
#######################################################
#                                                     #
#                        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   85 (   85),  selected   42 , name T0335TS168_3
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS168_3.T0335.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:    42         1 - 42          3.64     3.64
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    39         4 - 42          1.87     3.93
  LCS_AVERAGE:     88.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        22 - 41          0.75     4.08
  LCS_AVERAGE:     39.91

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:   42
LCS_GDT     M       1     M       1      5    5   42     3    3    5    5    5   13   18   19   19   19   20   21   22   22   22   25   41   41   41   41 
LCS_GDT     I       2     I       2      5    5   42     3    3    5    5    5    7   18   19   19   19   29   31   35   37   38   40   41   41   41   41 
LCS_GDT     S       3     S       3      5   37   42     3    3   11   14   17   18   36   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     N       4     N       4     16   39   42     4   14   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       5     A       5     16   39   42     6   12   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K       6     K       6     16   39   42     7   13   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I       7     I       7     16   39   42     7   13   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       8     A       8     16   39   42     7   14   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R       9     R       9     16   39   42     7   13   18   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      10     I      10     16   39   42     7   13   18   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     N      11     N      11     16   39   42     7   13   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      12     E      12     16   39   42     7   13   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      13     L      13     16   39   42     7   13   16   23   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      14     A      14     16   39   42     7   13   16   29   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      15     A      15     16   39   42     7   14   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      16     K      16     16   39   42     6   13   16   21   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      17     A      17     16   39   42     5   13   16   16   17   31   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      18     K      18     16   39   42     5   13   19   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      19     A      19     16   39   42     5   12   18   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      20     G      20     15   39   42     7   15   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     V      21     V      21     15   39   42     3    3   10   23   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      22     I      22     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     T      23     T      23     20   39   42     3   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      24     E      24     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      25     E      25     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      26     E      26     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      27     K      27     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      28     A      28     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      29     E      29     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      30     Q      30     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      31     Q      31     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      32     K      32     20   39   42     4   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      33     L      33     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      34     R      34     20   39   42    10   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      35     Q      35     20   39   42     9   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      36     E      36     20   39   42     9   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     Y      37     Y      37     20   39   42     9   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      38     L      38     20   39   42     9   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      39     K      39     20   39   42     9   18   21   27   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      40     G      40     20   39   42     8   15   20   24   32   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     F      41     F      41     20   39   42     8   18   21   30   33   36   38   39   39   39   40   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      42     R      42      3   39   42     3    3    3    3    6   12   37   39   39   39   40   40   40   40   40   40   40   40   41   41 
LCS_AVERAGE  LCS_A:  76.27  (  39.91   88.89  100.00 )

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     10     18     21     30     33     36     38     39     39     39     40     40     40     40     40     40     41     41     41     41 
GDT PERCENT_CA  23.81  42.86  50.00  71.43  78.57  85.71  90.48  92.86  92.86  92.86  95.24  95.24  95.24  95.24  95.24  95.24  97.62  97.62  97.62  97.62
GDT RMS_LOCAL    0.33   0.65   0.94   1.35   1.47   1.63   1.78   1.87   1.87   1.87   2.10   2.10   2.10   2.10   2.10   2.10   3.53   3.53   2.83   2.83
GDT RMS_ALL_CA   4.13   4.08   3.78   3.94   3.95   3.91   3.86   3.93   3.93   3.93   3.84   3.84   3.84   3.84   3.84   3.84   3.65   3.65   3.71   3.71

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         17.232
LGA    I       2      I       2         13.120
LGA    S       3      S       3          6.489
LGA    N       4      N       4          1.517
LGA    A       5      A       5          1.644
LGA    K       6      K       6          1.757
LGA    I       7      I       7          1.321
LGA    A       8      A       8          1.003
LGA    R       9      R       9          1.903
LGA    I      10      I      10          1.953
LGA    N      11      N      11          1.267
LGA    E      12      E      12          1.605
LGA    L      13      L      13          2.955
LGA    A      14      A      14          2.271
LGA    A      15      A      15          1.269
LGA    K      16      K      16          2.685
LGA    A      17      A      17          3.675
LGA    K      18      K      18          1.899
LGA    A      19      A      19          2.183
LGA    G      20      G      20          1.762
LGA    V      21      V      21          2.687
LGA    I      22      I      22          1.601
LGA    T      23      T      23          1.646
LGA    E      24      E      24          0.863
LGA    E      25      E      25          0.335
LGA    E      26      E      26          0.756
LGA    K      27      K      27          0.926
LGA    A      28      A      28          0.483
LGA    E      29      E      29          0.829
LGA    Q      30      Q      30          1.443
LGA    Q      31      Q      31          1.089
LGA    K      32      K      32          1.386
LGA    L      33      L      33          1.436
LGA    R      34      R      34          0.974
LGA    Q      35      Q      35          0.792
LGA    E      36      E      36          1.990
LGA    Y      37      Y      37          1.969
LGA    L      38      L      38          0.941
LGA    K      39      K      39          2.526
LGA    G      40      G      40          3.417
LGA    F      41      F      41          1.124
LGA    R      42      R      42          3.763

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   85   42    4.0     39    1.87    75.595    82.237     1.976

LGA_LOCAL      RMSD =  1.873  Number of atoms =   39  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.928  Number of atoms =   42 
Std_ALL_ATOMS  RMSD =  3.638  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.292407 * X  +   0.296353 * Y  +   0.909216 * Z  +   4.838801
  Y_new =   0.952986 * X  +  -0.169314 * Y  +  -0.251297 * Z  +   1.615276
  Z_new =   0.079471 * X  +   0.939951 * Y  +  -0.331929 * Z  +  -6.954117 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.910260   -1.231332  [ DEG:   109.4499    -70.5501 ]
  Theta =  -0.079555   -3.062038  [ DEG:    -4.5582   -175.4418 ]
  Phi   =   1.273083   -1.868509  [ DEG:    72.9423   -107.0577 ]
 
# 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: T0335TS168_3                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_3.T0335.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   85   42   4.0   39   1.87  82.237     3.64
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_3
PFRMAT TS
TARGET T0335
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -7.646 -17.728 -14.080  1.00 25.00           C
ATOM      2  CA  ILE     2      -6.241 -15.409 -11.455  1.00 25.00           C
ATOM      3  CA  SER     3      -3.356 -13.047 -11.082  1.00 25.00           C
ATOM      4  CA  ASN     4      -1.107 -10.098 -10.058  1.00 25.00           C
ATOM      5  CA  ALA     5       0.326 -10.547  -6.535  1.00 25.00           C
ATOM      6  CA  LYS     6       1.575  -6.928  -6.554  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.882  -5.714  -7.667  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.523  -7.734  -4.858  1.00 25.00           C
ATOM      9  CA  ARG     9      -1.087  -6.224  -2.317  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.884  -2.707  -3.605  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.635  -3.416  -3.295  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.127  -4.665   0.289  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.144  -1.501   1.137  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.933   0.671  -0.339  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.539  -1.227   1.730  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.437  -0.717   4.891  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.152   3.025   4.128  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.945   3.238   3.636  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.504   1.443   6.972  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.161   0.538  10.650  1.00 25.00           C
ATOM     21  CA  VAL    21      -6.725   2.166  10.549  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.874   5.351   9.865  1.00 25.00           C
ATOM     23  CA  THR    23      -2.078   5.170  12.411  1.00 25.00           C
ATOM     24  CA  GLU    24       1.176   6.519  10.906  1.00 25.00           C
ATOM     25  CA  GLU    25       3.104   3.242  10.448  1.00 25.00           C
ATOM     26  CA  GLU    26       0.247   1.829   8.325  1.00 25.00           C
ATOM     27  CA  LYS    27       0.242   5.000   6.178  1.00 25.00           C
ATOM     28  CA  ALA    28       4.032   4.715   5.703  1.00 25.00           C
ATOM     29  CA  GLU    29       3.651   1.047   4.673  1.00 25.00           C
ATOM     30  CA  GLN    30       0.924   2.009   2.162  1.00 25.00           C
ATOM     31  CA  GLN    31       3.182   4.747   0.722  1.00 25.00           C
ATOM     32  CA  LYS    32       6.056   2.237   0.389  1.00 25.00           C
ATOM     33  CA  LEU    33       3.731  -0.226  -1.399  1.00 25.00           C
ATOM     34  CA  ARG    34       2.595   2.543  -3.788  1.00 25.00           C
ATOM     35  CA  GLN    35       6.245   3.448  -4.513  1.00 25.00           C
ATOM     36  CA  GLU    36       7.043  -0.231  -5.215  1.00 25.00           C
ATOM     37  CA  TYR    37       4.047  -0.454  -7.589  1.00 25.00           C
ATOM     38  CA  LEU    38       5.220   2.706  -9.406  1.00 25.00           C
ATOM     39  CA  LYS    39       8.739   1.236  -9.744  1.00 25.00           C
ATOM     40  CA  GLY    40       7.274  -2.011 -11.152  1.00 25.00           C
ATOM     41  CA  PHE    41       5.194  -0.008 -13.669  1.00 25.00           C
ATOM     42  CA  ARG    42       8.312   1.946 -14.729  1.00 25.00           C
ATOM     43  CA  SER    43      10.241  -1.332 -15.187  1.00 25.00           C
ATOM     44  CA  SER    44       7.384  -2.744 -17.310  1.00 25.00           C
ATOM     45  CA  MET    45       7.378   0.428 -19.457  1.00 25.00           C
ATOM     46  CA  LYS    46      11.168   0.143 -19.932  1.00 25.00           C
ATOM     47  CA  ASN    47      10.787  -3.525 -20.963  1.00 25.00           C
ATOM     48  CA  THR    48       8.060  -2.563 -23.473  1.00 25.00           C
ATOM     49  CA  LEU    49      10.318   0.175 -24.913  1.00 25.00           C
ATOM     50  CA  LYS    50       7.094   2.181 -24.488  1.00 25.00           C
ATOM     51  CA  SER    51       3.745   1.315 -22.772  1.00 25.00           C
ATOM     52  CA  VAL    52       1.150  -1.073 -21.325  1.00 25.00           C
ATOM     53  CA  LYS    53      -2.295  -0.795 -19.731  1.00 25.00           C
ATOM     54  CA  ILE    54      -2.028   1.383 -16.650  1.00 25.00           C
ATOM     55  CA  ILE    55      -2.796   4.731 -14.983  1.00 25.00           C
ATOM     56  CA  ASP    56      -4.010   8.241 -15.741  1.00 25.00           C
ATOM     57  CA  PRO    57      -3.898   9.513 -19.341  1.00 25.00           C
ATOM     58  CA  GLU    58      -1.863  12.002 -21.462  1.00 25.00           C
ATOM     59  CA  GLY    59      -0.851  14.965 -19.240  1.00 25.00           C
ATOM     60  CA  ASN    60      -1.833  13.955 -15.697  1.00 25.00           C
ATOM     61  CA  ASP    61      -0.127  11.223 -13.600  1.00 25.00           C
ATOM     62  CA  VAL    62       1.201   7.805 -14.609  1.00 25.00           C
ATOM     63  CA  THR    63       4.149   9.215 -16.570  1.00 25.00           C
ATOM     64  CA  PRO    64       7.581  10.787 -16.524  1.00 25.00           C
ATOM     65  CA  GLU    65       9.942  13.587 -15.403  1.00 25.00           C
ATOM     66  CA  LYS    66       9.868  12.248 -11.816  1.00 25.00           C
ATOM     67  CA  LEU    67      10.662   8.724 -13.090  1.00 25.00           C
ATOM     68  CA  LYS    68      13.589  10.098 -15.142  1.00 25.00           C
ATOM     69  CA  ARG    69      14.907  11.955 -12.063  1.00 25.00           C
ATOM     70  CA  GLU    70      14.651   8.748  -9.988  1.00 25.00           C
ATOM     71  CA  GLN    71      16.551   6.815 -12.694  1.00 25.00           C
ATOM     72  CA  ARG    72      19.275   9.505 -12.738  1.00 25.00           C
ATOM     73  CA  ASN    73      19.559   9.314  -8.923  1.00 25.00           C
ATOM     74  CA  ASN    74      19.864   5.501  -9.113  1.00 25.00           C
ATOM     75  CA  LYS    75      23.410   4.716 -10.096  1.00 25.00           C
ATOM     76  CA  LEU    76      23.989   4.850  -6.354  1.00 25.00           C
ATOM     77  CA  HIS    77      21.626   3.451  -3.770  1.00 25.00           C
ATOM     78  CA  LEU    78      24.497   1.185  -2.587  1.00 25.00           C
ATOM     79  CA  GLU    79      24.448  -2.649  -2.406  1.00 25.00           C
ATOM     80  CA  HIS    80      20.737  -3.335  -2.882  1.00 25.00           C
ATOM     81  CA  HIS    81      18.445  -1.024  -0.859  1.00 25.00           C
ATOM     82  CA  HIS    82      18.406  -2.434   2.681  1.00 25.00           C
ATOM     83  CA  HIS    83      15.548  -4.329   4.262  1.00 25.00           C
ATOM     84  CA  HIS    84      15.428  -8.178   4.393  1.00 25.00           C
ATOM     85  CA  HIS    85      14.334  -7.923   8.067  1.00 25.00           C
TER
END
