T      44      T      44         12.119
LGA    F      45      F      45         14.211
LGA    P      46      P      46         16.084
LGA    M      47      M      47         12.049
LGA    A      48      A      48         11.946
LGA    A      49      A      49         10.092
LGA    E      50      E      50          9.872
LGA    Q      51      Q      51          6.021
LGA    A      52      A      52          2.499
LGA    M      53      M      53          5.164
LGA    T      54      T      54          3.923
LGA    E      55      E      55          4.997
LGA    L      56      L      56          8.394
LGA    G      57      G      57         11.153
LGA    I      58      I      58          8.097
LGA    A      59      A      59          9.311
LGA    A      60      A      60          6.466
LGA    S      61      S      61          5.854
LGA    E      62      E      62          2.336
LGA    F      63      F      63          1.432
LGA    D      64      D      64          0.910
LGA    H      65      H      65          0.929
LGA    F      66      F      66          0.398
LGA    Q      67      Q      67          0.293
LGA    A      68      A      68          0.660
LGA    Q      69      Q      69          0.787
LGA    Y      70      Y      70          1.093
LGA    E      71      E      71          1.183
LGA    D      72      D      72          1.777
LGA    V      73      V      73          2.370
LGA    M      74      M      74          1.954
LGA    A      75      A      75          1.591
LGA    S      76      S      76          1.706
LGA    H      77      H      77          1.642
LGA    Y      78      Y      78          0.826
LGA    D      79      D      79          3.953
LGA    Q      80      Q      80          5.852
LGA    I      81      I      81          6.124

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     28    2.38    45.000    39.715     1.128

LGA_LOCAL      RMSD =  2.381  Number of atoms =   28  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.127  Number of atoms =   65 
Std_ALL_ATOMS  RMSD =  6.255  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.653379 * X  +  -0.693732 * Y  +  -0.303038 * Z  +  24.738674
  Y_new =  -0.660701 * X  +   0.717968 * Y  +  -0.219079 * Z  +  20.582775
  Z_new =   0.369554 * X  +   0.057076 * Y  +  -0.927455 * Z  +  -1.926170 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.080130   -0.061463  [ DEG:   176.4784     -3.5216 ]
  Theta =  -0.378529   -2.763064  [ DEG:   -21.6881   -158.3119 ]
  Phi   =  -2.350623    0.790970  [ DEG:  -134.6808     45.3192 ]
 
# 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: T0324TS393_3-D2                               
REMARK     2: T0324_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0324TS393_3-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   28   2.38  39.715     6.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0324TS393_3-D2
PFRMAT TS
TARGET T0324
MODEL 3
PARENT N/A
ATOM     17  CA  SER    17      27.748  21.293   4.353  1.00 25.00           C
ATOM     18  CA  GLN    18      27.355  20.190   8.013  1.00 25.00           C
ATOM     19  CA  PRO    19      25.402  17.932  10.411  1.00 25.00           C
ATOM     20  CA  ALA    20      22.102  19.431   9.174  1.00 25.00           C
ATOM     21  CA  TYR    21      23.162  18.828   5.543  1.00 25.00           C
ATOM     22  CA  THR    22      24.054  15.199   6.380  1.00 25.00           C
ATOM     23  CA  THR    23      20.645  14.722   8.058  1.00 25.00           C
ATOM     24  CA  VAL    24      18.898  16.177   4.976  1.00 25.00           C
ATOM     25  CA  MET    25      20.874  13.809   2.707  1.00 25.00           C
ATOM     26  CA  ARG    26      19.895  10.837   4.915  1.00 25.00           C
ATOM     27  CA  GLU    27      16.220  11.897   4.755  1.00 25.00           C
ATOM     28  CA  VAL    28      16.435  12.162   0.941  1.00 25.00           C
ATOM     29  CA  LEU    29      17.998   8.669   0.763  1.00 25.00           C
ATOM     30  CA  ALA    30      15.199   7.277   2.977  1.00 25.00           C
ATOM     31  CA  THR    31      12.569   8.913   0.725  1.00 25.00           C
ATOM     32  CA  TYR    32       9.892   6.981   2.614  1.00 25.00           C
ATOM     33  CA  GLY    33       9.811   3.893   0.381  1.00 25.00           C
ATOM     34  CA  LYS    34      10.827   5.733  -2.754  1.00 25.00           C
ATOM     35  CA  PRO    35       7.900   7.214  -4.596  1.00 25.00           C
ATOM     36  CA  PHE    36       7.369  10.400  -2.613  1.00 25.00           C
ATOM     37  CA  SER    37       5.620  11.614  -5.726  1.00 25.00           C
ATOM     38  CA  PRO    38       4.149  15.137  -5.281  1.00 25.00           C
ATOM     39  CA  ALA    39       2.237  16.821  -2.421  1.00 25.00           C
ATOM     40  CA  GLN    40       3.891  14.466   0.105  1.00 25.00           C
ATOM     41  CA  ALA    41       7.336  15.273  -1.361  1.00 25.00           C
ATOM     42  CA  GLN    42       6.593  19.021  -1.108  1.00 25.00           C
ATOM     43  CA  LYS    43       5.513  18.587   2.540  1.00 25.00           C
ATOM     44  CA  THR    44       8.739  16.663   3.290  1.00 25.00           C
ATOM     45  CA  PHE    45      10.805  19.440   1.652  1.00 25.00           C
ATOM     46  CA  PRO    46       9.158  22.486   3.307  1.00 25.00           C
ATOM     47  CA  MET    47       9.125  21.453   6.968  1.00 25.00           C
ATOM     48  CA  ALA    48      12.618  20.662   8.334  1.00 25.00           C
ATOM     49  CA  ALA    49      12.506  23.264  11.116  1.00 25.00           C
ATOM     50  CA  GLU    50      10.064  24.314  13.872  1.00 25.00           C
ATOM     51  CA  GLN    51       7.464  21.833  12.549  1.00 25.00           C
ATOM     52  CA  ALA    52      10.095  19.052  12.523  1.00 25.00           C
ATOM     53  CA  MET    53      11.068  19.904  16.128  1.00 25.00           C
ATOM     54  CA  THR    54       7.385  19.798  17.173  1.00 25.00           C
ATOM     55  CA  GLU    55       6.979  16.388  15.477  1.00 25.00           C
ATOM     56  CA  LEU    56      10.089  15.086  17.293  1.00 25.00           C
ATOM     57  CA  GLY    57       8.060  13.804  20.208  1.00 25.00           C
ATOM     58  CA  ILE    58       4.919  12.037  18.843  1.00 25.00           C
ATOM     59  CA  ALA    59       4.805   9.198  21.362  1.00 25.00           C
ATOM     60  CA  ALA    60       5.430   5.739  19.897  1.00 25.00           C
ATOM     61  CA  SER    61       7.439   2.736  18.625  1.00 25.00           C
ATOM     62  CA  GLU    62       7.681   4.339  15.155  1.00 25.00           C
ATOM     63  CA  PHE    63       8.887   7.617  16.725  1.00 25.00           C
ATOM     64  CA  ASP    64      11.524   5.709  18.742  1.00 25.00           C
ATOM     65  CA  HIS    65      12.701   3.926  15.564  1.00 25.00           C
ATOM     66  CA  PHE    66      12.954   7.286  13.743  1.00 25.00           C
ATOM     67  CA  GLN    67      14.987   8.734  16.646  1.00 25.00           C
ATOM     68  CA  ALA    68      17.328   5.704  16.551  1.00 25.00           C
ATOM     69  CA  GLN    69      17.779   6.140  12.773  1.00 25.00           C
ATOM     70  CA  TYR    70      18.581   9.851  13.272  1.00 25.00           C
ATOM     71  CA  GLU    71      21.149   8.959  15.970  1.00 25.00           C
ATOM     72  CA  ASP    72      22.754   6.390  13.626  1.00 25.00           C
ATOM     73  CA  VAL    73      22.927   9.007  10.836  1.00 25.00           C
ATOM     74  CA  MET    74      24.562  11.500  13.241  1.00 25.00           C
ATOM     75  CA  ALA    75      27.119   8.850  14.288  1.00 25.00           C
ATOM     76  CA  SER    76      27.895   8.109  10.611  1.00 25.00           C
ATOM     77  CA  HIS    77      28.366  11.849   9.933  1.00 25.00           C
ATOM     78  CA  TYR    78      30.725  12.122  12.939  1.00 25.00           C
ATOM     79  CA  ASP    79      32.734   9.121  11.665  1.00 25.00           C
ATOM     80  CA  GLN    80      35.758  10.662   9.840  1.00 25.00           C
ATOM     81  CA  ILE    81      33.335  12.954   7.997  1.00 25.00           C
TER
END
