
#######################################################
#                                                     #
#                        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_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_3.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:    25        18 - 42          4.91    22.11
  LCS_AVERAGE:     38.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9         8 - 16          1.89    20.02
  LCS_AVERAGE:     10.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        10 - 14          0.96    23.01
  LONGEST_CONTINUOUS_SEGMENT:     5        12 - 16          0.81    18.55
  LONGEST_CONTINUOUS_SEGMENT:     5        33 - 37          0.94    22.04
  LCS_AVERAGE:      6.23

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    3   19     3    3    3    3    3    5    5    6    6   10   10   10   11   11   15   20   20   26   28   30 
LCS_GDT     A       3     A       3      3    3   19     3    3    3    3    3    7    7    7    9   10   10   12   18   21   24   25   27   32   36   36 
LCS_GDT     K       4     K       4      3    3   19     3    3    3    4    4    5    5    6   11   17   17   22   24   25   26   28   30   34   36   36 
LCS_GDT     F       5     F       5      3    3   20     1    3    3    4    4    5    5    8   13   17   22   22   24   25   26   28   33   34   36   37 
LCS_GDT     L       6     L       6      3    3   20     0    3    3    4    4    6    9   11   15   17   22   22   24   25   28   31   33   35   36   37 
LCS_GDT     E       7     E       7      4    7   20     3    4    5    5   10   12   16   16   18   19   22   22   24   25   29   31   33   35   36   37 
LCS_GDT     I       8     I       8      4    9   20     3    4    5    8    9   12   16   16   18   19   22   22   24   25   28   31   33   35   36   37 
LCS_GDT     L       9     L       9      4    9   20     3    4    5    8   10   12   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     V      10     V      10      5    9   20     4    4    5    6    8    9   12   15   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     C      11     C      11      5    9   20     4    4    5    6   12   13   16   16   18   19   22   22   24   25   29   31   33   35   36   37 
LCS_GDT     P      12     P      12      5    9   20     4    6    7    8   10   12   16   16   18   19   22   22   24   25   28   31   33   35   36   37 
LCS_GDT     L      13     L      13      5    9   20     4    6    7    8   10   12   16   16   18   19   22   22   24   25   26   28   33   34   36   37 
LCS_GDT     C      14     C      14      5    9   20     4    6    7   10   12   13   16   16   18   19   22   22   24   25   26   28   33   34   36   37 
LCS_GDT     K      15     K      15      5    9   20     4    6    7    8   10   12   16   16   18   19   22   22   24   25   29   31   33   35   36   37 
LCS_GDT     G      16     G      16      5    9   20     3    5    7    8   10   12   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     P      17     P      17      3    7   23     0    3    7    8   10   12   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     L      18     L      18      3    7   25     1    4    7    8   10   12   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     V      19     V      19      3    5   25     3    3    4    9    9   10   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     F      20     F      20      4    5   25     4    4    6    9    9   12   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     D      21     D      21      4    5   25     4    4    6    9    9   10   12   14   14   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     K      22     K      22      4    5   25     4    4    4    5    6    7    9   11   13   15   20   21   24   27   29   31   33   35   36   37 
LCS_GDT     S      23     S      23      4    5   25     4    4    4    5    8   10   12   14   14   16   20   21   24   27   29   31   33   35   36   37 
LCS_GDT     K      24     K      24      4    5   25     4    4    6    9    9   10   12   14   14   16   20   21   24   27   29   31   33   35   36   37 
LCS_GDT     D      25     D      25      4    5   25     4    4    5    5    5    5    8   11   13   13   15   19   24   27   29   31   33   35   36   37 
LCS_GDT     E      26     E      26      4    5   25     4    4    5    8   10   10   12   14   16   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     L      27     L      27      4    5   25     4    4    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     I      28     I      28      4    4   25     3    4    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     C      29     C      29      4    4   25     3    3    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     K      30     K      30      4    4   25     3    4    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     G      31     G      31      4    6   25     3    4    4    4    6    8   13   15   16   17   18   21   23   25   27   31   33   35   35   37 
LCS_GDT     D      32     D      32      4    8   25     3    4    4    6    7    7    9   14   16   19   20   22   24   27   29   31   33   35   35   37 
LCS_GDT     R      33     R      33      5    8   25     3    5    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   35   37 
LCS_GDT     L      34     L      34      5    8   25     3    5    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     A      35     A      35      5    8   25     1    5    8   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     F      36     F      36      5    8   25     2    5    7   10   12   13   13   15   18   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     P      37     P      37      5    8   25     2    6    8   10   12   13   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     I      38     I      38      3    8   25     4    6    7    8   10   12   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     K      39     K      39      3    8   25     3    4    5    9   10   13   16   16   18   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     D      40     D      40      3    6   25     3    3    4    5    8    8   12   14   16   19   22   22   24   27   29   31   33   35   36   37 
LCS_GDT     G      41     G      41      3    6   25     3    3    7   10   12   13   13   15   16   19   20   22   24   27   29   31   33   35   36   37 
LCS_GDT     I      42     I      42      3    6   25     3    3    3    5    7    9   10   14   15   17   20   22   23   25   28   30   33   35   35   37 
LCS_GDT     P      43     P      43      3    6   24     3    3    3    5    7    9   10   14   15   16   18   20   21   23   24   24   25   26   31   32 
LCS_GDT     M      44     M      44      4    6   24     3    3    4    5    6    9   10   14   15   16   18   20   21   23   24   24   27   28   31   32 
LCS_GDT     M      45     M      45      4    6   24     3    3    4    5    6    7   10   11   12   16   18   20   21   23   24   24   25   25   29   30 
LCS_GDT     L      46     L      46      4    5   24     3    3    4    4    6    7   10   11   12   16   18   18   21   23   24   24   25   25   25   28 
LCS_GDT     E      47     E      47      4    5   24     3    3    4    5    6    7   10   11   12   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     S      48     S      48      4    5   24     3    3    4    4    6    7   10   11   12   13   16   18   20   22   24   24   25   25   25   25 
LCS_GDT     E      49     E      49      4    5   24     0    3    4    4    5    6    9   11   12   13   17   18   21   23   24   24   25   25   25   25 
LCS_GDT     A      50     A      50      4    7   24     3    3    4    6    6    7   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     R      51     R      51      4    7   24     3    3    4    6    6    9   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     E      52     E      52      4    7   24     3    3    4    6    7    9   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     L      53     L      53      4    7   24     3    3    4    6    7    9   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     A      54     A      54      4    7   24     3    3    4    5    7    9   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     P      55     P      55      4    7   24     3    3    4    6    7    9   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     E      56     E      56      3    7   24     3    3    3    6    7    7   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     E      57     E      57      3    6   24     3    3    3    4    6    9   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     E      58     E      58      3    4   24     3    3    3    4    4    7   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     V      59     V      59      3    4   24     0    3    3    3    4    5   10   14   15   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     K      60     K      60      3    4   24     1    3    3    3    4    4    5   11   13   15   17   19   20   23   24   24   25   25   25   25 
LCS_GDT     L      61     L      61      3    4   24     0    3    3    3    4    4    5   10   14   16   18   20   21   23   24   24   25   25   25   25 
LCS_GDT     E      62     E      62      0    3   24     0    0    3    5    6    7    7    8    8   12   18   20   21   23   24   24   25   25   25   25 
LCS_AVERAGE  LCS_A:  18.19  (   6.23   10.05   38.30 )

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      4      6      8     10     12     13     16     16     18     19     22     22     24     27     29     31     33     35     36     37 
GDT PERCENT_CA   6.56   9.84  13.11  16.39  19.67  21.31  26.23  26.23  29.51  31.15  36.07  36.07  39.34  44.26  47.54  50.82  54.10  57.38  59.02  60.66
GDT RMS_LOCAL    0.32   0.64   1.15   1.31   1.64   1.78   2.61   2.61   2.88   3.58   3.99   3.99   4.34   5.17   5.52   5.79   6.00   6.23   6.44   6.56
GDT RMS_ALL_CA  23.83  19.56  22.77  22.68  22.54  22.65  19.92  19.92  19.70  22.49  21.32  21.32  21.79  22.21  22.34  22.44  22.55  22.45  22.75  22.47

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         15.738
LGA    A       3      A       3         12.850
LGA    K       4      K       4          7.505
LGA    F       5      F       5          6.923
LGA    L       6      L       6          7.016
LGA    E       7      E       7          3.516
LGA    I       8      I       8          2.352
LGA    L       9      L       9          1.808
LGA    V      10      V      10          4.322
LGA    C      11      C      11          2.951
LGA    P      12      P      12          1.897
LGA    L      13      L      13          1.077
LGA    C      14      C      14          1.866
LGA    K      15      K      15          1.893
LGA    G      16      G      16          3.078
LGA    P      17      P      17          3.045
LGA    L      18      L      18          2.199
LGA    V      19      V      19          3.847
LGA    F      20      F      20          3.565
LGA    D      21      D      21          7.068
LGA    K      22      K      22         14.390
LGA    S      23      S      23         14.639
LGA    K      24      K      24         10.690
LGA    D      25      D      25         13.557
LGA    E      26      E      26          7.720
LGA    L      27      L      27         10.011
LGA    I      28      I      28         13.066
LGA    C      29      C      29         10.766
LGA    K      30      K      30         15.014
LGA    G      31      G      31         17.813
LGA    D      32      D      32         17.375
LGA    R      33      R      33         17.215
LGA    L      34      L      34         12.714
LGA    A      35      A      35          9.674
LGA    F      36      F      36          5.091
LGA    P      37      P      37          2.935
LGA    I      38      I      38          2.226
LGA    K      39      K      39          2.124
LGA    D      40      D      40          8.431
LGA    G      41      G      41         10.711
LGA    I      42      I      42         13.853
LGA    P      43      P      43         15.630
LGA    M      44      M      44         17.065
LGA    M      45      M      45         22.205
LGA    L      46      L      46         26.578
LGA    E      47      E      47         31.899
LGA    S      48      S      48         32.788
LGA    E      49      E      49         31.453
LGA    A      50      A      50         32.988
LGA    R      51      R      51         31.898
LGA    E      52      E      52         35.580
LGA    L      53      L      53         36.166
LGA    A      54      A      54         40.876
LGA    P      55      P      55         43.510
LGA    E      56      E      56         37.860
LGA    E      57      E      57         35.075
LGA    E      58      E      58         37.070
LGA    V      59      V      59         34.924
LGA    K      60      K      60         29.965
LGA    L      61      L      61         27.519
LGA    E      62      E      62         27.224

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     16    2.61    25.820    22.156     0.591

LGA_LOCAL      RMSD =  2.606  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 20.011  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 15.634  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.855999 * X  +   0.325787 * Y  +  -0.401409 * Z  +  13.381611
  Y_new =   0.260434 * X  +   0.398988 * Y  +   0.879194 * Z  +  31.897369
  Z_new =   0.446587 * X  +  -0.857130 * Y  +   0.256687 * Z  +  47.767349 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.279824    1.861769  [ DEG:   -73.3285    106.6715 ]
  Theta =  -0.462947   -2.678645  [ DEG:   -26.5249   -153.4751 ]
  Phi   =   0.295348   -2.846245  [ DEG:    16.9222   -163.0778 ]
 
# 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_3                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_3.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   16   2.61  22.156    15.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_3
PFRMAT TS
TARGET T0348
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1       9.766  36.684  44.158  1.00 25.00           C
ATOM      2  CA  ASP     2       8.556  38.604  47.259  1.00 25.00           C
ATOM      3  CA  ALA     3       8.954  40.814  50.306  1.00 25.00           C
ATOM      4  CA  LYS     4       5.513  40.524  51.962  1.00 25.00           C
ATOM      5  CA  PHE     5       5.881  36.715  52.114  1.00 25.00           C
ATOM      6  CA  LEU     6       9.348  37.088  53.696  1.00 25.00           C
ATOM      7  CA  GLU     7       7.930  39.527  56.287  1.00 25.00           C
ATOM      8  CA  ILE     8       5.108  37.066  57.096  1.00 25.00           C
ATOM      9  CA  LEU     9       7.660  34.241  57.517  1.00 25.00           C
ATOM     10  CA  VAL    10       8.538  30.665  56.462  1.00 25.00           C
ATOM     11  CA  CYS    11       5.905  28.376  58.023  1.00 25.00           C
ATOM     12  CA  PRO    12       4.914  30.803  60.858  1.00 25.00           C
ATOM     13  CA  LEU    13       4.267  27.692  62.965  1.00 25.00           C
ATOM     14  CA  CYS    14       7.544  28.514  64.718  1.00 25.00           C
ATOM     15  CA  LYS    15       8.697  32.036  63.963  1.00 25.00           C
ATOM     16  CA  GLY    16      12.328  32.995  63.271  1.00 25.00           C
ATOM     17  CA  PRO    17      13.313  29.347  63.554  1.00 25.00           C
ATOM     18  CA  LEU    18      11.948  29.150  59.990  1.00 25.00           C
ATOM     19  CA  VAL    19      14.456  31.253  57.961  1.00 25.00           C
ATOM     20  CA  PHE    20      13.520  29.104  54.920  1.00 25.00           C
ATOM     21  CA  ASP    21      12.019  25.660  55.577  1.00 25.00           C
ATOM     22  CA  LYS    22       9.665  24.831  58.499  1.00 25.00           C
ATOM     23  CA  SER    23      10.275  21.149  57.643  1.00 25.00           C
ATOM     24  CA  LYS    24       7.842  21.406  54.696  1.00 25.00           C
ATOM     25  CA  ASP    25       5.120  23.119  56.725  1.00 25.00           C
ATOM     26  CA  GLU    26       5.058  25.566  53.804  1.00 25.00           C
ATOM     27  CA  LEU    27       2.003  26.172  51.672  1.00 25.00           C
ATOM     28  CA  ILE    28      -0.004  28.550  53.905  1.00 25.00           C
ATOM     29  CA  CYS    29       1.114  26.613  57.013  1.00 25.00           C
ATOM     30  CA  LYS    30       0.172  28.629  60.048  1.00 25.00           C
ATOM     31  CA  GLY    31      -2.664  30.025  57.957  1.00 25.00           C
ATOM     32  CA  ASP    32      -2.097  33.731  57.552  1.00 25.00           C
ATOM     33  CA  ARG    33       1.243  33.984  59.439  1.00 25.00           C
ATOM     34  CA  LEU    34       2.900  32.582  56.274  1.00 25.00           C
ATOM     35  CA  ALA    35       4.584  31.130  53.187  1.00 25.00           C
ATOM     36  CA  PHE    36       7.930  30.356  51.487  1.00 25.00           C
ATOM     37  CA  PRO    37       5.866  28.746  48.717  1.00 25.00           C
ATOM     38  CA  ILE    38       7.261  30.840  45.902  1.00 25.00           C
ATOM     39  CA  LYS    39       6.530  27.682  43.816  1.00 25.00           C
ATOM     40  CA  ASP    40       6.269  23.911  43.451  1.00 25.00           C
ATOM     41  CA  GLY    41       8.763  23.327  40.634  1.00 25.00           C
ATOM     42  CA  ILE    42      12.237  23.871  39.053  1.00 25.00           C
ATOM     43  CA  PRO    43      10.741  25.839  36.154  1.00 25.00           C
ATOM     44  CA  MET    44      11.048  29.555  35.488  1.00 25.00           C
ATOM     45  CA  MET    45      14.811  29.111  35.566  1.00 25.00           C
ATOM     46  CA  LEU    46      17.819  26.844  35.140  1.00 25.00           C
ATOM     47  CA  GLU    47      19.489  26.178  31.813  1.00 25.00           C
ATOM     48  CA  SER    48      19.886  29.830  30.785  1.00 25.00           C
ATOM     49  CA  GLU    49      19.263  31.738  27.587  1.00 25.00           C
ATOM     50  CA  ALA    50      16.309  33.137  25.549  1.00 25.00           C
ATOM     51  CA  ARG    51      15.171  35.651  28.147  1.00 25.00           C
ATOM     52  CA  GLU    52      16.778  38.709  29.830  1.00 25.00           C
ATOM     53  CA  LEU    53      20.213  40.363  30.328  1.00 25.00           C
ATOM     54  CA  ALA    54      20.254  44.071  29.647  1.00 25.00           C
ATOM     55  CA  PRO    55      23.997  44.563  30.303  1.00 25.00           C
ATOM     56  CA  GLU    56      23.861  42.562  33.497  1.00 25.00           C
ATOM     57  CA  GLU    57      26.917  43.226  35.632  1.00 25.00           C
ATOM     58  CA  GLU    58      30.005  41.356  34.379  1.00 25.00           C
ATOM     59  CA  VAL    59      32.110  38.152  34.279  1.00 25.00           C
ATOM     60  CA  LYS    60      34.943  36.513  36.267  1.00 25.00           C
ATOM     61  CA  LEU    61      34.357  34.887  39.660  1.00 25.00           C
ATOM     62  CA  GLU    62      34.037  35.451  43.425  1.00 25.00           C
ATOM     63  CA  HIS    63      34.638  31.917  44.861  1.00 25.00           C
ATOM     64  CA  HIS    64      33.287  28.421  44.126  1.00 25.00           C
ATOM     65  CA  HIS    65      30.200  29.282  46.211  1.00 25.00           C
ATOM     66  CA  HIS    66      27.637  29.844  48.964  1.00 25.00           C
ATOM     67  CA  HIS    67      28.752  32.312  51.635  1.00 25.00           C
ATOM     68  CA  HIS    68      26.174  35.035  50.907  1.00 25.00           C
TER
END
