
#######################################################
#                                                     #
#                        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   76 (   76),  selected   62 , name T0309TS393_4
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS393_4.T0309.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:    28        29 - 56          4.98    12.90
  LCS_AVERAGE:     35.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10         3 - 12          1.83    20.75
  LCS_AVERAGE:     12.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        35 - 42          0.57    21.96
  LCS_AVERAGE:      7.47

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:   62
LCS_GDT     A       2     A       2      4    6   17     0    4    4    5    7   10   12   15   20   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     S       3     S       3      4   10   17     2    4    6    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     K       4     K       4      4   10   17     2    4    6    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     K       5     K       5      6   10   17     2    5    6    7   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     V       6     V       6      6   10   17     0    5    6    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     H       7     H       7      6   10   17     4    5    6    9   10   12   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     Q       8     Q       8      6   10   17     4    5    6    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     I       9     I       9      6   10   17     4    5    6    9   10   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     N      10     N      10      6   10   17     4    5    6    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     V      11     V      11      5   10   17     3    4    6    9   11   14   16   20   21   24   25   27   29   30   34   38   39   41   43   46 
LCS_GDT     K      12     K      12      5   10   17     2    4    6    9   10   11   16   18   20   24   25   27   29   30   31   32   34   36   39   41 
LCS_GDT     G      13     G      13      5    9   17     3    3    5    6   10   11   13   17   20   24   25   26   27   30   31   31   33   34   36   37 
LCS_GDT     F      14     F      14      3    9   19     3    3    6    9   10   14   16   18   20   24   25   27   29   30   32   34   38   40   42   43 
LCS_GDT     F      15     F      15      3    9   19     3    3    5    9   10   12   15   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     D      16     D      16      3    5   19     1    3    3    5    8   11   14   18   20   24   25   27   29   31   35   38   39   42   43   46 
LCS_GDT     M      17     M      17      3    5   19     3    3    3    4    5    9   11   14   18   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     D      18     D      18      3    7   19     3    3    3    4    7    9   11   14   15   16   16   17   19   21   25   29   33   38   43   46 
LCS_GDT     V      19     V      19      3    7   19     3    3    5    6    7    9   11   14   15   16   16   17   19   21   25   28   33   35   43   46 
LCS_GDT     M      20     M      20      5    7   19     3    3    5    6    7    8   11   14   15   16   16   18   23   27   35   38   39   42   43   46 
LCS_GDT     E      21     E      21      5    7   19     3    4    5    6    7    8   11   14   15   19   22   26   29   32   35   38   39   42   43   46 
LCS_GDT     V      22     V      22      5    7   19     3    4    5    6    7    9   11   14   17   20   22   26   29   32   35   38   39   42   43   46 
LCS_GDT     T      23     T      23      5    7   19     3    4    5    6    7    9   11   14   17   20   22   24   29   31   35   38   39   42   43   46 
LCS_GDT     E      24     E      24      5    7   19     3    4    5    6    7   10   12   15   18   20   22   26   29   32   35   38   39   42   43   46 
LCS_GDT     Q      25     Q      25      4    7   19     3    3    4    6    7    8   11   14   15   16   16   19   25   30   34   37   39   42   43   46 
LCS_GDT     T      26     T      26      4    7   19     0    3    4    5    7    9   11   14   15   16   16   17   19   25   29   33   38   42   43   46 
LCS_GDT     K      27     K      27      3    6   19     0    3    4    5    7    8   11   14   15   16   16   17   18   19   22   25   31   36   38   42 
LCS_GDT     E      28     E      28      4    6   19     0    4    4    5    7    7    9   13   15   16   16   17   18   19   22   25   33   37   39   42 
LCS_GDT     A      29     A      29      4    6   28     3    4    4    5    7    9   11   14   15   16   16   19   25   29   32   34   38   41   43   46 
LCS_GDT     E      30     E      30      4    5   28     3    4    4    4    5    6    8    9   13   16   18   23   27   29   32   34   35   37   42   44 
LCS_GDT     Y      31     Y      31      4    5   28     3    4    4    4    7    9   11   14   15   16   18   20   23   29   32   34   38   41   43   46 
LCS_GDT     T      32     T      32      3    5   28     0    3    4    6    6    8   11   14   15   18   22   23   27   29   32   34   38   42   43   46 
LCS_GDT     Y      33     Y      33      3    5   28     3    3    4    4    5    8   11   12   15   18   22   24   27   29   32   34   35   41   42   46 
LCS_GDT     D      34     D      34      3    9   28     3    3    4    4    5    8    9   10   11   16   18   23   27   29   32   34   35   37   42   46 
LCS_GDT     F      35     F      35      8    9   28     6    7    8    8    8    8    9   11   12   17   22   23   27   29   32   34   39   42   43   46 
LCS_GDT     K      36     K      36      8    9   28     6    7    8    8    8    8   11   12   16   18   22   24   27   30   34   38   39   42   43   46 
LCS_GDT     E      37     E      37      8    9   28     6    7    8    8    8   10   13   16   20   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     I      38     I      38      8    9   28     6    7    8    8    8   10   12   15   18   22   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     L      39     L      39      8    9   28     6    7    8    8    8   10   13   18   20   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     S      40     S      40      8    9   28     6    7    8    8    8   11   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     E      41     E      41      8    9   28     6    7    8    8   10   14   16   20   21   23   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     F      42     F      42      8    9   28     4    7    8    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     N      43     N      43      5    8   28     3    5    5    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     G      44     G      44      5    8   28     3    5    5    7   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     K      45     K      45      5    8   28     3    5    5    9   11   14   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     N      46     N      46      5    8   28     3    5    5    6   10   11   16   20   21   23   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     V      47     V      47      5    8   28     3    5    5    7   10   12   16   20   21   24   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     S      48     S      48      5    8   28     1    5    5    7   10   10   13   16   21   23   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     I      49     I      49      3    8   28     3    3    5    7   10   11   16   20   21   23   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     T      50     T      50      3    8   28     3    3    5    7   10   12   16   20   21   23   25   27   29   32   35   38   39   42   43   46 
LCS_GDT     V      51     V      51      3    8   28     3    3    5    5    8   10   13   16   18   22   23   26   29   32   35   38   39   42   43   46 
LCS_GDT     K      52     K      52      3    6   28     3    3    4    5    7   10   13   15   18   22   23   26   29   32   35   38   39   42   43   46 
LCS_GDT     E      53     E      53      3    6   28     3    3    4    5    7   10   12   15   18   20   22   26   29   32   35   38   39   42   43   46 
LCS_GDT     E      54     E      54      4    6   28     3    3    4    5    8   10   13   15   18   22   23   26   29   32   35   38   39   42   43   46 
LCS_GDT     N      55     N      55      4    5   28     3    4    4    5    6    8    9   13   16   20   22   24   29   31   35   38   39   42   43   46 
LCS_GDT     E      56     E      56      4    7   28     3    3    4    4    6    8    9   11   13   15   22   24   27   29   32   33   37   42   43   46 
LCS_GDT     L      57     L      57      4    7   26     3    3    4    4    6    7    8    8    8   10   12   15   18   22   28   31   34   37   38   42 
LCS_GDT     P      58     P      58      4    7   11     2    3    5    5    6    7    8    8    8    8   10   10   12   14   15   18   28   32   38   39 
LCS_GDT     V      59     V      59      4    7   10     3    3    4    5    6    7    8    8    8    8    9    9   11   11   11   11   12   16   19   20 
LCS_GDT     K      60     K      60      3    7   10     3    3    5    5    6    7    8    8    8    8    9    9   10   11   11   11   12   14   14   15 
LCS_GDT     G      61     G      61      3    7   10     3    3    5    5    6    7    8    8    8    8    9    9    9   10   10   10   11   11   11   13 
LCS_GDT     V      62     V      62      3    7   10     3    3    5    5    6    7    8    8    8    8    9    9    9   10   10   10   11   11   11   13 
LCS_GDT     E      63     E      63      3    6   10     3    3    5    5    6    7    8    8    8    8    9    9    9   10   10   10   11   11   11   11 
LCS_AVERAGE  LCS_A:  18.40  (   7.47   12.36   35.38 )

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      6      7      8      9     11     14     16     20     21     24     25     27     29     32     35     38     39     42     43     46 
GDT PERCENT_CA   9.68  11.29  12.90  14.52  17.74  22.58  25.81  32.26  33.87  38.71  40.32  43.55  46.77  51.61  56.45  61.29  62.90  67.74  69.35  74.19
GDT RMS_LOCAL    0.26   0.34   0.57   1.30   1.69   2.01   2.29   2.84   2.92   3.55   3.47   3.74   4.01   4.92   5.30   5.64   5.75   6.27   6.36   6.83
GDT RMS_ALL_CA  22.02  21.90  21.96  20.19  16.77  16.73  17.04  15.84  15.81  16.59  16.24  16.01  15.63  13.00  12.68  12.63  12.51  12.04  12.06  11.87

#      Molecule1      Molecule2       DISTANCE
LGA    A       2      A       2          7.643
LGA    S       3      S       3          2.368
LGA    K       4      K       4          0.420
LGA    K       5      K       5          2.719
LGA    V       6      V       6          2.452
LGA    H       7      H       7          3.589
LGA    Q       8      Q       8          1.651
LGA    I       9      I       9          1.819
LGA    N      10      N      10          1.333
LGA    V      11      V      11          3.884
LGA    K      12      K      12          7.287
LGA    G      13      G      13          9.830
LGA    F      14      F      14          6.357
LGA    F      15      F      15          3.997
LGA    D      16      D      16          6.369
LGA    M      17      M      17          7.343
LGA    D      18      D      18         14.405
LGA    V      19      V      19         15.488
LGA    M      20      M      20         12.636
LGA    E      21      E      21          9.311
LGA    V      22      V      22         10.997
LGA    T      23      T      23         13.326
LGA    E      24      E      24         14.212
LGA    Q      25      Q      25         16.112
LGA    T      26      T      26         18.366
LGA    K      27      K      27         23.874
LGA    E      28      E      28         24.521
LGA    A      29      A      29         21.299
LGA    E      30      E      30         22.525
LGA    Y      31      Y      31         17.263
LGA    T      32      T      32         16.938
LGA    Y      33      Y      33         17.861
LGA    D      34      D      34         17.361
LGA    F      35      F      35         14.430
LGA    K      36      K      36         11.548
LGA    E      37      E      37          6.353
LGA    I      38      I      38          7.506
LGA    L      39      L      39          5.688
LGA    S      40      S      40          3.608
LGA    E      41      E      41          3.523
LGA    F      42      F      42          2.692
LGA    N      43      N      43          1.986
LGA    G      44      G      44          2.612
LGA    K      45      K      45          0.569
LGA    N      46      N      46          3.029
LGA    V      47      V      47          3.036
LGA    S      48      S      48          4.185
LGA    I      49      I      49          3.932
LGA    T      50      T      50          3.636
LGA    V      51      V      51          8.393
LGA    K      52      K      52         11.618
LGA    E      53      E      53         14.772
LGA    E      54      E      54         12.694
LGA    N      55      N      55         14.983
LGA    E      56      E      56         19.920
LGA    L      57      L      57         24.276
LGA    P      58      P      58         31.089
LGA    V      59      V      59         32.453
LGA    K      60      K      60         38.046
LGA    G      61      G      61         39.367
LGA    V      62      V      62         34.467
LGA    E      63      E      63         37.133

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   76   62    4.0     20    2.84    29.839    24.970     0.681

LGA_LOCAL      RMSD =  2.836  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.812  Number of atoms =   62 
Std_ALL_ATOMS  RMSD = 11.012  (standard rmsd on all 62 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.738374 * X  +   0.526860 * Y  +   0.420977 * Z  +  -6.814710
  Y_new =  -0.552597 * X  +  -0.114845 * Y  +  -0.825498 * Z  + -19.187323
  Z_new =  -0.386575 * X  +  -0.842157 * Y  +   0.375940 * Z  +   1.232921 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.150939    1.990654  [ DEG:   -65.9439    114.0561 ]
  Theta =   0.396915    2.744678  [ DEG:    22.7415    157.2585 ]
  Phi   =  -2.499118    0.642475  [ DEG:  -143.1889     36.8111 ]
 
# 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: T0309TS393_4                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309TS393_4.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   76   62   4.0   20   2.84  24.970    11.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS393_4
PFRMAT TS
TARGET T0309
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1     -22.482 -31.537  10.749  1.00 25.00           C
ATOM      2  CA  ALA     2     -21.330 -28.081  11.962  1.00 25.00           C
ATOM      3  CA  SER     3     -18.496 -27.387   9.478  1.00 25.00           C
ATOM      4  CA  LYS     4     -16.116 -25.478   7.265  1.00 25.00           C
ATOM      5  CA  LYS     5     -13.515 -23.335   5.479  1.00 25.00           C
ATOM      6  CA  VAL     6     -11.505 -20.449   4.048  1.00 25.00           C
ATOM      7  CA  HIS     7     -10.476 -22.438   0.946  1.00 25.00           C
ATOM      8  CA  GLN     8      -7.892 -19.889   0.042  1.00 25.00           C
ATOM      9  CA  ILE     9      -6.609 -18.756  -3.299  1.00 25.00           C
ATOM     10  CA  ASN    10      -3.326 -17.506  -4.714  1.00 25.00           C
ATOM     11  CA  VAL    11      -0.586 -14.939  -4.122  1.00 25.00           C
ATOM     12  CA  LYS    12       2.862 -13.572  -3.230  1.00 25.00           C
ATOM     13  CA  GLY    13       6.385 -12.450  -2.410  1.00 25.00           C
ATOM     14  CA  PHE    14       5.902 -10.156  -5.405  1.00 25.00           C
ATOM     15  CA  PHE    15       2.644  -8.287  -5.706  1.00 25.00           C
ATOM     16  CA  ASP    16       3.826  -6.618  -2.519  1.00 25.00           C
ATOM     17  CA  MET    17       1.452  -8.999  -0.802  1.00 25.00           C
ATOM     18  CA  ASP    18       1.654 -11.994   1.591  1.00 25.00           C
ATOM     19  CA  VAL    19      -1.912 -12.758   0.329  1.00 25.00           C
ATOM     20  CA  MET    20      -4.972 -13.778  -1.760  1.00 25.00           C
ATOM     21  CA  GLU    21      -4.905 -12.611  -5.411  1.00 25.00           C
ATOM     22  CA  VAL    22      -7.787 -14.843  -6.420  1.00 25.00           C
ATOM     23  CA  THR    23      -9.068 -17.256  -9.075  1.00 25.00           C
ATOM     24  CA  GLU    24     -11.414 -17.863 -12.039  1.00 25.00           C
ATOM     25  CA  GLN    25     -12.434 -14.989 -14.304  1.00 25.00           C
ATOM     26  CA  THR    26     -15.981 -15.741 -13.039  1.00 25.00           C
ATOM     27  CA  LYS    27     -18.969 -17.318 -11.261  1.00 25.00           C
ATOM     28  CA  GLU    28     -18.697 -19.174  -7.955  1.00 25.00           C
ATOM     29  CA  ALA    29     -16.241 -21.316  -9.825  1.00 25.00           C
ATOM     30  CA  GLU    30     -14.190 -23.512  -7.553  1.00 25.00           C
ATOM     31  CA  TYR    31     -10.972 -21.646  -6.643  1.00 25.00           C
ATOM     32  CA  THR    32     -12.967 -18.421  -6.102  1.00 25.00           C
ATOM     33  CA  TYR    33     -15.439 -20.298  -3.859  1.00 25.00           C
ATOM     34  CA  ASP    34     -14.216 -17.858  -1.206  1.00 25.00           C
ATOM     35  CA  PHE    35     -15.020 -14.141  -1.318  1.00 25.00           C
ATOM     36  CA  LYS    36     -11.806 -13.503  -3.301  1.00 25.00           C
ATOM     37  CA  GLU    37     -12.310  -9.723  -2.951  1.00 25.00           C
ATOM     38  CA  ILE    38     -12.835 -10.117   0.822  1.00 25.00           C
ATOM     39  CA  LEU    39      -9.633 -12.204   1.074  1.00 25.00           C
ATOM     40  CA  SER    40      -7.707  -9.529  -0.875  1.00 25.00           C
ATOM     41  CA  GLU    41      -9.063  -6.815   1.461  1.00 25.00           C
ATOM     42  CA  PHE    42      -8.005  -8.877   4.511  1.00 25.00           C
ATOM     43  CA  ASN    43      -9.866  -6.255   6.450  1.00 25.00           C
ATOM     44  CA  GLY    44     -12.728  -8.640   7.409  1.00 25.00           C
ATOM     45  CA  LYS    45      -9.956 -10.963   8.672  1.00 25.00           C
ATOM     46  CA  ASN    46      -6.943 -13.061   7.524  1.00 25.00           C
ATOM     47  CA  VAL    47      -8.208 -15.315   4.772  1.00 25.00           C
ATOM     48  CA  SER    48      -5.274 -16.418   2.519  1.00 25.00           C
ATOM     49  CA  ILE    49      -2.395 -17.736   0.355  1.00 25.00           C
ATOM     50  CA  THR    50       0.515 -19.101  -1.572  1.00 25.00           C
ATOM     51  CA  VAL    51      -0.735 -21.968  -3.812  1.00 25.00           C
ATOM     52  CA  LYS    52      -2.949 -23.071  -6.701  1.00 25.00           C
ATOM     53  CA  GLU    53      -1.779 -26.669  -7.093  1.00 25.00           C
ATOM     54  CA  GLU    54       1.263 -27.188  -9.217  1.00 25.00           C
ATOM     55  CA  ASN    55       3.153 -29.154  -6.590  1.00 25.00           C
ATOM     56  CA  GLU    56       0.213 -31.608  -6.691  1.00 25.00           C
ATOM     57  CA  LEU    57      -1.843 -31.916  -3.483  1.00 25.00           C
ATOM     58  CA  PRO    58      -4.873 -33.439  -5.327  1.00 25.00           C
ATOM     59  CA  VAL    59      -5.940 -29.798  -5.703  1.00 25.00           C
ATOM     60  CA  LYS    60      -7.218 -29.835  -2.118  1.00 25.00           C
ATOM     61  CA  GLY    61      -7.515 -26.250  -0.947  1.00 25.00           C
ATOM     62  CA  VAL    62      -4.046 -25.545  -2.381  1.00 25.00           C
ATOM     63  CA  GLU    63      -2.693 -23.545   0.539  1.00 25.00           C
ATOM     64  CA  MET    64      -0.783 -21.417   3.072  1.00 25.00           C
ATOM     65  CA  ALA    65      -3.745 -20.325   5.278  1.00 25.00           C
ATOM     66  CA  GLY    66      -1.422 -18.355   7.615  1.00 25.00           C
ATOM     67  CA  ASP    67      -1.637 -21.282  10.050  1.00 25.00           C
ATOM     68  CA  PRO    68       0.433 -24.235  11.375  1.00 25.00           C
ATOM     69  CA  LEU    69      -2.316 -25.067  13.869  1.00 25.00           C
ATOM     70  CA  GLU    70      -1.920 -27.423  16.839  1.00 25.00           C
ATOM     71  CA  HIS    71      -2.370 -29.114  20.184  1.00 25.00           C
ATOM     72  CA  HIS    72      -3.248 -26.001  22.108  1.00 25.00           C
ATOM     73  CA  HIS    73      -6.457 -25.547  24.073  1.00 25.00           C
ATOM     74  CA  HIS    74      -4.611 -22.679  25.682  1.00 25.00           C
ATOM     75  CA  HIS    75      -7.493 -21.961  28.121  1.00 25.00           C
ATOM     76  CA  HIS    76      -9.601 -21.400  25.017  1.00 25.00           C
TER
END
