
#######################################################
#                                                     #
#                        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   68 (   68),  selected   61 , name T0348TS168_2
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_2.T0348.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:    24        39 - 62          4.98    23.78
  LCS_AVERAGE:     31.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        11 - 17          1.91    22.10
  LONGEST_CONTINUOUS_SEGMENT:     7        34 - 40          1.84    21.70
  LONGEST_CONTINUOUS_SEGMENT:     7        40 - 46          1.97    25.99
  LONGEST_CONTINUOUS_SEGMENT:     7        50 - 56          1.99    34.74
  LCS_AVERAGE:      9.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        15 - 19          0.94    22.15
  LONGEST_CONTINUOUS_SEGMENT:     5        16 - 20          0.93    25.06
  LCS_AVERAGE:      6.18

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:   61
LCS_GDT     D       2     D       2      3    4    8     3    3    3    4    4    4    4    5    5    5    5   12   12   12   15   16   17   17   27   29 
LCS_GDT     A       3     A       3      3    4   12     3    3    3    4    4    5    6    6    8   10   10   12   12   13   15   16   17   26   28   33 
LCS_GDT     K       4     K       4      3    4   16     3    3    3    4    4    4    5    6    7    8   11   13   13   15   15   19   25   30   32   34 
LCS_GDT     F       5     F       5      3    4   17     1    3    3    4    4    6    7    8   11   12   13   14   16   16   17   19   24   28   32   34 
LCS_GDT     L       6     L       6      3    3   17     0    3    4    5    7    9    9    9   11   12   13   14   16   19   23   25   29   31   32   34 
LCS_GDT     E       7     E       7      4    5   17     3    4    4    5    7    9   10   11   14   16   17   19   23   27   29   30   31   32   32   34 
LCS_GDT     I       8     I       8      4    5   17     3    4    4    5    7    9   10   11   14   16   20   20   22   26   29   30   31   32   32   34 
LCS_GDT     L       9     L       9      4    6   17     3    4    4    6    7    9   10   11   14   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     V      10     V      10      4    6   17     3    4    4    6    7    9   10   11   14   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     C      11     C      11      4    7   17     3    4    5    5    7    9   10   14   15   16   20   20   22   25   29   30   31   32   32   34 
LCS_GDT     P      12     P      12      4    7   17     3    4    5    8    9   10   12   14   15   16   17   18   20   22   22   24   25   27   29   33 
LCS_GDT     L      13     L      13      4    7   17     1    4    5    8    9   10   12   14   15   16   16   18   20   22   22   23   24   24   28   28 
LCS_GDT     C      14     C      14      4    7   17     3    4    5    8    9   10   12   14   15   16   17   18   20   22   22   24   25   27   30   34 
LCS_GDT     K      15     K      15      5    7   17     3    4    5    5    7    9   10   11   13   15   16   18   20   22   22   25   28   31   32   34 
LCS_GDT     G      16     G      16      5    7   17     3    4    5    5    7    9   10   11   14   16   17   18   22   24   26   29   31   32   32   34 
LCS_GDT     P      17     P      17      5    7   17     3    4    5    6    7    9   10   11   14   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     L      18     L      18      5    6   17     3    4    5    5    7    9   10   11   13   13   18   20   23   27   29   30   31   32   32   34 
LCS_GDT     V      19     V      19      5    6   17     3    4    5    5    7    8   10   11   13   15   16   19   23   27   29   30   31   32   32   34 
LCS_GDT     F      20     F      20      5    6   17     3    4    5    5    6    6    8   10   14   15   16   19   23   27   29   30   31   32   32   34 
LCS_GDT     D      21     D      21      4    6   17     3    4    4    5    6    6    8    9   14   15   16   19   22   27   29   30   31   32   32   34 
LCS_GDT     K      22     K      22      4    6   17     3    4    4    5    6    6    9   10   14   15   16   19   22   27   29   30   31   32   32   34 
LCS_GDT     S      23     S      23      3    6   16     3    3    3    5    6    6    8   10   14   14   16   19   20   25   28   30   31   32   32   34 
LCS_GDT     K      24     K      24      3    6   16     3    3    4    5    6    6    8   10   14   15   16   19   23   27   29   30   31   32   32   34 
LCS_GDT     D      25     D      25      3    5   16     0    3    3    4    5    6    7   10   11   12   16   19   22   27   29   30   31   32   32   34 
LCS_GDT     E      26     E      26      3    5   17     0    3    3    4    5    5    7   10   11   12   16   20   23   27   29   30   31   32   32   34 
LCS_GDT     L      27     L      27      3    5   17     1    3    3    5    6    8    9   11   14   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     I      28     I      28      4    5   17     3    3    4    5    5    6    7   11   14   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     C      29     C      29      4    5   17     3    3    4    5    7    9   12   13   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     K      30     K      30      4    5   17     3    3    4    4    4    7   12   13   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     G      31     G      31      4    5   17     3    3    4    5    6    6    9   10   11   13   15   16   18   27   29   30   31   32   32   33 
LCS_GDT     D      32     D      32      4    5   17     3    3    5    5    7   10   12   14   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     R      33     R      33      4    6   17     3    3    5    8    9   10   12   14   15   16   20   20   23   27   29   30   31   32   32   33 
LCS_GDT     L      34     L      34      4    7   17     3    3    5    8    9   10   12   14   15   16   20   20   22   27   29   30   31   32   32   33 
LCS_GDT     A      35     A      35      4    7   17     3    3    5    8    9   10   12   14   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     F      36     F      36      4    7   17     3    3    5    8    9   10   12   14   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     P      37     P      37      4    7   17     3    4    4    6    7    9   11   14   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     I      38     I      38      4    7   18     3    4    5    8    9   10   12   14   15   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     K      39     K      39      4    7   24     3    4    4    6    7    8   10   14   14   16   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     D      40     D      40      4    7   24     3    4    4    6    7    8   10   14   15   17   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     G      41     G      41      4    7   24     3    3    5    5    9   10   11   14   15   17   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     I      42     I      42      4    7   24     3    3    5    5    8    9   12   14   15   17   20   20   23   27   29   30   31   32   32   34 
LCS_GDT     P      43     P      43      4    7   24     3    4    5    5    6    9    9   14   15   17   18   19   20   22   23   24   24   26   30   32 
LCS_GDT     M      44     M      44      4    7   24     3    4    5    5    8    9   10   14   15   17   18   19   20   22   23   24   25   28   32   32 
LCS_GDT     M      45     M      45      4    7   24     3    4    4    5    6    7   10   11   15   17   18   19   20   22   23   24   24   25   25   27 
LCS_GDT     L      46     L      46      4    7   24     3    4    4    5    6    7    8    9   10   12   13   16   19   20   23   24   24   25   26   30 
LCS_GDT     E      47     E      47      3    6   24     3    3    4    4    6    7    8    9   11   12   14   18   20   22   23   24   24   25   25   25 
LCS_GDT     S      48     S      48      4    6   24     3    3    5    5    6    7    8    9   10   12   13   16   20   22   23   24   24   25   25   25 
LCS_GDT     E      49     E      49      4    6   24     3    3    4    4    6    6    8    9   10   12   18   18   20   22   23   24   24   25   25   25 
LCS_GDT     A      50     A      50      4    7   24     3    3    4    5    6    8    9   13   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     R      51     R      51      4    7   24     3    3    4    5    8    9    9   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     E      52     E      52      4    7   24     3    4    4    5    8    9   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     L      53     L      53      4    7   24     3    4    4    5    8    9   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     A      54     A      54      3    7   24     3    4    4    5    8    9   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     P      55     P      55      3    7   24     3    3    4    5    6    8    9   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     E      56     E      56      3    7   24     3    4    4    4    8    9   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     E      57     E      57      3    5   24     3    3    4    5    8    9   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     E      58     E      58      3    5   24     3    3    4    4    5    6    9   11   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     V      59     V      59      3    5   24     3    3    4    5    7    9   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     K      60     K      60      3    5   24     3    3    4    4    5    6   10   14   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     L      61     L      61      3    4   24     3    3    3    4    4    6    7    7   15   17   18   19   20   22   23   24   24   25   25   25 
LCS_GDT     E      62     E      62      3    4   24     3    3    3    4    4    6    7    8   11   14   18   19   20   22   23   24   24   25   25   25 
LCS_AVERAGE  LCS_A:  15.96  (   6.18    9.78   31.93 )

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      3      4      5      8      9     10     12     14     15     17     20     20     23     27     29     30     31     32     32     34 
GDT PERCENT_CA   4.92   6.56   8.20  13.11  14.75  16.39  19.67  22.95  24.59  27.87  32.79  32.79  37.70  44.26  47.54  49.18  50.82  52.46  52.46  55.74
GDT RMS_LOCAL    0.02   0.52   0.93   1.53   1.80   1.98   2.58   2.91   2.97   3.45   4.12   4.12   5.38   5.63   5.77   5.97   6.03   6.19   6.19   6.93
GDT RMS_ALL_CA  24.82  23.18  25.06  22.76  22.56  22.60  22.62  23.00  22.69  24.31  22.61  22.61  22.47  22.45  22.52  22.35  22.38  22.39  22.39  22.61

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         32.742
LGA    A       3      A       3         30.662
LGA    K       4      K       4         26.199
LGA    F       5      F       5         21.979
LGA    L       6      L       6         20.838
LGA    E       7      E       7         16.696
LGA    I       8      I       8         15.228
LGA    L       9      L       9         11.151
LGA    V      10      V      10         10.602
LGA    C      11      C      11          3.501
LGA    P      12      P      12          0.899
LGA    L      13      L      13          3.748
LGA    C      14      C      14          3.515
LGA    K      15      K      15          4.917
LGA    G      16      G      16          6.697
LGA    P      17      P      17         11.931
LGA    L      18      L      18         13.530
LGA    V      19      V      19         19.057
LGA    F      20      F      20         19.620
LGA    D      21      D      21         21.870
LGA    K      22      K      22         23.761
LGA    S      23      S      23         21.733
LGA    K      24      K      24         20.232
LGA    D      25      D      25         16.713
LGA    E      26      E      26         10.879
LGA    L      27      L      27          6.713
LGA    I      28      I      28          8.117
LGA    C      29      C      29          5.851
LGA    K      30      K      30          6.142
LGA    G      31      G      31          7.930
LGA    D      32      D      32          3.606
LGA    R      33      R      33          1.721
LGA    L      34      L      34          2.022
LGA    A      35      A      35          2.930
LGA    F      36      F      36          1.110
LGA    P      37      P      37          2.703
LGA    I      38      I      38          2.721
LGA    K      39      K      39          3.991
LGA    D      40      D      40          3.463
LGA    G      41      G      41          3.507
LGA    I      42      I      42          7.318
LGA    P      43      P      43         13.838
LGA    M      44      M      44         15.257
LGA    M      45      M      45         20.462
LGA    L      46      L      46         19.762
LGA    E      47      E      47         23.909
LGA    S      48      S      48         24.674
LGA    E      49      E      49         25.695
LGA    A      50      A      50         28.499
LGA    R      51      R      51         25.686
LGA    E      52      E      52         28.836
LGA    L      53      L      53         31.803
LGA    A      54      A      54         34.193
LGA    P      55      P      55         37.360
LGA    E      56      E      56         41.432
LGA    E      57      E      57         41.639
LGA    E      58      E      58         45.774
LGA    V      59      V      59         48.061
LGA    K      60      K      60         49.498
LGA    L      61      L      61         49.212
LGA    E      62      E      62         50.281

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     14    2.91    22.951    19.242     0.465

LGA_LOCAL      RMSD =  2.909  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.068  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 15.656  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.421605 * X  +  -0.715091 * Y  +   0.557579 * Z  +  -1.676619
  Y_new =  -0.577349 * X  +   0.262464 * Y  +   0.773163 * Z  +  27.057238
  Z_new =  -0.699226 * X  +  -0.647887 * Y  +  -0.302201 * Z  +  48.054028 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.007238    1.134355  [ DEG:  -115.0062     64.9938 ]
  Theta =   0.774315    2.367278  [ DEG:    44.3650    135.6350 ]
  Phi   =  -0.940060    2.201533  [ DEG:   -53.8614    126.1385 ]
 
# 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: T0348TS168_2                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_2.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   68   61   4.0   14   2.91  19.242    15.66
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_2
PFRMAT TS
TARGET T0348
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1       0.829  19.676  45.700  1.00 25.00           C
ATOM      2  CA  ASP     2       0.507  18.635  49.337  1.00 25.00           C
ATOM      3  CA  ALA     3      -0.696  17.393  52.673  1.00 25.00           C
ATOM      4  CA  LYS     4      -3.259  20.202  53.134  1.00 25.00           C
ATOM      5  CA  PHE     5      -1.273  21.557  56.115  1.00 25.00           C
ATOM      6  CA  LEU     6       1.943  21.480  54.039  1.00 25.00           C
ATOM      7  CA  GLU     7       0.185  23.354  51.199  1.00 25.00           C
ATOM      8  CA  ILE     8      -1.077  25.982  53.683  1.00 25.00           C
ATOM      9  CA  LEU     9       2.464  26.398  55.080  1.00 25.00           C
ATOM     10  CA  VAL    10       2.431  24.559  58.367  1.00 25.00           C
ATOM     11  CA  CYS    11       5.462  26.670  59.287  1.00 25.00           C
ATOM     12  CA  PRO    12       3.273  29.763  59.632  1.00 25.00           C
ATOM     13  CA  LEU    13       3.139  31.160  63.116  1.00 25.00           C
ATOM     14  CA  CYS    14       6.907  30.461  63.440  1.00 25.00           C
ATOM     15  CA  LYS    15       9.011  27.264  63.582  1.00 25.00           C
ATOM     16  CA  GLY    16       6.546  25.634  66.047  1.00 25.00           C
ATOM     17  CA  PRO    17       4.041  24.089  63.683  1.00 25.00           C
ATOM     18  CA  LEU    18       0.993  26.389  63.114  1.00 25.00           C
ATOM     19  CA  VAL    19      -1.798  24.348  61.456  1.00 25.00           C
ATOM     20  CA  PHE    20      -2.175  27.305  59.186  1.00 25.00           C
ATOM     21  CA  ASP    21      -1.655  30.668  60.982  1.00 25.00           C
ATOM     22  CA  LYS    22      -2.526  32.181  57.604  1.00 25.00           C
ATOM     23  CA  SER    23       0.573  32.006  55.360  1.00 25.00           C
ATOM     24  CA  LYS    24       2.270  34.732  57.447  1.00 25.00           C
ATOM     25  CA  ASP    25       5.609  34.208  59.191  1.00 25.00           C
ATOM     26  CA  GLU    26       8.803  32.630  58.029  1.00 25.00           C
ATOM     27  CA  LEU    27       8.611  33.491  54.348  1.00 25.00           C
ATOM     28  CA  ILE    28       6.484  30.311  54.169  1.00 25.00           C
ATOM     29  CA  CYS    29       9.546  28.184  55.045  1.00 25.00           C
ATOM     30  CA  LYS    30      10.633  27.314  58.614  1.00 25.00           C
ATOM     31  CA  GLY    31      11.515  23.990  56.946  1.00 25.00           C
ATOM     32  CA  ASP    32      11.289  22.692  60.575  1.00 25.00           C
ATOM     33  CA  ARG    33       9.836  19.653  58.788  1.00 25.00           C
ATOM     34  CA  LEU    34       6.733  21.850  58.604  1.00 25.00           C
ATOM     35  CA  ALA    35       6.721  23.786  55.354  1.00 25.00           C
ATOM     36  CA  PHE    36       6.616  25.432  51.910  1.00 25.00           C
ATOM     37  CA  PRO    37       9.371  24.772  49.393  1.00 25.00           C
ATOM     38  CA  ILE    38       7.000  26.651  47.058  1.00 25.00           C
ATOM     39  CA  LYS    39       9.389  29.229  45.482  1.00 25.00           C
ATOM     40  CA  ASP    40       7.106  32.254  44.881  1.00 25.00           C
ATOM     41  CA  GLY    41       5.994  34.787  42.254  1.00 25.00           C
ATOM     42  CA  ILE    42       4.043  32.480  39.878  1.00 25.00           C
ATOM     43  CA  PRO    43       4.539  31.056  36.387  1.00 25.00           C
ATOM     44  CA  MET    44       2.085  28.203  35.785  1.00 25.00           C
ATOM     45  CA  MET    45      -0.119  30.962  34.450  1.00 25.00           C
ATOM     46  CA  LEU    46      -2.950  28.865  35.773  1.00 25.00           C
ATOM     47  CA  GLU    47      -2.604  25.759  33.629  1.00 25.00           C
ATOM     48  CA  SER    48      -3.877  27.018  30.310  1.00 25.00           C
ATOM     49  CA  GLU    49      -4.729  25.064  27.112  1.00 25.00           C
ATOM     50  CA  ALA    50      -4.181  21.270  26.943  1.00 25.00           C
ATOM     51  CA  ARG    51      -3.959  18.629  29.673  1.00 25.00           C
ATOM     52  CA  GLU    52      -7.298  17.619  31.260  1.00 25.00           C
ATOM     53  CA  LEU    53     -10.344  19.731  32.144  1.00 25.00           C
ATOM     54  CA  ALA    54     -12.949  17.018  31.819  1.00 25.00           C
ATOM     55  CA  PRO    55     -14.535  18.575  34.967  1.00 25.00           C
ATOM     56  CA  GLU    56     -17.576  19.296  32.808  1.00 25.00           C
ATOM     57  CA  GLU    57     -18.170  23.051  32.596  1.00 25.00           C
ATOM     58  CA  GLU    58     -21.510  23.579  34.449  1.00 25.00           C
ATOM     59  CA  VAL    59     -20.240  27.077  35.269  1.00 25.00           C
ATOM     60  CA  LYS    60     -20.955  30.648  34.229  1.00 25.00           C
ATOM     61  CA  LEU    61     -20.563  34.335  35.010  1.00 25.00           C
ATOM     62  CA  GLU    62     -19.898  34.244  38.743  1.00 25.00           C
ATOM     63  CA  HIS    63     -17.574  37.222  38.937  1.00 25.00           C
ATOM     64  CA  HIS    64     -14.693  37.925  41.334  1.00 25.00           C
ATOM     65  CA  HIS    65     -15.289  37.968  45.062  1.00 25.00           C
ATOM     66  CA  HIS    66     -15.339  34.246  46.056  1.00 25.00           C
ATOM     67  CA  HIS    67     -16.850  34.527  49.521  1.00 25.00           C
ATOM     68  CA  HIS    68     -15.648  30.894  49.836  1.00 25.00           C
TER
END
