
#######################################################
#                                                     #
#                        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 T0358TS393_5-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS393_5-D1.T0358_D1.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:    47        24 - 70          4.97    11.55
  LCS_AVERAGE:     62.20

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        12 - 26          1.98    14.57
  LCS_AVERAGE:     15.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        14 - 24          0.28    14.73
  LCS_AVERAGE:      8.54

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     G      10     G      10      3    3   19     0    3    5    5    5    6    6   11   15   16   18   20   24   28   30   32   35   36   40   42 
LCS_GDT     P      11     P      11      3    9   19     0    3    5    5    6    9   12   14   16   16   19   23   24   28   31   32   35   36   40   42 
LCS_GDT     F      12     F      12      3   15   19     1    3    6   10   13   16   17   18   20   21   23   24   26   29   31   32   35   36   39   42 
LCS_GDT     T      13     T      13      3   15   19     3    3    5   10   13   16   18   18   20   21   23   24   26   29   31   34   35   36   39   40 
LCS_GDT     R      14     R      14     11   15   21    11   12   12   13   15   16   18   18   20   21   23   24   26   29   32   34   37   39   39   40 
LCS_GDT     R      15     R      15     11   15   22    11   12   12   13   15   16   18   18   20   21   23   24   26   29   32   34   38   39   39   40 
LCS_GDT     Q      16     Q      16     11   15   22    11   12   12   13   15   16   18   18   20   21   23   24   26   29   32   34   38   39   39   40 
LCS_GDT     A      17     A      17     11   15   22    11   12   12   13   15   16   18   18   20   21   23   24   26   30   32   34   38   39   39   41 
LCS_GDT     Q      18     Q      18     11   15   22    11   12   12   13   15   16   18   18   20   21   23   24   26   30   32   34   38   39   39   41 
LCS_GDT     A      19     A      19     11   15   22    11   12   12   13   15   16   18   18   20   21   23   24   26   30   32   34   38   39   39   41 
LCS_GDT     V      20     V      20     11   15   22    11   12   12   13   15   16   18   18   20   21   23   24   26   30   32   34   38   40   44   46 
LCS_GDT     T      21     T      21     11   15   22    11   12   12   13   15   16   18   18   20   21   23   26   27   31   35   39   41   44   46   48 
LCS_GDT     T      22     T      22     11   15   42    11   12   12   13   15   16   18   18   20   21   23   26   27   31   35   39   41   41   44   46 
LCS_GDT     T      23     T      23     11   15   46    11   12   12   13   15   16   18   18   20   21   23   26   27   31   35   39   41   42   44   46 
LCS_GDT     Y      24     Y      24     11   15   47    11   12   12   13   15   16   18   18   21   24   32   36   40   42   45   45   47   47   47   48 
LCS_GDT     S      25     S      25      5   15   47     3    5    5    9   15   17   22   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     N      26     N      26      5   15   47     4    6    9   13   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     I      27     I      27      5    9   47     4    5    8   11   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     T      28     T      28      5    9   47     4    6    9   11   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     L      29     L      29      5    9   47     4    6    9   11   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     E      30     E      30      3    9   47     1    3    4    6    7   10   14   21   26   29   35   40   41   43   45   45   47   47   47   48 
LCS_GDT     D      31     D      31      3    9   47     0    3    4    7    9   12   19   25   30   34   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     D      32     D      32      3    9   47     3    3    4    7    8   16   22   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     Q      33     Q      33      3    9   47     3    3    5    6   10   18   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     G      34     G      34      3    9   47     3    3    7   11   15   20   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     S      35     S      35      4    9   47     3    5    7   11   15   20   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     H      36     H      36      4    9   47     3    5    6   10   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     F      37     F      37      4    9   47     3    4    5   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     R      38     R      38      4    9   47     3    4    5   10   12   20   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     L      39     L      39      4    9   47     3    6    9   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     V      40     V      40      4    9   47     3    4    5   10   12   17   19   24   30   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     V      41     V      41      4    9   47     3    6    7   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     R      42     R      42      4    9   47     3    6    9   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     D      43     D      43      4    8   47     3    3    8   10   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     T      44     T      44      4    8   47     3    5    8   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     E      45     E      45      3    8   47     3    5    8   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     G      46     G      46      3    7   47     3    3    3    5    6    8   13   19   28   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     R      47     R      47      4    8   47     4    5    8   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     M      48     M      48      4    8   47     4    6    9   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     V      49     V      49      4    9   47     4    4    5    9   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     W      50     W      50      4    9   47     4    6    9   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     R      51     R      51      4    9   47     4    4    7   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     A      52     A      52      4    9   47     4    6    9   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     W      53     W      53      4    9   47     4    6    9   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     N      54     N      54      4    9   47     4    4    9   11   13   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     F      55     F      55      5    9   47     3    5    7   12   15   21   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     E      56     E      56      5    9   47     3    5    7   11   15   20   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     P      57     P      57      5    9   47     3    5    7   11   15   20   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     D      58     D      58      5    9   47     3    5    6   11   14   18   22   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     A      59     A      59      5   10   47     3    4    8    9   12   15   19   25   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     G      60     G      60      3   10   47     3    5    7   11   15   20   23   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     E      61     E      61      8   10   47     8    8    9    9   11   12   19   24   26   32   38   40   41   42   45   45   47   47   47   48 
LCS_GDT     G      62     G      62      8   10   47     8    8    9    9   15   15   16   21   30   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     L      63     L      63      8   10   47     8    8    9   13   15   16   19   26   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     N      64     N      64      8   10   47     8   12   12   13   14   15   18   26   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     R      65     R      65      8   10   47     8   10   12   13   14   15   21   27   31   35   39   40   41   43   45   45   47   47   47   48 
LCS_GDT     Y      66     Y      66      8   10   47     8    8    9    9   13   13   14   15   24   29   32   36   41   43   45   45   47   47   47   48 
LCS_GDT     I      67     I      67      8   10   47     8    8    9    9   11   12   15   22   26   29   33   36   41   43   45   45   47   47   47   48 
LCS_GDT     R      68     R      68      8   10   47     8    8    9    9   11   16   19   24   30   33   36   39   41   43   45   45   47   47   47   48 
LCS_GDT     T      69     T      69      3    9   47     3    3    4    4    6   10   15   22   24   28   31   34   37   42   44   45   47   47   47   48 
LCS_GDT     S      70     S      70      3    4   47     3    3    4    4    6    9   14   22   26   28   32   34   37   42   44   45   47   47   47   48 
LCS_GDT     G      71     G      71      3    4   20     3    3    4    4    8    9   11   12   14   20   22   27   29   32   34   36   40   44   46   47 
LCS_GDT     I      72     I      72      3    4   20     3    3    4    5    6    7    9   11   14   15   16   19   22   23   23   26   28   30   33   35 
LCS_GDT     R      73     R      73      3    4   20     3    3    4    4    6    7    9   11   14   15   15   16   18   19   20   22   27   29   33   33 
LCS_GDT     T      74     T      74      3    4   20     3    3    3    4    5    7    9   11   14   15   15   16   18   18   20   22   24   26   26   32 
LCS_AVERAGE  LCS_A:  28.69  (   8.54   15.31   62.20 )

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     12     12     13     15     21     23     27     31     35     39     40     41     43     45     45     47     47     47     48 
GDT PERCENT_CA  16.92  18.46  18.46  20.00  23.08  32.31  35.38  41.54  47.69  53.85  60.00  61.54  63.08  66.15  69.23  69.23  72.31  72.31  72.31  73.85
GDT RMS_LOCAL    0.28   0.39   0.39   0.69   1.62   2.23   2.38   2.74   3.16   3.41   3.74   3.82   3.92   4.32   4.55   4.55   4.97   4.97   4.97   5.26
GDT RMS_ALL_CA  14.73  14.80  14.80  14.68  14.63  11.85  12.06  12.39  12.58  12.40  12.19  12.24  12.28  11.80  11.83  11.83  11.55  11.55  11.55  11.48

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10         24.386
LGA    P      11      P      11         21.828
LGA    F      12      F      12         20.980
LGA    T      13      T      13         24.689
LGA    R      14      R      14         22.249
LGA    R      15      R      15         23.094
LGA    Q      16      Q      16         19.810
LGA    A      17      A      17         16.848
LGA    Q      18      Q      18         18.426
LGA    A      19      A      19         18.335
LGA    V      20      V      20         14.063
LGA    T      21      T      21         12.647
LGA    T      22      T      22         14.722
LGA    T      23      T      23         13.485
LGA    Y      24      Y      24          8.779
LGA    S      25      S      25          3.709
LGA    N      26      N      26          2.844
LGA    I      27      I      27          3.308
LGA    T      28      T      28          3.999
LGA    L      29      L      29          3.669
LGA    E      30      E      30          8.113
LGA    D      31      D      31          7.873
LGA    D      32      D      32          6.274
LGA    Q      33      Q      33          6.382
LGA    G      34      G      34          2.396
LGA    S      35      S      35          2.737
LGA    H      36      H      36          2.677
LGA    F      37      F      37          2.870
LGA    R      38      R      38          3.798
LGA    L      39      L      39          2.123
LGA    V      40      V      40          4.583
LGA    V      41      V      41          2.075
LGA    R      42      R      42          1.359
LGA    D      43      D      43          2.675
LGA    T      44      T      44          2.358
LGA    E      45      E      45          2.351
LGA    G      46      G      46          5.326
LGA    R      47      R      47          2.196
LGA    M      48      M      48          2.308
LGA    V      49      V      49          5.241
LGA    W      50      W      50          2.814
LGA    R      51      R      51          1.338
LGA    A      52      A      52          2.656
LGA    W      53      W      53          1.742
LGA    N      54      N      54          3.882
LGA    F      55      F      55          0.882
LGA    E      56      E      56          1.298
LGA    P      57      P      57          3.347
LGA    D      58      D      58          4.911
LGA    A      59      A      59          5.568
LGA    G      60      G      60          3.075
LGA    E      61      E      61          6.348
LGA    G      62      G      62          5.933
LGA    L      63      L      63          6.552
LGA    N      64      N      64          6.835
LGA    R      65      R      65          5.745
LGA    Y      66      Y      66         10.633
LGA    I      67      I      67         12.319
LGA    R      68      R      68         10.672
LGA    T      69      T      69         16.333
LGA    S      70      S      70         15.795
LGA    G      71      G      71         19.307
LGA    I      72      I      72         24.749
LGA    R      73      R      73         29.715
LGA    T      74      T      74         33.791

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     27    2.74    37.308    33.275     0.952

LGA_LOCAL      RMSD =  2.738  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.391  Number of atoms =   65 
Std_ALL_ATOMS  RMSD = 10.262  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.926944 * X  +  -0.366259 * Y  +  -0.081426 * Z  +  -1.175784
  Y_new =  -0.077924 * X  +  -0.024363 * Y  +   0.996662 * Z  +   6.476145
  Z_new =  -0.367020 * X  +   0.930194 * Y  +  -0.005958 * Z  +   6.180801 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.577201   -1.564391  [ DEG:    90.3670    -89.6330 ]
  Theta =   0.375803    2.765790  [ DEG:    21.5319    158.4681 ]
  Phi   =  -3.057724    0.083869  [ DEG:  -175.1947      4.8053 ]
 
# 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: T0358TS393_5-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_5-D1.T0358_D1.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   2.74  33.275    10.26
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_5-D1
PFRMAT TS
TARGET T0358
MODEL 5
PARENT N/A
ATOM     10  CA  GLY    10      -8.992  18.529   8.109  1.00 25.00           C
ATOM     11  CA  PRO    11      -8.590  18.953   4.366  1.00 25.00           C
ATOM     12  CA  PHE    12      -8.626  15.133   4.384  1.00 25.00           C
ATOM     13  CA  THR    13     -12.460  14.767   4.327  1.00 25.00           C
ATOM     14  CA  ARG    14     -11.956  10.961   4.297  1.00 25.00           C
ATOM     15  CA  ARG    15     -10.692  11.571   0.734  1.00 25.00           C
ATOM     16  CA  GLN    16      -7.233  10.245   1.709  1.00 25.00           C
ATOM     17  CA  ALA    17      -8.835   7.127   3.250  1.00 25.00           C
ATOM     18  CA  GLN    18     -10.874   6.565   0.057  1.00 25.00           C
ATOM     19  CA  ALA    19      -7.700   6.909  -2.059  1.00 25.00           C
ATOM     20  CA  VAL    20      -5.900   4.382   0.186  1.00 25.00           C
ATOM     21  CA  THR    21      -8.836   1.947  -0.162  1.00 25.00           C
ATOM     22  CA  THR    22      -8.752   2.351  -3.969  1.00 25.00           C
ATOM     23  CA  THR    23      -4.982   1.677  -3.983  1.00 25.00           C
ATOM     24  CA  TYR    24      -5.511  -1.463  -1.854  1.00 25.00           C
ATOM     25  CA  SER    25      -5.087  -5.098  -2.927  1.00 25.00           C
ATOM     26  CA  ASN    26      -2.925  -5.642   0.203  1.00 25.00           C
ATOM     27  CA  ILE    27       0.145  -3.885  -1.195  1.00 25.00           C
ATOM     28  CA  THR    28      -0.551  -0.538  -2.879  1.00 25.00           C
ATOM     29  CA  LEU    29       0.696   2.465  -4.796  1.00 25.00           C
ATOM     30  CA  GLU    30       2.090   4.112  -7.879  1.00 25.00           C
ATOM     31  CA  ASP    31      -0.824   5.458  -9.894  1.00 25.00           C
ATOM     32  CA  ASP    32       0.061   7.744 -12.759  1.00 25.00           C
ATOM     33  CA  GLN    33       1.352  11.273 -13.568  1.00 25.00           C
ATOM     34  CA  GLY    34      -0.789  12.228 -10.529  1.00 25.00           C
ATOM     35  CA  SER    35       1.264  11.022  -7.561  1.00 25.00           C
ATOM     36  CA  HIS    36      -0.039   9.732  -4.197  1.00 25.00           C
ATOM     37  CA  PHE    37      -0.813   6.523  -2.292  1.00 25.00           C
ATOM     38  CA  ARG    38       1.764   4.893  -0.065  1.00 25.00           C
ATOM     39  CA  LEU    39      -1.128   2.599   1.040  1.00 25.00           C
ATOM     40  CA  VAL    40      -1.550  -0.737   2.805  1.00 25.00           C
ATOM     41  CA  VAL    41      -4.509  -2.636   4.267  1.00 25.00           C
ATOM     42  CA  ARG    42      -7.514  -4.816   3.229  1.00 25.00           C
ATOM     43  CA  ASP    43      -8.019  -7.730   0.827  1.00 25.00           C
ATOM     44  CA  THR    44     -11.219  -9.638   1.498  1.00 25.00           C
ATOM     45  CA  GLU    45     -14.068  -9.443  -0.994  1.00 25.00           C
ATOM     46  CA  GLY    46     -16.427  -7.084   0.810  1.00 25.00           C
ATOM     47  CA  ARG    47     -14.451  -4.154   2.156  1.00 25.00           C
ATOM     48  CA  MET    48     -11.563  -1.670   1.990  1.00 25.00           C
ATOM     49  CA  VAL    49     -11.390   1.372   4.222  1.00 25.00           C
ATOM     50  CA  TRP    50      -7.565   1.500   4.660  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.145   3.097   5.009  1.00 25.00           C
ATOM     52  CA  ALA    52      -3.005   6.737   4.557  1.00 25.00           C
ATOM     53  CA  TRP    53      -0.809   8.804   2.170  1.00 25.00           C
ATOM     54  CA  ASN    54       2.224  10.898   1.373  1.00 25.00           C
ATOM     55  CA  PHE    55       5.837  10.228   0.288  1.00 25.00           C
ATOM     56  CA  GLU    56       6.291   9.252   3.902  1.00 25.00           C
ATOM     57  CA  PRO    57       9.984   8.624   3.355  1.00 25.00           C
ATOM     58  CA  ASP    58      10.806   4.893   3.391  1.00 25.00           C
ATOM     59  CA  ALA    59       8.103   4.133   0.777  1.00 25.00           C
ATOM     60  CA  GLY    60       7.955   0.783   2.628  1.00 25.00           C
ATOM     61  CA  GLU    61       4.238   1.541   2.955  1.00 25.00           C
ATOM     62  CA  GLY    62       5.366   4.386   5.257  1.00 25.00           C
ATOM     63  CA  LEU    63       1.723   5.447   5.773  1.00 25.00           C
ATOM     64  CA  ASN    64       0.764   1.836   6.613  1.00 25.00           C
ATOM     65  CA  ARG    65       3.645   1.631   9.129  1.00 25.00           C
ATOM     66  CA  TYR    66       2.507   4.915  10.737  1.00 25.00           C
ATOM     67  CA  ILE    67      -1.075   3.581  10.985  1.00 25.00           C
ATOM     68  CA  ARG    68       0.211   0.362  12.613  1.00 25.00           C
ATOM     69  CA  THR    69       2.249   2.416  15.122  1.00 25.00           C
ATOM     70  CA  SER    70       4.679  -0.520  15.393  1.00 25.00           C
ATOM     71  CA  GLY    71       4.837   0.190  19.185  1.00 25.00           C
ATOM     72  CA  ILE    72       4.821   4.008  19.337  1.00 25.00           C
ATOM     73  CA  ARG    73       7.083   3.840  22.415  1.00 25.00           C
ATOM     74  CA  THR    74       5.863   7.357  23.194  1.00 25.00           C
TER
END
