
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358TS393_3-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:    41        21 - 61          4.97    14.65
  LONGEST_CONTINUOUS_SEGMENT:    41        22 - 62          4.93    14.74
  LONGEST_CONTINUOUS_SEGMENT:    41        23 - 63          4.78    14.91
  LONGEST_CONTINUOUS_SEGMENT:    41        24 - 64          4.98    14.82
  LCS_AVERAGE:     55.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        38 - 51          1.98    16.69
  LONGEST_CONTINUOUS_SEGMENT:    14        39 - 52          1.95    16.81
  LCS_AVERAGE:     15.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        14 - 24          0.28    18.40
  LCS_AVERAGE:      9.40

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      4    4   22     3    3    4    4    5    7   13   15   17   19   21   23   26   27   30   31   34   36   38   38 
LCS_GDT     P      11     P      11      4    4   22     3    3    4    4    4    5    9   11   13   19   21   23   26   27   30   31   31   36   38   38 
LCS_GDT     F      12     F      12      4    4   22     3    3    4    4    5    7   10   14   17   19   21   23   26   27   30   31   34   36   38   38 
LCS_GDT     T      13     T      13      4   12   22     3    3    4    4    8   12   14   15   19   20   21   23   26   30   30   31   34   36   38   39 
LCS_GDT     R      14     R      14     11   12   22    11   11   11   11   12   14   17   18   19   21   21   24   26   30   30   31   32   36   38   39 
LCS_GDT     R      15     R      15     11   12   22    11   11   11   11   12   14   17   18   19   21   22   25   26   30   30   32   34   35   38   39 
LCS_GDT     Q      16     Q      16     11   12   31    11   11   11   11   12   14   17   18   19   22   23   25   26   30   30   32   34   37   38   40 
LCS_GDT     A      17     A      17     11   12   35    11   11   11   11   12   14   17   18   19   21   23   25   30   33   34   35   38   43   46   47 
LCS_GDT     Q      18     Q      18     11   12   35    11   11   11   11   12   14   17   18   19   21   22   24   26   29   32   35   38   41   43   47 
LCS_GDT     A      19     A      19     11   12   36    11   11   11   11   12   14   17   18   19   21   23   24   26   30   33   35   41   43   46   47 
LCS_GDT     V      20     V      20     11   12   37    11   11   11   11   11   14   17   18   22   27   30   33   35   38   42   43   45   46   46   47 
LCS_GDT     T      21     T      21     11   12   41    11   11   11   11   11   14   17   18   22   27   30   33   35   38   42   43   45   46   46   47 
LCS_GDT     T      22     T      22     11   12   41    11   11   11   11   12   14   17   18   22   26   29   33   35   38   42   43   45   46   46   47 
LCS_GDT     T      23     T      23     11   12   41    11   11   11   11   12   14   17   18   25   29   32   34   36   38   42   43   45   46   46   47 
LCS_GDT     Y      24     Y      24     11   12   41    11   11   11   11   12   13   15   22   26   30   32   34   37   38   42   43   45   46   46   47 
LCS_GDT     S      25     S      25      5   12   41     3    5    8   11   12   14   17   21   25   27   32   34   35   38   42   43   45   46   46   47 
LCS_GDT     N      26     N      26      5    7   41     3    5    8   11   12   14   18   23   28   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     I      27     I      27      5    7   41     3    5    8   11   12   15   19   26   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     T      28     T      28      5    7   41     3    5    6   11   12   14   18   23   28   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     L      29     L      29      3    7   41     2    4    8   11   12   15   20   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     E      30     E      30      3    7   41     3    5    7   11   12   14   17   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     D      31     D      31      3    6   41     3    3    3    6   10   14   21   25   27   31   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     D      32     D      32      4    6   41     3    5    6    8   12   15   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     Q      33     Q      33      4    5   41     3    5    6    8   12   15   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     G      34     G      34      4    6   41     3    4    6    8   12   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     S      35     S      35      4    6   41     1    4    5    7   11   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     H      36     H      36      4    6   41     3    3    4    7   11   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     F      37     F      37      4    7   41     3    3    5    7    9   12   21   26   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     R      38     R      38      4   14   41     3    3    6   11   13   15   17   23   28   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     L      39     L      39      4   14   41     0    5    8   11   13   15   18   23   28   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     V      40     V      40      6   14   41     1    5    8   11   13   15   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     V      41     V      41      8   14   41     4    6    9   11   13   15   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     R      42     R      42      8   14   41     4    6    9   11   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     D      43     D      43      8   14   41     4    6    9   11   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     T      44     T      44      8   14   41     4    6    9   11   13   17   22   27   29   32   34   35   37   38   41   43   45   46   46   47 
LCS_GDT     E      45     E      45      8   14   41     3    6    9   10   12   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     G      46     G      46      8   14   41     3    6    9   10   11   15   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     R      47     R      47      8   14   41     3    6    9   11   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     M      48     M      48      8   14   41     3    6    9   11   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     V      49     V      49      7   14   41     3    5    9   10   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     W      50     W      50      4   14   41     3    5    9   10   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     R      51     R      51      4   14   41     3    4    5   11   13   15   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     A      52     A      52      4   14   41     3    4    6   11   13   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     W      53     W      53      3    9   41     3    3    5    6    9   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     N      54     N      54      4    9   41     3    4    5    7   10   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     F      55     F      55      4    9   41     3    4    5    7   10   17   22   27   29   31   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     E      56     E      56      4    9   41     3    4    5    7   10   17   22   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     P      57     P      57      4    9   41     3    5    6    8   11   17   22   27   29   32   34   35   37   38   40   41   45   46   46   46 
LCS_GDT     D      58     D      58      3    9   41     3    4    6    8   11   17   22   27   29   32   34   35   37   38   39   41   44   46   46   46 
LCS_GDT     A      59     A      59      3   10   41     3    3    8    9   11   14   21   27   29   32   34   35   37   38   42   43   45   46   46   47 
LCS_GDT     G      60     G      60      3   10   41     3    3    3    5    6    9   15   20   25   30   32   34   37   38   42   43   45   46   46   47 
LCS_GDT     E      61     E      61      8   10   41     8    8    8    9   11   14   18   22   26   30   32   35   37   38   42   43   45   46   46   47 
LCS_GDT     G      62     G      62      8   10   41     8    8    8    9   11   13   15   18   19   22   23   30   35   38   42   43   45   46   46   47 
LCS_GDT     L      63     L      63      8   10   41     8    8    8    9   11   13   15   18   20   22   27   33   35   38   42   43   45   46   46   47 
LCS_GDT     N      64     N      64      8   10   41     8    8    8    9   11   13   15   18   19   24   26   33   35   38   42   43   45   46   46   47 
LCS_GDT     R      65     R      65      8   10   24     8    8    8    9   11   13   15   18   19   22   23   25   33   36   40   43   45   46   46   47 
LCS_GDT     Y      66     Y      66      8   10   24     8    8    8    9   11   13   15   18   19   22   23   25   26   30   32   33   39   42   45   47 
LCS_GDT     I      67     I      67      8   10   24     8    8    8    9   11   13   15   18   19   22   23   25   26   30   32   33   38   42   45   47 
LCS_GDT     R      68     R      68      8   10   24     8    8    8    9   11   13   15   18   19   21   23   24   26   29   32   34   39   42   45   47 
LCS_GDT     T      69     T      69      3    9   24     3    3    5    5    6    8   11   12   17   22   23   25   26   30   30   32   34   35   38   41 
LCS_GDT     S      70     S      70      3    4   24     3    3    4    4    6    8    9   11   12   16   21   25   26   30   30   32   34   35   38   39 
LCS_GDT     G      71     G      71      3    4   22     3    3    4    4    5    7    9   11   14   22   22   25   26   30   30   32   34   35   38   39 
LCS_GDT     I      72     I      72      3    4   22     3    3    4    4    5    6    9   12   15   22   22   25   26   30   30   32   34   35   38   39 
LCS_GDT     R      73     R      73      3    4   22     3    3    4    4    5    6    9   11   12   15   18   19   22   30   30   32   33   34   38   39 
LCS_GDT     T      74     T      74      3    4   22     3    3    3    3    5    6    9   12   14   16   21   24   26   30   30   32   34   35   38   39 
LCS_AVERAGE  LCS_A:  26.64  (   9.40   15.10   55.43 )

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     11     11     11     13     17     22     27     29     32     34     35     37     38     42     43     45     46     46     47 
GDT PERCENT_CA  16.92  16.92  16.92  16.92  20.00  26.15  33.85  41.54  44.62  49.23  52.31  53.85  56.92  58.46  64.62  66.15  69.23  70.77  70.77  72.31
GDT RMS_LOCAL    0.28   0.28   0.28   0.28   1.73   2.29   2.63   2.95   3.08   3.42   3.54   3.77   4.11   4.25   5.21   5.23   5.57   5.68   5.68   6.22
GDT RMS_ALL_CA  18.40  18.40  18.40  18.40  16.52  17.16  16.87  16.63  16.53  16.24  16.26  15.91  15.51  15.43  13.69  13.74  13.71  13.87  13.87  13.07

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10         26.980
LGA    P      11      P      11         24.130
LGA    F      12      F      12         25.548
LGA    T      13      T      13         26.054
LGA    R      14      R      14         24.266
LGA    R      15      R      15         26.291
LGA    Q      16      Q      16         21.166
LGA    A      17      A      17         16.572
LGA    Q      18      Q      18         20.212
LGA    A      19      A      19         18.355
LGA    V      20      V      20         12.301
LGA    T      21      T      21         13.751
LGA    T      22      T      22         16.388
LGA    T      23      T      23         10.994
LGA    Y      24      Y      24          9.963
LGA    S      25      S      25          9.899
LGA    N      26      N      26          5.788
LGA    I      27      I      27          4.495
LGA    T      28      T      28          5.618
LGA    L      29      L      29          3.842
LGA    E      30      E      30          3.991
LGA    D      31      D      31          5.558
LGA    D      32      D      32          3.483
LGA    Q      33      Q      33          3.836
LGA    G      34      G      34          0.818
LGA    S      35      S      35          2.859
LGA    H      36      H      36          3.250
LGA    F      37      F      37          4.275
LGA    R      38      R      38          5.513
LGA    L      39      L      39          5.444
LGA    V      40      V      40          3.010
LGA    V      41      V      41          3.560
LGA    R      42      R      42          0.684
LGA    D      43      D      43          2.237
LGA    T      44      T      44          2.145
LGA    E      45      E      45          3.642
LGA    G      46      G      46          3.778
LGA    R      47      R      47          2.409
LGA    M      48      M      48          2.249
LGA    V      49      V      49          2.182
LGA    W      50      W      50          2.698
LGA    R      51      R      51          2.949
LGA    A      52      A      52          1.619
LGA    W      53      W      53          3.673
LGA    N      54      N      54          3.015
LGA    F      55      F      55          3.574
LGA    E      56      E      56          2.901
LGA    P      57      P      57          2.303
LGA    D      58      D      58          1.992
LGA    A      59      A      59          3.808
LGA    G      60      G      60         10.369
LGA    E      61      E      61          9.752
LGA    G      62      G      62         12.490
LGA    L      63      L      63         12.889
LGA    N      64      N      64         15.985
LGA    R      65      R      65         18.863
LGA    Y      66      Y      66         20.937
LGA    I      67      I      67         21.926
LGA    R      68      R      68         25.685
LGA    T      69      T      69         31.625
LGA    S      70      S      70         34.375
LGA    G      71      G      71         34.567
LGA    I      72      I      72         34.322
LGA    R      73      R      73         40.740
LGA    T      74      T      74         44.312

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   65   65    4.0     27    2.95    35.385    30.570     0.885

LGA_LOCAL      RMSD =  2.949  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.475  Number of atoms =   65 
Std_ALL_ATOMS  RMSD = 11.343  (standard rmsd on all 65 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.498351 * X  +  -0.839001 * Y  +   0.218456 * Z  +  -7.307914
  Y_new =  -0.383689 * X  +   0.439390 * Y  +   0.812231 * Z  +   8.017572
  Z_new =  -0.777450 * X  +   0.320957 * Y  +  -0.540886 * Z  +   7.042463 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.606046   -0.535546  [ DEG:   149.3155    -30.6845 ]
  Theta =   0.890602    2.250991  [ DEG:    51.0277    128.9723 ]
  Phi   =  -2.485466    0.656126  [ DEG:  -142.4067     37.5933 ]
 
# 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_3-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358TS393_3-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   2.95  30.570    11.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS393_3-D1
PFRMAT TS
TARGET T0358
MODEL 3
PARENT N/A
ATOM     10  CA  GLY    10     -12.346  -0.297  18.435  1.00 25.00           C
ATOM     11  CA  PRO    11      -8.663   0.753  18.258  1.00 25.00           C
ATOM     12  CA  PHE    12      -8.599   4.529  18.037  1.00 25.00           C
ATOM     13  CA  THR    13      -4.817   4.890  17.747  1.00 25.00           C
ATOM     14  CA  ARG    14      -5.411   5.150  13.974  1.00 25.00           C
ATOM     15  CA  ARG    15      -5.880   1.358  13.710  1.00 25.00           C
ATOM     16  CA  GLN    16      -6.469   1.670   9.938  1.00 25.00           C
ATOM     17  CA  ALA    17      -3.295   3.785   9.593  1.00 25.00           C
ATOM     18  CA  GLN    18      -1.308   1.170  11.565  1.00 25.00           C
ATOM     19  CA  ALA    19      -2.671  -1.605   9.306  1.00 25.00           C
ATOM     20  CA  VAL    20      -1.684   0.405   6.199  1.00 25.00           C
ATOM     21  CA  THR    21       1.837   0.915   7.617  1.00 25.00           C
ATOM     22  CA  THR    22       2.128  -2.841   8.312  1.00 25.00           C
ATOM     23  CA  THR    23       1.007  -3.614   4.733  1.00 25.00           C
ATOM     24  CA  TYR    24       3.606  -1.159   3.361  1.00 25.00           C
ATOM     25  CA  SER    25       2.695  -1.224  -0.327  1.00 25.00           C
ATOM     26  CA  ASN    26      -0.552  -3.215  -0.822  1.00 25.00           C
ATOM     27  CA  ILE    27      -2.015  -0.343   1.223  1.00 25.00           C
ATOM     28  CA  THR    28      -1.945   2.932  -0.704  1.00 25.00           C
ATOM     29  CA  LEU    29      -2.185   5.511  -3.424  1.00 25.00           C
ATOM     30  CA  GLU    30      -3.405   8.534  -5.314  1.00 25.00           C
ATOM     31  CA  ASP    31      -2.100   6.674  -8.367  1.00 25.00           C
ATOM     32  CA  ASP    32      -3.492   9.068 -10.976  1.00 25.00           C
ATOM     33  CA  GLN    33      -1.917  12.271 -12.146  1.00 25.00           C
ATOM     34  CA  GLY    34       0.974  11.140  -9.874  1.00 25.00           C
ATOM     35  CA  SER    35       1.481  10.060  -6.235  1.00 25.00           C
ATOM     36  CA  HIS    36       0.825   9.579  -2.474  1.00 25.00           C
ATOM     37  CA  PHE    37      -1.593   8.819   0.325  1.00 25.00           C
ATOM     38  CA  ARG    38      -5.186   9.464   1.578  1.00 25.00           C
ATOM     39  CA  LEU    39      -5.873   6.005   0.070  1.00 25.00           C
ATOM     40  CA  VAL    40      -7.262   2.647  -0.849  1.00 25.00           C
ATOM     41  CA  VAL    41      -6.999  -1.070   0.106  1.00 25.00           C
ATOM     42  CA  ARG    42      -7.878  -4.465   1.575  1.00 25.00           C
ATOM     43  CA  ASP    43      -6.755  -8.074   2.017  1.00 25.00           C
ATOM     44  CA  THR    44      -8.074 -10.877  -0.091  1.00 25.00           C
ATOM     45  CA  GLU    45     -10.681 -12.082   2.375  1.00 25.00           C
ATOM     46  CA  GLY    46     -12.859  -9.189   1.126  1.00 25.00           C
ATOM     47  CA  ARG    47     -12.375  -6.295   3.574  1.00 25.00           C
ATOM     48  CA  MET    48     -11.563  -2.641   4.522  1.00 25.00           C
ATOM     49  CA  VAL    49      -8.397  -0.555   4.920  1.00 25.00           C
ATOM     50  CA  TRP    50      -5.890   2.161   4.011  1.00 25.00           C
ATOM     51  CA  ARG    51      -5.625   5.784   5.062  1.00 25.00           C
ATOM     52  CA  ALA    52      -1.815   6.032   4.994  1.00 25.00           C
ATOM     53  CA  TRP    53       1.308   4.622   3.374  1.00 25.00           C
ATOM     54  CA  ASN    54       4.401   6.678   2.480  1.00 25.00           C
ATOM     55  CA  PHE    55       7.488   7.802   0.471  1.00 25.00           C
ATOM     56  CA  GLU    56       7.725  10.509   3.182  1.00 25.00           C
ATOM     57  CA  PRO    57      10.737   9.402   5.245  1.00 25.00           C
ATOM     58  CA  ASP    58       9.530   5.839   6.025  1.00 25.00           C
ATOM     59  CA  ALA    59       6.464   7.670   7.336  1.00 25.00           C
ATOM     60  CA  GLY    60       6.044  10.754   9.534  1.00 25.00           C
ATOM     61  CA  GLU    61       2.338  10.143   9.153  1.00 25.00           C
ATOM     62  CA  GLY    62       1.961  13.207   6.888  1.00 25.00           C
ATOM     63  CA  LEU    63      -0.745  11.407   4.861  1.00 25.00           C
ATOM     64  CA  ASN    64      -2.590  10.494   8.090  1.00 25.00           C
ATOM     65  CA  ARG    65      -2.405  14.138   9.255  1.00 25.00           C
ATOM     66  CA  TYR    66      -3.787  15.312   5.881  1.00 25.00           C
ATOM     67  CA  ILE    67      -6.653  12.786   6.148  1.00 25.00           C
ATOM     68  CA  ARG    68      -7.439  14.015   9.690  1.00 25.00           C
ATOM     69  CA  THR    69      -7.462  17.640   8.453  1.00 25.00           C
ATOM     70  CA  SER    70      -6.529  20.141   5.801  1.00 25.00           C
ATOM     71  CA  GLY    71      -9.525  22.237   6.796  1.00 25.00           C
ATOM     72  CA  ILE    72     -12.491  20.371   8.190  1.00 25.00           C
ATOM     73  CA  ARG    73     -13.733  23.912   9.026  1.00 25.00           C
ATOM     74  CA  THR    74     -11.941  23.945  12.420  1.00 25.00           C
TER
END
