
#######################################################
#                                                     #
#                        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_1
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_1.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          5.00    24.76
  LONGEST_CONTINUOUS_SEGMENT:    21        41 - 61          4.96    23.91
  LONGEST_CONTINUOUS_SEGMENT:    21        42 - 62          4.95    22.30
  LCS_AVERAGE:     29.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        18 - 25          1.54    20.78
  LCS_AVERAGE:      9.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        10 - 14          0.79    24.09
  LONGEST_CONTINUOUS_SEGMENT:     5        18 - 22          0.80    19.94
  LONGEST_CONTINUOUS_SEGMENT:     5        21 - 25          0.91    23.57
  LONGEST_CONTINUOUS_SEGMENT:     5        52 - 56          0.68    24.57
  LONGEST_CONTINUOUS_SEGMENT:     5        53 - 57          0.99    23.74
  LCS_AVERAGE:      6.48

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   17     3    3    3    3    4    5    5    6    6    7    8   10   12   13   15   22   25   26   26   27 
LCS_GDT     A       3     A       3      3    4   17     3    4    5    5    5    5    5    6    7    9   12   16   19   20   24   24   27   27   28   30 
LCS_GDT     K       4     K       4      3    4   17     3    3    3    4    7    8   11   14   16   17   19   20   21   23   24   24   27   27   29   30 
LCS_GDT     F       5     F       5      3    4   17     1    3    3    7    8    9   11   14   16   17   19   20   21   23   24   25   27   27   29   30 
LCS_GDT     L       6     L       6      3    3   17     1    3    4    7    8    9   11   14   16   17   19   20   21   23   24   25   27   27   29   30 
LCS_GDT     E       7     E       7      4    6   17     3    4    4    6    7    9   11   15   15   17   19   20   21   23   24   25   27   27   29   30 
LCS_GDT     I       8     I       8      4    7   17     3    4    4    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     L       9     L       9      4    7   17     3    4    4    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     V      10     V      10      5    7   17     3    4    5    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     C      11     C      11      5    7   17     3    4    5    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     P      12     P      12      5    7   17     3    4    5    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     L      13     L      13      5    7   17     3    4    5    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     C      14     C      14      5    7   17     3    4    5    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     K      15     K      15      4    5   17     3    4    5    6    8    8   11   12   14   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     G      16     G      16      4    5   17     3    4    4    6    7    9   11   12   14   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     P      17     P      17      3    6   17     1    3    4    6    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     L      18     L      18      5    8   17     3    5    6    7    8    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     V      19     V      19      5    8   16     3    5    6    7    8    8    9   10   10   11   14   15   17   20   21   23   25   26   29   30 
LCS_GDT     F      20     F      20      5    8   15     3    5    6    7    8    8    9   10   10   11   14   15   16   19   20   23   23   25   26   27 
LCS_GDT     D      21     D      21      5    8   15     3    5    6    7    8    8    9   10   10   11   14   15   16   19   20   22   23   25   26   27 
LCS_GDT     K      22     K      22      5    8   15     3    5    6    7    8    8    9   10   10   11   12   13   15   17   19   19   22   25   26   27 
LCS_GDT     S      23     S      23      5    8   15     3    4    6    7    8    8    9   10   10   11   12   13   15   17   19   19   23   25   26   27 
LCS_GDT     K      24     K      24      5    8   15     3    4    6    7    8    8    9   10   10   11   14   17   18   20   20   22   23   25   26   27 
LCS_GDT     D      25     D      25      5    8   15     3    5    6    7    8    8    9   10   10   11   14   17   18   20   20   22   23   25   26   27 
LCS_GDT     E      26     E      26      3    4   17     3    3    4    4    5    5    7    9   10   13   15   18   18   20   20   22   23   25   26   29 
LCS_GDT     L      27     L      27      3    4   17     3    3    4    6    6    6   11   11   13   14   15   18   18   20   20   22   24   25   29   30 
LCS_GDT     I      28     I      28      3    5   17     3    3    5    6    8   10   10   11   13   14   15   18   18   20   20   23   24   26   29   30 
LCS_GDT     C      29     C      29      3    5   17     3    3    5    6    8   10   10   11   13   15   17   18   19   22   23   25   27   27   29   30 
LCS_GDT     K      30     K      30      4    6   17     3    4    5    6    8    8    9   11   13   14   15   18   18   20   20   22   23   25   28   29 
LCS_GDT     G      31     G      31      4    6   17     3    4    5    5    8   10   10   11   12   12   13   18   18   18   19   23   23   25   27   29 
LCS_GDT     D      32     D      32      4    6   17     3    4    5    6    8   10   10   11   13   15   17   18   19   22   23   25   27   27   29   30 
LCS_GDT     R      33     R      33      4    6   17     3    4    4    5    7   10   10   11   12   15   17   18   20   22   23   25   27   27   29   30 
LCS_GDT     L      34     L      34      4    6   17     3    4    4    5    8   10   10   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     A      35     A      35      4    7   17     3    4    4    5    8   10   10   11   12   13   17   19   21   23   24   25   27   27   29   30 
LCS_GDT     F      36     F      36      4    7   17     3    4    4    7    8   10   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     P      37     P      37      3    7   17     3    3    4    5    8   10   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     I      38     I      38      3    7   17     2    3    4    6    7    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     K      39     K      39      3    7   17     2    3    4    6    7    9   11   15   15   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     D      40     D      40      3    7   21     3    3    3    4    6    7    9   11   14   16   18   20   21   23   24   25   27   27   29   30 
LCS_GDT     G      41     G      41      4    7   21     3    4    5    5    6    7    9   10   12   14   17   18   20   23   24   25   27   27   29   30 
LCS_GDT     I      42     I      42      4    6   21     3    3    5    5    8   10   10   11   13   14   16   18   19   20   23   25   27   27   28   29 
LCS_GDT     P      43     P      43      4    6   21     3    4    5    5    5    7   10   10   13   14   16   18   19   20   23   24   24   25   25   25 
LCS_GDT     M      44     M      44      4    6   21     3    4    5    5    5    7   10   10   13   14   16   18   19   20   23   24   24   25   25   25 
LCS_GDT     M      45     M      45      4    6   21     3    5    5    6    6    7   10   11   13   15   16   18   19   20   23   24   24   25   25   25 
LCS_GDT     L      46     L      46      4    6   21     3    5    5    6    6    7    9   10   14   15   18   20   20   21   23   24   24   25   25   25 
LCS_GDT     E      47     E      47      4    6   21     3    5    5    6    6    8   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     S      48     S      48      4    6   21     3    5    5    6    6    7    9   10   10   12   14   15   16   21   22   22   23   25   25   25 
LCS_GDT     E      49     E      49      3    5   21     3    3    3    4    4    7   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     A      50     A      50      3    5   21     3    3    4    6    6   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     R      51     R      51      3    5   21     3    5    5    6    6   10   10   13   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     E      52     E      52      5    6   21     3    5    6    6    7   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     L      53     L      53      5    6   21     3    5    6    6    7   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     A      54     A      54      5    6   21     3    5    6    6    8   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     P      55     P      55      5    6   21     3    5    6    7    8   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     E      56     E      56      5    6   21     3    5    6    7    8   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     E      57     E      57      5    6   21     3    3    6    7    8   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     E      58     E      58      3    4   21     3    3    3    3    4    4    8   11   14   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     V      59     V      59      3    4   21     3    3    4    7    8   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     K      60     K      60      3    3   21     3    3    4    7    8   10   11   14   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     L      61     L      61      3    3   21     3    3    3    3    4    5    9   13   16   17   19   20   20   21   23   24   24   25   25   25 
LCS_GDT     E      62     E      62      3    3   21     3    3    3    4    5    7    8   11   14   17   19   20   20   21   23   24   24   25   25   25 
LCS_AVERAGE  LCS_A:  15.39  (   6.48    9.70   29.99 )

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      5      6      7      8     10     11     15     16     17     19     20     21     23     24     25     27     27     29     30 
GDT PERCENT_CA   4.92   8.20   9.84  11.48  13.11  16.39  18.03  24.59  26.23  27.87  31.15  32.79  34.43  37.70  39.34  40.98  44.26  44.26  47.54  49.18
GDT RMS_LOCAL    0.02   0.56   0.81   1.16   1.54   2.15   2.40   3.01   3.15   3.36   3.74   3.90   4.08   4.45   4.62   5.08   5.42   5.42   6.14   6.26
GDT RMS_ALL_CA  28.24  28.79  19.90  20.15  20.78  22.99  19.80  21.23  20.06  20.05  19.79  19.83  21.62  21.99  22.22  22.57  22.54  22.54  22.34  22.45

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         12.113
LGA    A       3      A       3          9.392
LGA    K       4      K       4          8.244
LGA    F       5      F       5          7.461
LGA    L       6      L       6          5.818
LGA    E       7      E       7          3.309
LGA    I       8      I       8          1.460
LGA    L       9      L       9          1.898
LGA    V      10      V      10          3.921
LGA    C      11      C      11          2.653
LGA    P      12      P      12          3.359
LGA    L      13      L      13          2.643
LGA    C      14      C      14          3.569
LGA    K      15      K      15          6.863
LGA    G      16      G      16          6.257
LGA    P      17      P      17          3.339
LGA    L      18      L      18          3.701
LGA    V      19      V      19         10.308
LGA    F      20      F      20         14.941
LGA    D      21      D      21         20.360
LGA    K      22      K      22         24.422
LGA    S      23      S      23         27.526
LGA    K      24      K      24         24.600
LGA    D      25      D      25         18.465
LGA    E      26      E      26         16.790
LGA    L      27      L      27         12.896
LGA    I      28      I      28         11.522
LGA    C      29      C      29          9.626
LGA    K      30      K      30         15.383
LGA    G      31      G      31         16.661
LGA    D      32      D      32         10.837
LGA    R      33      R      33          9.201
LGA    L      34      L      34          3.782
LGA    A      35      A      35          5.116
LGA    F      36      F      36          3.426
LGA    P      37      P      37          3.370
LGA    I      38      I      38          0.639
LGA    K      39      K      39          1.690
LGA    D      40      D      40          6.358
LGA    G      41      G      41          8.757
LGA    I      42      I      42         10.141
LGA    P      43      P      43         14.029
LGA    M      44      M      44         18.259
LGA    M      45      M      45         22.706
LGA    L      46      L      46         24.360
LGA    E      47      E      47         28.911
LGA    S      48      S      48         31.388
LGA    E      49      E      49         29.766
LGA    A      50      A      50         31.722
LGA    R      51      R      51         35.873
LGA    E      52      E      52         41.120
LGA    L      53      L      53         39.576
LGA    A      54      A      54         43.370
LGA    P      55      P      55         43.067
LGA    E      56      E      56         42.750
LGA    E      57      E      57         38.037
LGA    E      58      E      58         39.103
LGA    V      59      V      59         36.121
LGA    K      60      K      60         29.143
LGA    L      61      L      61         29.269
LGA    E      62      E      62         27.557

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     15    3.01    21.311    18.481     0.483

LGA_LOCAL      RMSD =  3.007  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 21.233  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 15.067  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.335231 * X  +   0.881117 * Y  +   0.333545 * Z  +  12.359461
  Y_new =  -0.539561 * X  +  -0.110670 * Y  +   0.834641 * Z  +  34.183548
  Z_new =   0.772330 * X  +  -0.459765 * Y  +   0.438317 * Z  +  49.110458 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.809276    2.332316  [ DEG:   -46.3681    133.6319 ]
  Theta =  -0.882501   -2.259091  [ DEG:   -50.5636   -129.4364 ]
  Phi   =  -1.014861    2.126732  [ DEG:   -58.1472    121.8528 ]
 
# 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_1                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_1.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   15   3.01  18.481    15.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_1
PFRMAT TS
TARGET T0348
MODEL 1
PARENT N/A
ATOM      1  CA  MET     1       3.502  38.903  45.774  1.00 25.00           C
ATOM      2  CA  ASP     2       0.913  39.367  48.596  1.00 25.00           C
ATOM      3  CA  ALA     3       3.923  40.575  50.594  1.00 25.00           C
ATOM      4  CA  LYS     4       3.362  40.502  54.382  1.00 25.00           C
ATOM      5  CA  PHE     5       3.275  36.673  54.319  1.00 25.00           C
ATOM      6  CA  LEU     6       6.538  36.608  52.315  1.00 25.00           C
ATOM      7  CA  GLU     7       8.162  38.990  54.835  1.00 25.00           C
ATOM      8  CA  ILE     8       7.007  36.759  57.725  1.00 25.00           C
ATOM      9  CA  LEU     9       8.455  33.682  55.963  1.00 25.00           C
ATOM     10  CA  VAL    10       5.786  31.627  57.782  1.00 25.00           C
ATOM     11  CA  CYS    11       4.627  28.805  60.045  1.00 25.00           C
ATOM     12  CA  PRO    12       2.333  27.635  62.893  1.00 25.00           C
ATOM     13  CA  LEU    13       5.531  28.126  64.920  1.00 25.00           C
ATOM     14  CA  CYS    14       9.226  28.351  64.061  1.00 25.00           C
ATOM     15  CA  LYS    15       8.449  25.640  61.579  1.00 25.00           C
ATOM     16  CA  GLY    16      12.193  25.472  61.195  1.00 25.00           C
ATOM     17  CA  PRO    17      11.804  28.996  59.812  1.00 25.00           C
ATOM     18  CA  LEU    18      11.837  32.795  59.601  1.00 25.00           C
ATOM     19  CA  VAL    19       9.815  33.237  62.734  1.00 25.00           C
ATOM     20  CA  PHE    20       5.983  33.455  62.495  1.00 25.00           C
ATOM     21  CA  ASP    21       2.886  35.534  61.624  1.00 25.00           C
ATOM     22  CA  LYS    22       0.600  32.793  63.063  1.00 25.00           C
ATOM     23  CA  SER    23      -2.765  31.665  61.625  1.00 25.00           C
ATOM     24  CA  LYS    24      -2.850  34.743  59.346  1.00 25.00           C
ATOM     25  CA  ASP    25      -0.243  33.010  57.235  1.00 25.00           C
ATOM     26  CA  GLU    26      -3.211  30.993  55.815  1.00 25.00           C
ATOM     27  CA  LEU    27      -0.800  30.518  52.869  1.00 25.00           C
ATOM     28  CA  ILE    28       3.009  30.772  52.567  1.00 25.00           C
ATOM     29  CA  CYS    29       3.425  27.994  55.171  1.00 25.00           C
ATOM     30  CA  LYS    30       1.182  25.544  53.434  1.00 25.00           C
ATOM     31  CA  GLY    31      -1.673  25.917  55.984  1.00 25.00           C
ATOM     32  CA  ASP    32      -0.676  24.909  59.513  1.00 25.00           C
ATOM     33  CA  ARG    33       2.686  23.693  58.211  1.00 25.00           C
ATOM     34  CA  LEU    34       6.235  24.254  57.151  1.00 25.00           C
ATOM     35  CA  ALA    35       8.317  27.312  56.349  1.00 25.00           C
ATOM     36  CA  PHE    36       7.796  28.891  52.898  1.00 25.00           C
ATOM     37  CA  PRO    37      10.002  27.036  50.389  1.00 25.00           C
ATOM     38  CA  ILE    38       7.882  28.996  47.826  1.00 25.00           C
ATOM     39  CA  LYS    39       5.554  28.009  44.973  1.00 25.00           C
ATOM     40  CA  ASP    40       8.763  26.630  43.463  1.00 25.00           C
ATOM     41  CA  GLY    41      12.289  25.587  42.571  1.00 25.00           C
ATOM     42  CA  ILE    42      12.944  28.886  40.763  1.00 25.00           C
ATOM     43  CA  PRO    43      11.939  29.470  37.155  1.00 25.00           C
ATOM     44  CA  MET    44      12.279  32.560  34.934  1.00 25.00           C
ATOM     45  CA  MET    45      16.032  32.194  35.719  1.00 25.00           C
ATOM     46  CA  LEU    46      15.802  35.520  37.622  1.00 25.00           C
ATOM     47  CA  GLU    47      14.617  38.797  36.073  1.00 25.00           C
ATOM     48  CA  SER    48      16.564  41.998  36.932  1.00 25.00           C
ATOM     49  CA  GLU    49      14.615  43.628  34.100  1.00 25.00           C
ATOM     50  CA  ALA    50      15.366  41.220  31.243  1.00 25.00           C
ATOM     51  CA  ARG    51      18.443  41.905  29.165  1.00 25.00           C
ATOM     52  CA  GLU    52      19.840  45.389  29.422  1.00 25.00           C
ATOM     53  CA  LEU    53      22.266  46.127  32.239  1.00 25.00           C
ATOM     54  CA  ALA    54      25.105  45.833  29.774  1.00 25.00           C
ATOM     55  CA  PRO    55      27.678  43.245  30.979  1.00 25.00           C
ATOM     56  CA  GLU    56      29.252  46.380  32.536  1.00 25.00           C
ATOM     57  CA  GLU    57      28.875  46.574  36.316  1.00 25.00           C
ATOM     58  CA  GLU    58      31.620  46.828  38.978  1.00 25.00           C
ATOM     59  CA  VAL    59      32.896  43.238  38.969  1.00 25.00           C
ATOM     60  CA  LYS    60      31.743  41.821  42.274  1.00 25.00           C
ATOM     61  CA  LEU    61      35.114  39.958  42.378  1.00 25.00           C
ATOM     62  CA  GLU    62      33.311  37.555  44.701  1.00 25.00           C
ATOM     63  CA  HIS    63      32.938  33.807  44.140  1.00 25.00           C
ATOM     64  CA  HIS    64      31.052  30.457  44.430  1.00 25.00           C
ATOM     65  CA  HIS    65      29.705  31.124  47.931  1.00 25.00           C
ATOM     66  CA  HIS    66      27.894  33.295  50.450  1.00 25.00           C
ATOM     67  CA  HIS    67      27.262  35.667  53.338  1.00 25.00           C
ATOM     68  CA  HIS    68      25.197  38.905  53.319  1.00 25.00           C
TER
END
