
#######################################################
#                                                     #
#                        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_4
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_4.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:    23        40 - 62          4.88    19.54
  LCS_AVERAGE:     33.49

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        18 - 25          1.98    21.55
  LONGEST_CONTINUOUS_SEGMENT:     8        40 - 47          1.77    28.61
  LONGEST_CONTINUOUS_SEGMENT:     8        50 - 57          1.70    29.75
  LCS_AVERAGE:     10.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        21 - 25          0.70    23.83
  LONGEST_CONTINUOUS_SEGMENT:     5        28 - 32          0.85    21.54
  LONGEST_CONTINUOUS_SEGMENT:     5        34 - 38          0.90    23.42
  LONGEST_CONTINUOUS_SEGMENT:     5        35 - 39          0.92    23.49
  LONGEST_CONTINUOUS_SEGMENT:     5        50 - 54          0.86    29.49
  LCS_AVERAGE:      6.53

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   14     3    3    3    3    4    5    5    6    6    6   10   10   10   11   15   16   19   20   23   27 
LCS_GDT     A       3     A       3      3    4   16     3    3    3    3    4    5    7    8   10   12   13   15   16   17   17   19   20   21   23   27 
LCS_GDT     K       4     K       4      3    4   16     3    3    3    3    4    5    6    8   10   15   17   17   19   22   24   25   28   28   30   31 
LCS_GDT     F       5     F       5      3    4   16     1    3    3    3    4    5    5    8   12   15   17   20   20   22   24   26   28   29   31   31 
LCS_GDT     L       6     L       6      3    3   16     0    3    3    3    4    5    6    8   12   15   17   20   20   22   24   25   28   29   31   31 
LCS_GDT     E       7     E       7      3    5   16     3    3    3    5    5    6   13   14   15   15   17   20   22   23   26   27   28   29   31   31 
LCS_GDT     I       8     I       8      3    6   16     3    4    4    6    8   11   13   16   21   22   24   25   25   27   27   28   28   29   31   31 
LCS_GDT     L       9     L       9      4    6   16     3    4    4    5    8   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     V      10     V      10      4    6   16     3    4    4    6    7   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     C      11     C      11      4    6   16     3    3    4    5    9   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     P      12     P      12      4    6   16     3    3    4    6    9   10   13   16   19   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     L      13     L      13      3    6   16     3    3    4    5    6   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     C      14     C      14      3    5   16     3    3    4    6    8   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     K      15     K      15      3    5   16     3    3    4    6    9   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     G      16     G      16      3    5   21     3    3    4    5    8   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     P      17     P      17      4    5   21     4    4    4    6    8   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     L      18     L      18      4    8   21     4    4    4    4    7   10   11   13   15   18   20   24   26   27   27   28   28   29   31   31 
LCS_GDT     V      19     V      19      4    8   21     4    4    4    6    7    8   11   11   12   14   17   19   22   24   25   27   27   29   29   30 
LCS_GDT     F      20     F      20      4    8   21     4    4    4    5    7   10   11   11   12   14   17   18   20   24   24   27   27   29   29   30 
LCS_GDT     D      21     D      21      5    8   21     4    4    5    6    7    8   10   11   12   15   16   18   19   21   22   23   24   26   28   29 
LCS_GDT     K      22     K      22      5    8   21     4    4    5    6    7    8    9   11   12   15   16   18   19   21   22   23   24   25   27   29 
LCS_GDT     S      23     S      23      5    8   21     4    4    5    6    7    8   10   11   12   15   16   18   19   21   22   23   25   25   26   29 
LCS_GDT     K      24     K      24      5    8   21     4    4    5    6    7    8    9   11   12   15   16   18   19   22   23   23   25   26   28   29 
LCS_GDT     D      25     D      25      5    8   21     3    4    5    6    7    8    9   10   12   15   17   20   21   24   24   26   27   29   29   30 
LCS_GDT     E      26     E      26      3    5   21     3    4    4    7    7    9   11   15   16   18   19   22   24   26   27   28   28   29   31   31 
LCS_GDT     L      27     L      27      3    6   21     0    4    7    7    9   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     I      28     I      28      5    6   21     3    4    5    5    9   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     C      29     C      29      5    6   21     4    4    5    7    7   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     K      30     K      30      5    6   21     4    4    5    5    7   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     G      31     G      31      5    6   21     4    4    5    5    6   10   13   15   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     D      32     D      32      5    6   21     4    4    5    7    7   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     R      33     R      33      3    6   21     3    3    5    7    7   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     L      34     L      34      5    6   21     3    4    7    7    7   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     A      35     A      35      5    6   21     4    4    7    7    7   10   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     F      36     F      36      5    6   21     4    4    7    7    8   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     P      37     P      37      5    6   18     4    4    7    7    9   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     I      38     I      38      5    6   18     4    4    7    7    9   11   13   16   21   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     K      39     K      39      5    6   18     3    4    7    7    9   10   10   16   19   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     D      40     D      40      4    8   23     3    4    6    6    9   10   13   16   19   22   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     G      41     G      41      4    8   23     3    4    5    7    7   10   10   16   18   20   24   25   26   27   27   28   28   29   31   31 
LCS_GDT     I      42     I      42      4    8   23     3    4    6    6    7    8   10   13   17   20   21   23   26   27   27   28   28   29   31   31 
LCS_GDT     P      43     P      43      4    8   23     3    5    6    6    8    9    9   13   14   15   17   20   21   22   23   23   24   27   27   29 
LCS_GDT     M      44     M      44      4    8   23     3    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     M      45     M      45      4    8   23     3    5    6    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   26 
LCS_GDT     L      46     L      46      4    8   23     3    5    6    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      47     E      47      4    8   23     3    4    6    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     S      48     S      48      4    7   23     4    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      49     E      49      4    5   23     4    4    4    4    5    6    8   10   12   13   15   18   21   22   23   23   24   25   26   28 
LCS_GDT     A      50     A      50      5    8   23     4    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     R      51     R      51      5    8   23     4    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      52     E      52      5    8   23     3    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     L      53     L      53      5    8   23     3    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     A      54     A      54      5    8   23     3    4    5    5    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     P      55     P      55      3    8   23     3    5    5    6    8    9   10   13   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      56     E      56      3    8   23     3    3    5    6    8    8    8   11   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      57     E      57      3    8   23     3    3    3    4    8    8    8    9   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      58     E      58      3    5   23     3    3    4    4    5    7   10   11   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     V      59     V      59      3    5   23     3    3    3    4    5    7   10   11   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     K      60     K      60      3    5   23     3    3    3    4    4    7   10   11   14   16   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     L      61     L      61      3    4   23     3    3    3    4    4    7    9   11   14   17   18   20   21   22   23   23   24   25   26   28 
LCS_GDT     E      62     E      62      3    4   23     1    3    3    3    4    5    6    8    8    9   16   16   21   22   23   23   24   25   26   28 
LCS_AVERAGE  LCS_A:  16.83  (   6.53   10.48   33.49 )

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      7      7      9     11     13     16     21     22     24     25     26     27     27     28     28     29     31     31 
GDT PERCENT_CA   6.56   8.20  11.48  11.48  14.75  18.03  21.31  26.23  34.43  36.07  39.34  40.98  42.62  44.26  44.26  45.90  45.90  47.54  50.82  50.82
GDT RMS_LOCAL    0.14   0.61   1.06   1.06   2.03   2.06   2.32   2.84   3.48   3.54   3.85   4.02   4.24   7.49   4.32   4.52   4.52   4.92   5.60   5.84
GDT RMS_ALL_CA  22.87  30.51  23.40  23.40  21.32  23.86  23.86  23.23  22.37  22.38  23.02  23.10  22.90  22.90  23.10  23.03  23.03  23.27  23.70  23.94

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         23.444
LGA    A       3      A       3         20.987
LGA    K       4      K       4         13.428
LGA    F       5      F       5         10.854
LGA    L       6      L       6         11.365
LGA    E       7      E       7          7.557
LGA    I       8      I       8          3.082
LGA    L       9      L       9          0.695
LGA    V      10      V      10          3.945
LGA    C      11      C      11          3.216
LGA    P      12      P      12          5.210
LGA    L      13      L      13          3.182
LGA    C      14      C      14          3.637
LGA    K      15      K      15          2.035
LGA    G      16      G      16          3.262
LGA    P      17      P      17          2.643
LGA    L      18      L      18          6.198
LGA    V      19      V      19         13.108
LGA    F      20      F      20         14.518
LGA    D      21      D      21         19.246
LGA    K      22      K      22         19.009
LGA    S      23      S      23         20.959
LGA    K      24      K      24         18.356
LGA    D      25      D      25         12.879
LGA    E      26      E      26          7.239
LGA    L      27      L      27          3.057
LGA    I      28      I      28          5.446
LGA    C      29      C      29          5.465
LGA    K      30      K      30          6.098
LGA    G      31      G      31          5.439
LGA    D      32      D      32          7.013
LGA    R      33      R      33          3.532
LGA    L      34      L      34          2.111
LGA    A      35      A      35          2.895
LGA    F      36      F      36          2.190
LGA    P      37      P      37          3.742
LGA    I      38      I      38          3.942
LGA    K      39      K      39          7.035
LGA    D      40      D      40          9.560
LGA    G      41      G      41         11.778
LGA    I      42      I      42         11.385
LGA    P      43      P      43         15.975
LGA    M      44      M      44         17.376
LGA    M      45      M      45         20.873
LGA    L      46      L      46         23.150
LGA    E      47      E      47         28.729
LGA    S      48      S      48         30.279
LGA    E      49      E      49         29.950
LGA    A      50      A      50         31.013
LGA    R      51      R      51         31.789
LGA    E      52      E      52         38.586
LGA    L      53      L      53         40.905
LGA    A      54      A      54         45.522
LGA    P      55      P      55         50.390
LGA    E      56      E      56         48.416
LGA    E      57      E      57         44.140
LGA    E      58      E      58         47.203
LGA    V      59      V      59         45.401
LGA    K      60      K      60         40.957
LGA    L      61      L      61         41.648
LGA    E      62      E      62         42.929

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     16    2.84    22.951    21.329     0.544

LGA_LOCAL      RMSD =  2.842  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 22.952  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 14.889  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.644046 * X  +   0.564078 * Y  +  -0.516741 * Z  +   6.881823
  Y_new =   0.697908 * X  +   0.709865 * Y  +  -0.094952 * Z  +  33.802994
  Z_new =   0.313257 * X  +  -0.421791 * Y  +  -0.850860 * Z  +  46.044010 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.681372    0.460220  [ DEG:  -153.6313     26.3687 ]
  Theta =  -0.318620   -2.822972  [ DEG:   -18.2556   -161.7444 ]
  Phi   =   2.316079   -0.825514  [ DEG:   132.7016    -47.2985 ]
 
# 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_4                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_4.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   2.84  21.329    14.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_4
PFRMAT TS
TARGET T0348
MODEL 4
PARENT N/A
ATOM      1  CA  MET     1      13.973  34.321  44.047  1.00 25.00           C
ATOM      2  CA  ASP     2      15.875  34.771  47.271  1.00 25.00           C
ATOM      3  CA  ALA     3      15.940  36.554  50.576  1.00 25.00           C
ATOM      4  CA  LYS     4      12.588  38.385  50.291  1.00 25.00           C
ATOM      5  CA  PHE     5      10.723  35.159  51.179  1.00 25.00           C
ATOM      6  CA  LEU     6      12.998  34.652  54.218  1.00 25.00           C
ATOM      7  CA  GLU     7      12.347  38.257  55.337  1.00 25.00           C
ATOM      8  CA  ILE     8       8.573  37.714  54.972  1.00 25.00           C
ATOM      9  CA  LEU     9       8.810  34.501  57.043  1.00 25.00           C
ATOM     10  CA  VAL    10      10.964  31.334  57.384  1.00 25.00           C
ATOM     11  CA  CYS    11       7.584  29.538  57.259  1.00 25.00           C
ATOM     12  CA  PRO    12       8.183  27.883  60.681  1.00 25.00           C
ATOM     13  CA  LEU    13       5.673  25.590  62.322  1.00 25.00           C
ATOM     14  CA  CYS    14       3.637  28.655  63.485  1.00 25.00           C
ATOM     15  CA  LYS    15       6.881  29.687  65.252  1.00 25.00           C
ATOM     16  CA  GLY    16      10.047  27.712  65.610  1.00 25.00           C
ATOM     17  CA  PRO    17      11.690  30.437  63.448  1.00 25.00           C
ATOM     18  CA  LEU    18       9.589  33.167  61.838  1.00 25.00           C
ATOM     19  CA  VAL    19       5.968  34.335  61.865  1.00 25.00           C
ATOM     20  CA  PHE    20       3.881  32.957  59.075  1.00 25.00           C
ATOM     21  CA  ASP    21       0.874  30.806  59.892  1.00 25.00           C
ATOM     22  CA  LYS    22       2.676  27.946  58.091  1.00 25.00           C
ATOM     23  CA  SER    23       0.030  27.988  55.322  1.00 25.00           C
ATOM     24  CA  LYS    24       0.635  31.729  54.767  1.00 25.00           C
ATOM     25  CA  ASP    25       4.335  32.091  53.878  1.00 25.00           C
ATOM     26  CA  GLU    26       5.516  28.640  52.612  1.00 25.00           C
ATOM     27  CA  LEU    27       9.279  29.234  52.491  1.00 25.00           C
ATOM     28  CA  ILE    28      13.108  29.241  52.577  1.00 25.00           C
ATOM     29  CA  CYS    29      13.094  25.954  54.542  1.00 25.00           C
ATOM     30  CA  LYS    30      14.616  27.723  57.548  1.00 25.00           C
ATOM     31  CA  GLY    31      12.793  25.764  60.223  1.00 25.00           C
ATOM     32  CA  ASP    32      14.416  22.616  58.798  1.00 25.00           C
ATOM     33  CA  ARG    33      11.248  21.246  57.234  1.00 25.00           C
ATOM     34  CA  LEU    34       8.293  22.802  59.089  1.00 25.00           C
ATOM     35  CA  ALA    35       7.822  24.747  55.799  1.00 25.00           C
ATOM     36  CA  PHE    36       6.370  23.519  52.463  1.00 25.00           C
ATOM     37  CA  PRO    37       9.235  23.180  49.968  1.00 25.00           C
ATOM     38  CA  ILE    38       9.473  25.560  46.960  1.00 25.00           C
ATOM     39  CA  LYS    39       7.969  22.928  44.663  1.00 25.00           C
ATOM     40  CA  ASP    40       4.362  22.936  43.434  1.00 25.00           C
ATOM     41  CA  GLY    41       1.284  24.697  42.139  1.00 25.00           C
ATOM     42  CA  ILE    42       2.964  26.078  39.069  1.00 25.00           C
ATOM     43  CA  PRO    43       4.638  24.611  36.002  1.00 25.00           C
ATOM     44  CA  MET    44       6.408  27.230  33.946  1.00 25.00           C
ATOM     45  CA  MET    45       4.793  30.713  33.760  1.00 25.00           C
ATOM     46  CA  LEU    46       8.318  32.230  33.760  1.00 25.00           C
ATOM     47  CA  GLU    47      11.363  33.904  32.212  1.00 25.00           C
ATOM     48  CA  SER    48      11.807  32.031  28.899  1.00 25.00           C
ATOM     49  CA  GLU    49      11.387  34.339  25.896  1.00 25.00           C
ATOM     50  CA  ALA    50       8.422  32.150  25.078  1.00 25.00           C
ATOM     51  CA  ARG    51       5.051  33.973  25.482  1.00 25.00           C
ATOM     52  CA  GLU    52       3.891  36.899  23.357  1.00 25.00           C
ATOM     53  CA  LEU    53       5.506  40.322  22.937  1.00 25.00           C
ATOM     54  CA  ALA    54       2.766  42.697  21.629  1.00 25.00           C
ATOM     55  CA  PRO    55       2.229  46.293  22.770  1.00 25.00           C
ATOM     56  CA  GLU    56       5.990  46.729  22.771  1.00 25.00           C
ATOM     57  CA  GLU    57       8.215  47.904  25.606  1.00 25.00           C
ATOM     58  CA  GLU    58       7.078  50.817  27.751  1.00 25.00           C
ATOM     59  CA  VAL    59       7.317  49.397  31.248  1.00 25.00           C
ATOM     60  CA  LYS    60       8.503  50.514  34.695  1.00 25.00           C
ATOM     61  CA  LEU    61       4.972  51.569  35.522  1.00 25.00           C
ATOM     62  CA  GLU    62       3.878  50.093  38.908  1.00 25.00           C
ATOM     63  CA  HIS    63       0.973  48.295  40.551  1.00 25.00           C
ATOM     64  CA  HIS    64      -2.516  47.843  39.008  1.00 25.00           C
ATOM     65  CA  HIS    65      -6.102  46.468  38.844  1.00 25.00           C
ATOM     66  CA  HIS    66      -4.984  42.869  39.016  1.00 25.00           C
ATOM     67  CA  HIS    67      -5.671  42.576  42.774  1.00 25.00           C
ATOM     68  CA  HIS    68      -2.589  43.220  44.990  1.00 25.00           C
TER
END
