
#######################################################
#                                                     #
#                        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 T0348TS393_3
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS393_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:    21        40 - 60          4.92    24.77
  LCS_AVERAGE:     30.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        18 - 25          1.91    19.98
  LCS_AVERAGE:      9.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4         7 - 10          0.43    23.00
  LONGEST_CONTINUOUS_SEGMENT:     4        10 - 13          0.97    27.55
  LONGEST_CONTINUOUS_SEGMENT:     4        12 - 15          0.84    22.28
  LONGEST_CONTINUOUS_SEGMENT:     4        20 - 23          0.65    28.17
  LONGEST_CONTINUOUS_SEGMENT:     4        30 - 33          0.98    25.73
  LONGEST_CONTINUOUS_SEGMENT:     4        35 - 38          0.62    21.63
  LONGEST_CONTINUOUS_SEGMENT:     4        36 - 39          0.83    22.49
  LONGEST_CONTINUOUS_SEGMENT:     4        41 - 44          0.63    26.59
  LONGEST_CONTINUOUS_SEGMENT:     4        43 - 46          0.94    22.09
  LONGEST_CONTINUOUS_SEGMENT:     4        45 - 48          0.33    27.08
  LONGEST_CONTINUOUS_SEGMENT:     4        47 - 50          0.97    33.54
  LONGEST_CONTINUOUS_SEGMENT:     4        52 - 55          0.55    24.99
  LONGEST_CONTINUOUS_SEGMENT:     4        57 - 60          0.72    40.37
  LCS_AVERAGE:      5.99

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    9     0    2    3    3    3    4    5    5    6    7    8   10   13   15   17   18   19   22   24   24 
LCS_GDT     A       3     A       3      3    4   17     1    3    5    5    5    5    6    8    8    9   17   20   21   21   23   23   24   25   25   30 
LCS_GDT     K       4     K       4      3    4   17     0    3    3    3    3    5    7    9   13   16   19   20   21   21   23   23   27   27   28   30 
LCS_GDT     F       5     F       5      3    4   17     1    3    4    4    4    6    7    8    9   16   19   20   21   21   23   23   27   27   28   30 
LCS_GDT     L       6     L       6      3    3   17     0    3    4    4    5    6    7   10   14   16   19   20   21   21   23   23   27   27   28   30 
LCS_GDT     E       7     E       7      4    4   17     3    4    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     I       8     I       8      4    4   17     3    4    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     L       9     L       9      4    6   17     3    4    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     V      10     V      10      4    6   17     3    4    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     C      11     C      11      4    6   17     3    3    4    6    6    8    9   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     P      12     P      12      4    6   17     3    3    5    6    6    7    9   11   14   15   18   19   23   24   26   27   28   28   29   30 
LCS_GDT     L      13     L      13      4    6   17     3    3    5    6    6    7    9   11   14   15   18   19   22   22   26   27   28   28   29   30 
LCS_GDT     C      14     C      14      4    6   17     3    3    5    6    7    8    9   11   14   15   18   19   22   24   26   27   28   28   29   30 
LCS_GDT     K      15     K      15      4    4   17     3    3    5    5    5    7    8   11   14   15   18   19   22   22   24   27   28   28   28   30 
LCS_GDT     G      16     G      16      3    5   17     3    4    5    6    7    8    8    8   13   15   19   22   23   24   26   27   28   28   29   30 
LCS_GDT     P      17     P      17      3    5   17     3    4    5    6    7    8    9   10   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     L      18     L      18      3    8   17     3    3    5    6    8    9   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     V      19     V      19      3    8   17     3    4    6    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     F      20     F      20      4    8   18     4    5    6    6    7    8    8    9   13   15   17   19   19   21   23   24   26   27   29   30 
LCS_GDT     D      21     D      21      4    8   18     3    5    6    6    7    8    8    9   12   14   15   16   17   18   21   22   24   26   27   27 
LCS_GDT     K      22     K      22      4    8   18     3    4    4    5    7    8    8    9   11   13   15   16   17   18   18   19   20   22   23   25 
LCS_GDT     S      23     S      23      4    8   18     4    5    6    6    7    8    8    9   12   14   15   16   17   18   18   19   21   23   25   26 
LCS_GDT     K      24     K      24      3    8   18     4    5    6    6    7    8    8    9   12   14   15   16   17   18   22   22   24   26   27   27 
LCS_GDT     D      25     D      25      3    8   18     4    5    6    6    7    8    8    9   12   14   15   16   18   19   22   22   24   26   27   29 
LCS_GDT     E      26     E      26      3    6   18     3    3    4    4    6    8    9   11   14   15   17   17   21   21   24   24   27   27   28   30 
LCS_GDT     L      27     L      27      3    7   18     3    3    4    6    7    8    9   11   14   15   17   19   21   21   24   25   27   27   29   30 
LCS_GDT     I      28     I      28      3    7   18     3    3    4    6    7    8    9   11   13   15   17   19   21   23   26   26   28   28   29   30 
LCS_GDT     C      29     C      29      3    7   18     3    3    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     K      30     K      30      4    7   18     3    3    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     G      31     G      31      4    7   18     3    3    5    6    7    7    9   11   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     D      32     D      32      4    7   18     3    3    4    6    7    8   10   11   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     R      33     R      33      4    7   18     3    3    4    6    7    7    8   10   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     L      34     L      34      3    5   18     3    3    5    6    6    8    9   10   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     A      35     A      35      4    5   18     3    4    5    6    6    8    9   10   12   16   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     F      36     F      36      4    6   18     3    4    5    6    7    8   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     P      37     P      37      4    6   18     3    4    4    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     I      38     I      38      4    6   18     3    4    5    6    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     K      39     K      39      4    6   20     3    3    4    5    8   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     D      40     D      40      3    6   21     3    3    4    4    5    7    9   11   15   15   17   19   22   22   24   27   28   28   29   30 
LCS_GDT     G      41     G      41      4    6   21     3    4    5    5    7   11   13   14   15   19   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     I      42     I      42      4    5   21     3    4    5    5    7    8   10   12   13   17   21   22   23   24   26   27   28   28   29   30 
LCS_GDT     P      43     P      43      4    5   21     3    4    5    5    7    8   10   12   12   15   16   17   18   20   22   23   24   25   26   29 
LCS_GDT     M      44     M      44      4    5   21     3    4    5    5    7    8   10   12   12   15   16   17   18   20   22   22   23   24   26   27 
LCS_GDT     M      45     M      45      4    5   21     4    5    5    5    5    7    9   11   12   15   16   17   18   21   22   23   24   25   25   25 
LCS_GDT     L      46     L      46      4    5   21     4    5    5    5    5    6    9   11   13   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      47     E      47      4    5   21     4    5    5    5    5    6    9   11   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     S      48     S      48      4    5   21     4    5    5    5    5    7    9   10   11   15   17   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      49     E      49      4    5   21     3    3    4    4    5    6    7   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     A      50     A      50      4    6   21     3    4    5    6    6    8   10   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     R      51     R      51      3    6   21     3    5    5    6    6    7    8    9   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      52     E      52      4    6   21     3    4    5    6    7    8   10   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     L      53     L      53      4    6   21     3    4    5    6    6    8   10   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     A      54     A      54      4    6   21     3    4    5    6    6    8   10   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     P      55     P      55      4    6   21     3    4    5    6    7    8   10   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      56     E      56      3    6   21     3    3    4    5    7    8   10   12   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      57     E      57      4    6   21     3    3    4    5    7    8   10   12   13   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      58     E      58      4    6   21     3    3    4    5    6    7    8   10   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     V      59     V      59      4    6   21     3    3    4    5    6    7    8    9   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     K      60     K      60      4    6   21     3    3    4    5    6    7    8   10   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     L      61     L      61      3    6   20     3    3    4    5    6    7    8   11   14   16   19   20   21   21   23   23   24   25   25   25 
LCS_GDT     E      62     E      62      3    6   18     3    3    3    4    5    6    8   11   11   11   12   18   21   21   23   23   24   25   25   25 
LCS_AVERAGE  LCS_A:  15.43  (   5.99    9.67   30.61 )

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      5      6      6      8     11     13     14     15     19     21     22     23     24     26     27     28     28     29     30 
GDT PERCENT_CA   6.56   8.20   9.84   9.84  13.11  18.03  21.31  22.95  24.59  31.15  34.43  36.07  37.70  39.34  42.62  44.26  45.90  45.90  47.54  49.18
GDT RMS_LOCAL    0.33   0.48   0.69   0.69   1.81   2.17   2.56   2.84   3.06   3.82   4.01   4.28   4.59   4.81   5.15   5.32   5.46   5.46   5.83   5.96
GDT RMS_ALL_CA  27.08  20.46  20.26  20.26  22.78  23.26  23.09  23.12  23.33  22.28  22.34  22.36  22.43  22.44  22.56  22.77  22.81  22.81  22.85  22.93

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         22.354
LGA    A       3      A       3         17.231
LGA    K       4      K       4         15.824
LGA    F       5      F       5         14.750
LGA    L       6      L       6         10.843
LGA    E       7      E       7          3.798
LGA    I       8      I       8          3.421
LGA    L       9      L       9          2.618
LGA    V      10      V      10          3.311
LGA    C      11      C      11          3.793
LGA    P      12      P      12          9.753
LGA    L      13      L      13         11.477
LGA    C      14      C      14         11.849
LGA    K      15      K      15         12.953
LGA    G      16      G      16          8.790
LGA    P      17      P      17          6.184
LGA    L      18      L      18          2.580
LGA    V      19      V      19          1.035
LGA    F      20      F      20          7.723
LGA    D      21      D      21         13.554
LGA    K      22      K      22         20.446
LGA    S      23      S      23         23.815
LGA    K      24      K      24         21.482
LGA    D      25      D      25         17.244
LGA    E      26      E      26         12.765
LGA    L      27      L      27          9.054
LGA    I      28      I      28          6.713
LGA    C      29      C      29          3.813
LGA    K      30      K      30          3.211
LGA    G      31      G      31          7.523
LGA    D      32      D      32          8.306
LGA    R      33      R      33          7.329
LGA    L      34      L      34          6.919
LGA    A      35      A      35          5.440
LGA    F      36      F      36          2.915
LGA    P      37      P      37          2.063
LGA    I      38      I      38          1.959
LGA    K      39      K      39          3.086
LGA    D      40      D      40          6.295
LGA    G      41      G      41          2.602
LGA    I      42      I      42          5.745
LGA    P      43      P      43         11.965
LGA    M      44      M      44         14.756
LGA    M      45      M      45         18.132
LGA    L      46      L      46         18.306
LGA    E      47      E      47         23.240
LGA    S      48      S      48         23.795
LGA    E      49      E      49         25.094
LGA    A      50      A      50         29.259
LGA    R      51      R      51         34.387
LGA    E      52      E      52         39.918
LGA    L      53      L      53         43.579
LGA    A      54      A      54         50.011
LGA    P      55      P      55         52.258
LGA    E      56      E      56         51.830
LGA    E      57      E      57         46.197
LGA    E      58      E      58         48.303
LGA    V      59      V      59         47.156
LGA    K      60      K      60         41.141
LGA    L      61      L      61         40.755
LGA    E      62      E      62         41.741

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     14    2.84    21.311    19.179     0.476

LGA_LOCAL      RMSD =  2.841  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.174  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 15.250  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.182634 * X  +   0.290086 * Y  +   0.939412 * Z  +   6.518776
  Y_new =  -0.777475 * X  +   0.627469 * Y  +  -0.042609 * Z  +  36.702984
  Z_new =  -0.601812 * X  +  -0.722588 * Y  +   0.340132 * Z  +  50.391563 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.130851    2.010742  [ DEG:   -64.7930    115.2070 ]
  Theta =   0.645768    2.495825  [ DEG:    36.9998    143.0002 ]
  Phi   =  -1.340073    1.801519  [ DEG:   -76.7805    103.2195 ]
 
# 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: T0348TS393_3                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS393_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   14   2.84  19.179    15.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS393_3
PFRMAT TS
TARGET T0348
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -2.668  32.011  50.826  1.00 25.00           C
ATOM      2  CA  ASP     2      -2.942  30.121  54.086  1.00 25.00           C
ATOM      3  CA  ALA     3      -1.598  32.666  56.531  1.00 25.00           C
ATOM      4  CA  LYS     4       0.121  34.493  59.424  1.00 25.00           C
ATOM      5  CA  PHE     5       2.713  31.687  59.690  1.00 25.00           C
ATOM      6  CA  LEU     6       3.359  31.893  55.921  1.00 25.00           C
ATOM      7  CA  GLU     7       3.807  35.688  56.180  1.00 25.00           C
ATOM      8  CA  ILE     8       6.270  35.224  59.075  1.00 25.00           C
ATOM      9  CA  LEU     9       8.232  32.650  57.027  1.00 25.00           C
ATOM     10  CA  VAL    10       8.310  29.729  59.549  1.00 25.00           C
ATOM     11  CA  CYS    11       9.013  32.137  62.450  1.00 25.00           C
ATOM     12  CA  PRO    12      11.956  34.261  61.512  1.00 25.00           C
ATOM     13  CA  LEU    13      14.158  31.194  62.249  1.00 25.00           C
ATOM     14  CA  CYS    14      17.303  29.089  61.886  1.00 25.00           C
ATOM     15  CA  LYS    15      18.890  31.635  59.545  1.00 25.00           C
ATOM     16  CA  GLY    16      16.955  34.827  59.873  1.00 25.00           C
ATOM     17  CA  PRO    17      14.516  35.687  57.109  1.00 25.00           C
ATOM     18  CA  LEU    18      13.549  31.982  57.242  1.00 25.00           C
ATOM     19  CA  VAL    19      15.519  28.718  56.986  1.00 25.00           C
ATOM     20  CA  PHE    20      12.821  27.311  59.363  1.00 25.00           C
ATOM     21  CA  ASP    21      10.940  26.705  62.624  1.00 25.00           C
ATOM     22  CA  LYS    22      10.750  28.224  66.108  1.00 25.00           C
ATOM     23  CA  SER    23       7.891  25.803  66.895  1.00 25.00           C
ATOM     24  CA  LYS    24       5.403  28.135  65.154  1.00 25.00           C
ATOM     25  CA  ASP    25       6.000  25.997  62.091  1.00 25.00           C
ATOM     26  CA  GLU    26       4.360  23.284  59.962  1.00 25.00           C
ATOM     27  CA  LEU    27       3.755  25.331  56.829  1.00 25.00           C
ATOM     28  CA  ILE    28       6.116  23.218  54.677  1.00 25.00           C
ATOM     29  CA  CYS    29       8.926  23.709  57.233  1.00 25.00           C
ATOM     30  CA  LYS    30      11.353  22.436  59.895  1.00 25.00           C
ATOM     31  CA  GLY    31      14.461  22.015  57.658  1.00 25.00           C
ATOM     32  CA  ASP    32      12.466  19.230  55.926  1.00 25.00           C
ATOM     33  CA  ARG    33      11.075  21.569  53.254  1.00 25.00           C
ATOM     34  CA  LEU    34      12.878  24.902  53.888  1.00 25.00           C
ATOM     35  CA  ALA    35      10.754  27.914  54.831  1.00 25.00           C
ATOM     36  CA  PHE    36       7.037  28.217  54.045  1.00 25.00           C
ATOM     37  CA  PRO    37       7.898  27.409  50.459  1.00 25.00           C
ATOM     38  CA  ILE    38       6.178  29.594  47.923  1.00 25.00           C
ATOM     39  CA  LYS    39       8.543  28.992  45.023  1.00 25.00           C
ATOM     40  CA  ASP    40      11.704  30.938  44.362  1.00 25.00           C
ATOM     41  CA  GLY    41      10.688  33.790  41.995  1.00 25.00           C
ATOM     42  CA  ILE    42       7.159  35.026  41.127  1.00 25.00           C
ATOM     43  CA  PRO    43       5.135  33.558  38.261  1.00 25.00           C
ATOM     44  CA  MET    44       1.954  35.347  37.091  1.00 25.00           C
ATOM     45  CA  MET    45       3.778  38.508  38.186  1.00 25.00           C
ATOM     46  CA  LEU    46       1.020  39.472  40.579  1.00 25.00           C
ATOM     47  CA  GLU    47      -2.451  39.229  38.923  1.00 25.00           C
ATOM     48  CA  SER    48      -2.905  42.686  40.428  1.00 25.00           C
ATOM     49  CA  GLU    49      -6.027  44.382  39.056  1.00 25.00           C
ATOM     50  CA  ALA    50      -7.659  42.501  36.114  1.00 25.00           C
ATOM     51  CA  ARG    51      -6.058  44.477  33.276  1.00 25.00           C
ATOM     52  CA  GLU    52      -5.826  48.020  34.592  1.00 25.00           C
ATOM     53  CA  LEU    53      -4.680  51.603  35.055  1.00 25.00           C
ATOM     54  CA  ALA    54      -4.674  55.086  33.558  1.00 25.00           C
ATOM     55  CA  PRO    55      -1.017  55.880  34.099  1.00 25.00           C
ATOM     56  CA  GLU    56       1.388  55.365  31.185  1.00 25.00           C
ATOM     57  CA  GLU    57       4.647  54.634  32.946  1.00 25.00           C
ATOM     58  CA  GLU    58       6.045  57.254  35.401  1.00 25.00           C
ATOM     59  CA  VAL    59       6.555  55.823  38.873  1.00 25.00           C
ATOM     60  CA  LYS    60       9.593  53.470  38.838  1.00 25.00           C
ATOM     61  CA  LEU    61      11.820  56.046  40.627  1.00 25.00           C
ATOM     62  CA  GLU    62      11.626  54.872  44.205  1.00 25.00           C
ATOM     63  CA  HIS    63      14.118  52.549  45.961  1.00 25.00           C
ATOM     64  CA  HIS    64      11.754  52.333  48.891  1.00 25.00           C
ATOM     65  CA  HIS    65       9.439  53.231  51.749  1.00 25.00           C
ATOM     66  CA  HIS    66       5.809  52.282  51.030  1.00 25.00           C
ATOM     67  CA  HIS    67       5.331  52.163  54.834  1.00 25.00           C
ATOM     68  CA  HIS    68       7.879  49.388  55.266  1.00 25.00           C
TER
END
