
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS168_5.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          4.71    24.18
  LCS_AVERAGE:     33.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        50 - 57          1.81    34.04
  LCS_AVERAGE:      9.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        50 - 54          0.71    33.58
  LCS_AVERAGE:      5.78

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    8     0    3    3    3    3    5    5    6    6    6    6    8    9   12   12   17   19   19   23   25 
LCS_GDT     A       3     A       3      3    3   16     1    3    3    3    3    5    5    6    7    9   10   12   12   13   24   25   27   32   33   37 
LCS_GDT     K       4     K       4      3    3   18     0    3    4    4    4    5    5    6    8   11   14   17   20   22   27   30   33   34   35   37 
LCS_GDT     F       5     F       5      3    3   18     1    3    4    4    4    5    5    6   10   12   14   17   20   25   27   31   33   34   35   37 
LCS_GDT     L       6     L       6      3    3   18     0    3    4    4    5    6    6    8   10   14   16   19   23   27   30   31   33   34   35   37 
LCS_GDT     E       7     E       7      4    5   18     3    4    5    5    6    7    9   12   16   17   19   21   25   27   30   31   33   34   35   37 
LCS_GDT     I       8     I       8      4    5   18     3    4    5    6    7    8    9   11   15   17   19   21   25   27   30   31   33   34   35   37 
LCS_GDT     L       9     L       9      4    5   18     3    4    5    6    7    8    9   12   16   17   19   21   25   27   30   31   33   34   35   37 
LCS_GDT     V      10     V      10      4    5   18     3    4    5    7    9    9   11   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     C      11     C      11      4    5   18     3    4    5    8    9   10   12   13   16   20   20   22   24   26   30   31   33   34   35   37 
LCS_GDT     P      12     P      12      4    5   18     3    4    4    6    7    8    9   12   13   16   18   20   21   22   25   26   30   32   35   37 
LCS_GDT     L      13     L      13      3    5   18     3    3    4    5    6    8    9   12   15   17   19   20   24   25   29   31   33   34   35   37 
LCS_GDT     C      14     C      14      3    5   18     3    3    5    7    9    9   11   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     K      15     K      15      3    5   18     1    3    4    7    9    9   11   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     G      16     G      16      3    5   18     0    3    4    5    6    7    8   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     P      17     P      17      3    5   18     3    3    3    4    6    7    8   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     L      18     L      18      3    5   19     3    4    5    5    6    7    8   12   16   19   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     V      19     V      19      4    5   19     3    3    4    5    5    7    9   10   11   15   19   20   25   27   30   31   33   34   35   37 
LCS_GDT     F      20     F      20      4    5   19     3    3    4    5    5    7    9   10   15   16   19   21   25   27   30   31   33   34   35   37 
LCS_GDT     D      21     D      21      4    7   19     3    3    4    6    6    8    9   10   15   16   19   21   25   27   30   31   33   34   35   37 
LCS_GDT     K      22     K      22      4    7   19     3    3    4    5    7    8    9   10   11   13   17   21   25   27   30   31   33   34   35   37 
LCS_GDT     S      23     S      23      3    7   19     3    3    4    5    7    8    9   10   11   13   15   17   22   24   25   26   31   34   35   36 
LCS_GDT     K      24     K      24      3    7   19     3    3    4    5    7    8    9   10   11   13   15   18   22   24   29   31   33   34   35   37 
LCS_GDT     D      25     D      25      3    7   19     3    3    4    4    7    8    9   10   11   13   15   19   23   27   30   31   33   34   35   37 
LCS_GDT     E      26     E      26      3    7   19     3    3    4    5    7    8    9   11   16   19   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     L      27     L      27      3    7   19     3    3    6    8    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     I      28     I      28      3    7   19     3    3    6    8    9   10   12   13   18   20   20   22   24   27   30   31   33   34   35   37 
LCS_GDT     C      29     C      29      4    6   19     4    4    6    8    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     K      30     K      30      4    6   19     4    4    6    8    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     G      31     G      31      4    6   19     4    4    5    6    7    9   12   13   16   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     D      32     D      32      4    6   19     4    4    5    6    7    7    9   11   16   17   19   21   24   27   30   31   33   34   35   37 
LCS_GDT     R      33     R      33      3    5   19     3    3    3    6    7   10   12   13   18   20   20   22   23   26   29   31   32   34   35   36 
LCS_GDT     L      34     L      34      3    6   19     3    3    5    8    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     A      35     A      35      4    6   19     3    3    4    6    8   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     F      36     F      36      4    6   19     3    3    6    8    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     P      37     P      37      4    6   18     3    3    4    7    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     I      38     I      38      4    6   22     3    3    5    7    9   10   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     K      39     K      39      4    6   24     3    3    4    6    7    8   12   13   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     D      40     D      40      4    5   24     3    3    4    4    6   10   11   12   18   20   20   22   25   27   30   31   33   34   35   37 
LCS_GDT     G      41     G      41      3    5   24     3    3    6    8    9   10   12   13   18   20   20   22   24   27   30   31   33   34   35   37 
LCS_GDT     I      42     I      42      3    5   24     3    3    3    4    5   10   12   13   15   16   20   21   23   26   29   31   32   34   35   37 
LCS_GDT     P      43     P      43      3    5   24     3    3    4    4    6   10   11   12   15   16   19   20   22   24   24   24   25   25   27   28 
LCS_GDT     M      44     M      44      3    5   24     3    3    4    6    6   10   11   12   15   16   19   20   22   24   24   24   25   25   27   28 
LCS_GDT     M      45     M      45      3    5   24     3    3    4    6    6    8    9   10   12   15   17   20   22   24   24   24   25   25   25   27 
LCS_GDT     L      46     L      46      3    5   24     3    3    4    6    6    8    9   11   13   15   17   20   22   24   24   24   25   25   25   25 
LCS_GDT     E      47     E      47      3    6   24     3    3    4    5    6    8    9   11   14   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     S      48     S      48      4    6   24     3    3    4    6    6    8    9   10   13   15   17   19   22   24   24   24   25   25   25   25 
LCS_GDT     E      49     E      49      4    6   24     3    3    4    5    6    6    9    9   11   15   17   19   22   24   24   24   25   25   25   25 
LCS_GDT     A      50     A      50      5    8   24     4    5    5    5    6    8   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     R      51     R      51      5    8   24     4    5    5    6    6   10   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     E      52     E      52      5    8   24     4    5    5    6    6   10   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     L      53     L      53      5    8   24     4    5    5    5    6   10   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     A      54     A      54      5    8   24     3    5    5    5    6   10   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     P      55     P      55      3    8   24     3    3    4    4    6    8    9   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     E      56     E      56      3    8   24     3    4    5    5    6    8   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     E      57     E      57      3    8   24     3    3    3    4    5    8    9   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     E      58     E      58      3    5   24     3    3    3    4    5    7    9   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     V      59     V      59      3    5   24     3    3    3    4    5   10   11   12   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     K      60     K      60      3    5   24     3    3    3    4    5    6    8   10   15   16   17   19   20   24   24   24   25   25   25   25 
LCS_GDT     L      61     L      61      3    4   24     3    3    3    4    4    6    7   11   15   16   19   20   22   24   24   24   25   25   25   25 
LCS_GDT     E      62     E      62      3    4   24     0    3    3    4    5    5    7    9   14   16   19   20   22   24   24   24   25   25   25   25 
LCS_AVERAGE  LCS_A:  16.25  (   5.78    9.30   33.67 )

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      8      9     10     12     13     18     20     20     22     25     27     30     31     33     34     35     37 
GDT PERCENT_CA   6.56   8.20   9.84  13.11  14.75  16.39  19.67  21.31  29.51  32.79  32.79  36.07  40.98  44.26  49.18  50.82  54.10  55.74  57.38  60.66
GDT RMS_LOCAL    0.20   0.71   1.17   1.38   1.58   1.75   2.27   2.47   3.43   3.59   3.59   3.94   4.94   5.05   5.52   5.58   5.81   6.00   6.13   6.45
GDT RMS_ALL_CA  23.27  33.58  23.25  23.21  23.35  23.38  23.28  23.19  22.85  22.81  22.81  22.64  21.53  21.38  21.84  21.88  21.91  22.03  22.07  22.09

#      Molecule1      Molecule2       DISTANCE
LGA    D       2      D       2         24.757
LGA    A       3      A       3         23.316
LGA    K       4      K       4         23.770
LGA    F       5      F       5         17.911
LGA    L       6      L       6         17.950
LGA    E       7      E       7         18.502
LGA    I       8      I       8         17.562
LGA    L       9      L       9         12.816
LGA    V      10      V      10          7.138
LGA    C      11      C      11          0.993
LGA    P      12      P      12          6.482
LGA    L      13      L      13          5.736
LGA    C      14      C      14          5.476
LGA    K      15      K      15          8.608
LGA    G      16      G      16         10.365
LGA    P      17      P      17         10.289
LGA    L      18      L      18         10.964
LGA    V      19      V      19         17.125
LGA    F      20      F      20         17.463
LGA    D      21      D      21         16.924
LGA    K      22      K      22         19.076
LGA    S      23      S      23         23.206
LGA    K      24      K      24         20.709
LGA    D      25      D      25         14.806
LGA    E      26      E      26          9.265
LGA    L      27      L      27          2.194
LGA    I      28      I      28          1.405
LGA    C      29      C      29          1.818
LGA    K      30      K      30          2.105
LGA    G      31      G      31          3.844
LGA    D      32      D      32          6.662
LGA    R      33      R      33          3.429
LGA    L      34      L      34          2.049
LGA    A      35      A      35          3.952
LGA    F      36      F      36          1.667
LGA    P      37      P      37          2.396
LGA    I      38      I      38          3.966
LGA    K      39      K      39          4.273
LGA    D      40      D      40          5.064
LGA    G      41      G      41          1.345
LGA    I      42      I      42          4.962
LGA    P      43      P      43         11.644
LGA    M      44      M      44         14.282
LGA    M      45      M      45         16.658
LGA    L      46      L      46         21.142
LGA    E      47      E      47         26.181
LGA    S      48      S      48         28.463
LGA    E      49      E      49         25.997
LGA    A      50      A      50         28.786
LGA    R      51      R      51         27.501
LGA    E      52      E      52         32.827
LGA    L      53      L      53         36.667
LGA    A      54      A      54         39.558
LGA    P      55      P      55         43.514
LGA    E      56      E      56         47.425
LGA    E      57      E      57         45.837
LGA    E      58      E      58         47.029
LGA    V      59      V      59         50.100
LGA    K      60      K      60         48.971
LGA    L      61      L      61         46.847
LGA    E      62      E      62         49.002

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   68   61    4.0     13    2.47    23.361    20.113     0.505

LGA_LOCAL      RMSD =  2.473  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 23.340  Number of atoms =   61 
Std_ALL_ATOMS  RMSD = 15.602  (standard rmsd on all 61 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.662954 * X  +   0.282454 * Y  +   0.693334 * Z  +   1.575830
  Y_new =   0.720984 * X  +   0.008609 * Y  +  -0.692899 * Z  +  32.758392
  Z_new =  -0.201681 * X  +   0.959242 * Y  +  -0.197937 * Z  +  49.766903 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.774287   -1.367306  [ DEG:   101.6592    -78.3408 ]
  Theta =   0.203074    2.938519  [ DEG:    11.6353    168.3647 ]
  Phi   =   0.827305   -2.314288  [ DEG:    47.4011   -132.5989 ]
 
# 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_5                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS168_5.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   13   2.47  20.113    15.60
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS168_5
PFRMAT TS
TARGET T0348
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -1.270  27.815  46.882  1.00 25.00           C
ATOM      2  CA  ASP     2      -3.015  26.800  50.123  1.00 25.00           C
ATOM      3  CA  ALA     3      -4.700  25.112  53.040  1.00 25.00           C
ATOM      4  CA  LYS     4      -2.043  22.395  52.562  1.00 25.00           C
ATOM      5  CA  PHE     5       0.684  24.829  53.703  1.00 25.00           C
ATOM      6  CA  LEU     6      -1.381  25.731  56.800  1.00 25.00           C
ATOM      7  CA  GLU     7      -1.852  22.016  57.599  1.00 25.00           C
ATOM      8  CA  ILE     8       1.917  21.435  57.240  1.00 25.00           C
ATOM      9  CA  LEU     9       2.618  24.384  59.581  1.00 25.00           C
ATOM     10  CA  VAL    10       3.708  27.966  58.858  1.00 25.00           C
ATOM     11  CA  CYS    11       7.258  29.132  59.533  1.00 25.00           C
ATOM     12  CA  PRO    12       9.292  28.421  62.696  1.00 25.00           C
ATOM     13  CA  LEU    13       8.551  24.987  63.982  1.00 25.00           C
ATOM     14  CA  CYS    14       5.382  22.998  64.280  1.00 25.00           C
ATOM     15  CA  LYS    15       2.022  24.583  65.015  1.00 25.00           C
ATOM     16  CA  GLY    16       1.843  26.714  68.158  1.00 25.00           C
ATOM     17  CA  PRO    17       5.309  28.025  67.253  1.00 25.00           C
ATOM     18  CA  LEU    18       3.845  29.171  63.953  1.00 25.00           C
ATOM     19  CA  VAL    19       0.279  29.425  62.656  1.00 25.00           C
ATOM     20  CA  PHE    20       1.414  32.644  61.060  1.00 25.00           C
ATOM     21  CA  ASP    21       3.375  32.864  57.827  1.00 25.00           C
ATOM     22  CA  LYS    22       6.123  34.250  60.013  1.00 25.00           C
ATOM     23  CA  SER    23       7.046  33.118  63.554  1.00 25.00           C
ATOM     24  CA  LYS    24      10.597  34.476  63.088  1.00 25.00           C
ATOM     25  CA  ASP    25      11.205  32.372  59.936  1.00 25.00           C
ATOM     26  CA  GLU    26       9.724  32.339  56.371  1.00 25.00           C
ATOM     27  CA  LEU    27      11.361  29.617  54.207  1.00 25.00           C
ATOM     28  CA  ILE    28      12.528  26.064  55.028  1.00 25.00           C
ATOM     29  CA  CYS    29      11.851  26.674  58.747  1.00 25.00           C
ATOM     30  CA  LYS    30      13.251  25.004  61.901  1.00 25.00           C
ATOM     31  CA  GLY    31      11.751  21.614  61.150  1.00 25.00           C
ATOM     32  CA  ASP    32      12.429  21.598  57.401  1.00 25.00           C
ATOM     33  CA  ARG    33       9.294  19.416  57.158  1.00 25.00           C
ATOM     34  CA  LEU    34       6.970  21.768  59.029  1.00 25.00           C
ATOM     35  CA  ALA    35       7.117  24.902  56.815  1.00 25.00           C
ATOM     36  CA  PHE    36       5.936  26.524  53.567  1.00 25.00           C
ATOM     37  CA  PRO    37       6.906  24.245  50.683  1.00 25.00           C
ATOM     38  CA  ILE    38       5.386  26.251  47.893  1.00 25.00           C
ATOM     39  CA  LYS    39       8.528  26.904  45.920  1.00 25.00           C
ATOM     40  CA  ASP    40       8.435  30.708  45.860  1.00 25.00           C
ATOM     41  CA  GLY    41      10.141  33.699  44.241  1.00 25.00           C
ATOM     42  CA  ILE    42       7.675  35.783  42.322  1.00 25.00           C
ATOM     43  CA  PRO    43       8.021  34.553  38.695  1.00 25.00           C
ATOM     44  CA  MET    44       5.123  32.835  36.872  1.00 25.00           C
ATOM     45  CA  MET    45       2.551  35.156  38.542  1.00 25.00           C
ATOM     46  CA  LEU    46       4.461  37.819  36.667  1.00 25.00           C
ATOM     47  CA  GLU    47       2.597  36.278  33.657  1.00 25.00           C
ATOM     48  CA  SER    48       1.778  38.355  30.539  1.00 25.00           C
ATOM     49  CA  GLU    49      -1.349  36.615  29.426  1.00 25.00           C
ATOM     50  CA  ALA    50      -2.606  33.175  28.251  1.00 25.00           C
ATOM     51  CA  ARG    51      -4.208  32.758  31.674  1.00 25.00           C
ATOM     52  CA  GLU    52      -7.967  32.272  31.345  1.00 25.00           C
ATOM     53  CA  LEU    53     -10.067  35.281  32.106  1.00 25.00           C
ATOM     54  CA  ALA    54     -13.431  34.793  33.770  1.00 25.00           C
ATOM     55  CA  PRO    55     -13.805  37.360  36.589  1.00 25.00           C
ATOM     56  CA  GLU    56     -15.329  40.088  34.389  1.00 25.00           C
ATOM     57  CA  GLU    57     -13.590  43.529  34.184  1.00 25.00           C
ATOM     58  CA  GLU    58     -13.747  45.185  37.614  1.00 25.00           C
ATOM     59  CA  VAL    59     -11.040  47.729  36.786  1.00 25.00           C
ATOM     60  CA  LYS    60      -8.766  50.392  35.355  1.00 25.00           C
ATOM     61  CA  LEU    61      -7.296  52.358  38.280  1.00 25.00           C
ATOM     62  CA  GLU    62      -8.023  51.639  41.929  1.00 25.00           C
ATOM     63  CA  HIS    63      -4.372  52.226  42.890  1.00 25.00           C
ATOM     64  CA  HIS    64      -1.538  52.659  45.462  1.00 25.00           C
ATOM     65  CA  HIS    65      -3.369  50.819  48.289  1.00 25.00           C
ATOM     66  CA  HIS    66      -2.609  47.295  49.536  1.00 25.00           C
ATOM     67  CA  HIS    67      -5.379  47.479  52.193  1.00 25.00           C
ATOM     68  CA  HIS    68      -5.901  43.689  51.950  1.00 25.00           C
TER
END
