
#######################################################
#                                                     #
#                        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 T0335TS393_2
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS393_2.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          3.82     3.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28        14 - 41          1.99     3.94
  LCS_AVERAGE:     58.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21        21 - 41          0.95     4.12
  LCS_AVERAGE:     42.23

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      4    5   42     0    4    4    4    5    7    9   13   14   19   20   20   20   20   20   20   22   35   38   40 
LCS_GDT     I       2     I       2      4    5   42     3    4    4    4    5    7   12   17   19   19   21   26   28   40   40   40   41   41   41   41 
LCS_GDT     S       3     S       3      4   19   42     3    4    8   15   17   18   19   34   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     N       4     N       4     17   19   42     4   12   16   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       5     A       5     17   19   42     6   12   16   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     K       6     K       6     17   19   42     7   13   16   22   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     I       7     I       7     17   19   42     7   13   16   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A       8     A       8     17   19   42     7   13   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     R       9     R       9     17   19   42     7   13   16   22   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      10     I      10     17   19   42     7   13   16   16   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     N      11     N      11     17   19   42     7   13   16   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      12     E      12     17   19   42     7   13   16   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      13     L      13     17   19   42     6   13   16   16   19   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      14     A      14     17   28   42     6   13   16   16   21   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      15     A      15     17   28   42     6   13   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      16     K      16     17   28   42     6   13   16   16   20   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      17     A      17     17   28   42     5   13   16   16   17   18   18   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      18     K      18     17   28   42     5   13   16   21   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      19     A      19     17   28   42     5   12   16   21   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      20     G      20     17   28   42     3    3    3   20   28   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     V      21     V      21     21   28   42     3    6   17   24   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     I      22     I      22     21   28   42     3   11   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     T      23     T      23     21   28   42     5   16   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      24     E      24     21   28   42     3   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      25     E      25     21   28   42     8   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      26     E      26     21   28   42     8   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      27     K      27     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     A      28     A      28     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      29     E      29     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      30     Q      30     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      31     Q      31     21   28   42     8   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      32     K      32     21   28   42     4   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      33     L      33     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      34     R      34     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     Q      35     Q      35     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     E      36     E      36     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     Y      37     Y      37     21   28   42     9   17   19   24   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     L      38     L      38     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     K      39     K      39     21   28   42     9   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     G      40     G      40     21   28   42     8   16   19   23   28   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     F      41     F      41     21   28   42     8   17   19   25   30   35   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_GDT     R      42     R      42      3   26   42     3    3    3    3   23   34   37   38   39   39   39   40   40   40   40   40   41   41   41   41 
LCS_AVERAGE  LCS_A:  66.86  (  42.23   58.33  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      9     17     19     25     30     35     37     38     39     39     39     40     40     40     40     40     41     41     41     41 
GDT PERCENT_CA  21.43  40.48  45.24  59.52  71.43  83.33  88.10  90.48  92.86  92.86  92.86  95.24  95.24  95.24  95.24  95.24  97.62  97.62  97.62  97.62
GDT RMS_LOCAL    0.31   0.62   0.72   1.38   1.57   1.89   2.04   2.11   2.23   2.23   2.23   2.50   2.50   2.50   2.50   2.50   3.00   3.00   3.00   3.00
GDT RMS_ALL_CA   4.29   4.11   4.13   4.07   4.14   4.05   4.12   4.13   4.13   4.13   4.13   4.02   4.02   4.02   4.02   4.02   3.90   3.90   3.90   3.90

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         17.926
LGA    I       2      I       2         11.941
LGA    S       3      S       3          7.703
LGA    N       4      N       4          1.734
LGA    A       5      A       5          1.838
LGA    K       6      K       6          2.326
LGA    I       7      I       7          2.159
LGA    A       8      A       8          1.443
LGA    R       9      R       9          2.433
LGA    I      10      I      10          2.803
LGA    N      11      N      11          1.845
LGA    E      12      E      12          2.062
LGA    L      13      L      13          3.932
LGA    A      14      A      14          3.171
LGA    A      15      A      15          1.371
LGA    K      16      K      16          3.542
LGA    A      17      A      17          4.990
LGA    K      18      K      18          2.546
LGA    A      19      A      19          2.304
LGA    G      20      G      20          3.233
LGA    V      21      V      21          2.434
LGA    I      22      I      22          1.383
LGA    T      23      T      23          1.942
LGA    E      24      E      24          1.237
LGA    E      25      E      25          0.932
LGA    E      26      E      26          1.077
LGA    K      27      K      27          1.118
LGA    A      28      A      28          0.800
LGA    E      29      E      29          0.858
LGA    Q      30      Q      30          1.443
LGA    Q      31      Q      31          1.474
LGA    K      32      K      32          1.567
LGA    L      33      L      33          1.323
LGA    R      34      R      34          1.271
LGA    Q      35      Q      35          0.793
LGA    E      36      E      36          1.610
LGA    Y      37      Y      37          2.098
LGA    L      38      L      38          1.434
LGA    K      39      K      39          2.083
LGA    G      40      G      40          3.126
LGA    F      41      F      41          1.535
LGA    R      42      R      42          3.698

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   85   42    4.0     38    2.11    71.429    72.248     1.716

LGA_LOCAL      RMSD =  2.114  Number of atoms =   38  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.135  Number of atoms =   42 
Std_ALL_ATOMS  RMSD =  3.825  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.147415 * X  +  -0.628728 * Y  +   0.763525 * Z  +   4.720786
  Y_new =  -0.964695 * X  +  -0.261736 * Y  +  -0.029273 * Z  +   1.619264
  Z_new =   0.218247 * X  +  -0.732254 * Y  +  -0.645115 * Z  +  -6.913813 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.293014    0.848579  [ DEG:  -131.3800     48.6200 ]
  Theta =  -0.220017   -2.921575  [ DEG:   -12.6061   -167.3939 ]
  Phi   =  -1.419160    1.722433  [ DEG:   -81.3119     98.6881 ]
 
# 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: T0335TS393_2                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_2.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   38   2.11  72.248     3.82
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_2
PFRMAT TS
TARGET T0335
MODEL 2
PARENT N/A
ATOM      1  CA  MET     1      -3.257 -19.739  -8.946  1.00 25.00           C
ATOM      2  CA  ILE     2      -0.607 -16.993  -9.097  1.00 25.00           C
ATOM      3  CA  SER     3      -3.116 -14.415 -10.403  1.00 25.00           C
ATOM      4  CA  ASN     4      -1.290 -11.093  -9.850  1.00 25.00           C
ATOM      5  CA  ALA     5       0.594 -10.826  -6.526  1.00 25.00           C
ATOM      6  CA  LYS     6       1.382  -7.146  -7.240  1.00 25.00           C
ATOM      7  CA  ILE     7      -2.305  -6.486  -8.038  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.343  -8.188  -4.768  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.825  -6.052  -2.828  1.00 25.00           C
ATOM     10  CA  ILE    10      -2.192  -2.886  -4.493  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.765  -3.916  -3.577  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.688  -4.519   0.048  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.020  -1.073   0.151  1.00 25.00           C
ATOM     14  CA  ALA    14      -6.206   0.538  -1.232  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.298  -1.261   1.424  1.00 25.00           C
ATOM     16  CA  LYS    16      -5.915  -0.042   4.162  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.180   3.541   2.834  1.00 25.00           C
ATOM     18  CA  LYS    18     -10.002   3.283   2.835  1.00 25.00           C
ATOM     19  CA  ALA    19      -9.939   1.996   6.441  1.00 25.00           C
ATOM     20  CA  GLY    20      -9.511   4.253   9.457  1.00 25.00           C
ATOM     21  CA  VAL    21      -7.056   2.497  11.755  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.218   3.380   9.436  1.00 25.00           C
ATOM     23  CA  THR    23      -2.776   6.394  11.230  1.00 25.00           C
ATOM     24  CA  GLU    24       1.079   6.300  11.285  1.00 25.00           C
ATOM     25  CA  GLU    25       3.608   3.470  10.775  1.00 25.00           C
ATOM     26  CA  GLU    26       0.977   1.427   8.885  1.00 25.00           C
ATOM     27  CA  LYS    27       0.186   4.448   6.668  1.00 25.00           C
ATOM     28  CA  ALA    28       3.917   4.924   5.944  1.00 25.00           C
ATOM     29  CA  GLU    29       4.238   1.219   5.030  1.00 25.00           C
ATOM     30  CA  GLN    30       1.221   1.511   2.688  1.00 25.00           C
ATOM     31  CA  GLN    31       2.774   4.596   1.033  1.00 25.00           C
ATOM     32  CA  LYS    32       6.076   2.713   0.567  1.00 25.00           C
ATOM     33  CA  LEU    33       4.202  -0.237  -1.000  1.00 25.00           C
ATOM     34  CA  ARG    34       2.375   2.151  -3.372  1.00 25.00           C
ATOM     35  CA  GLN    35       5.710   3.753  -4.366  1.00 25.00           C
ATOM     36  CA  GLU    36       7.203   0.290  -5.032  1.00 25.00           C
ATOM     37  CA  TYR    37       4.176  -0.628  -7.190  1.00 25.00           C
ATOM     38  CA  LEU    38       4.559   2.636  -9.158  1.00 25.00           C
ATOM     39  CA  LYS    39       8.279   1.901  -9.699  1.00 25.00           C
ATOM     40  CA  GLY    40       7.428  -1.626 -10.927  1.00 25.00           C
ATOM     41  CA  PHE    41       4.829  -0.186 -13.343  1.00 25.00           C
ATOM     42  CA  ARG    42       7.407   2.323 -14.659  1.00 25.00           C
ATOM     43  CA  SER    43       9.936  -0.508 -15.169  1.00 25.00           C
ATOM     44  CA  SER    44       7.305  -2.551 -17.059  1.00 25.00           C
ATOM     45  CA  MET    45       6.515   0.470 -19.276  1.00 25.00           C
ATOM     46  CA  LYS    46      10.246   0.945 -20.000  1.00 25.00           C
ATOM     47  CA  ASN    47      10.565  -2.759 -20.915  1.00 25.00           C
ATOM     48  CA  THR    48       7.549  -2.467 -23.256  1.00 25.00           C
ATOM     49  CA  LEU    49       9.103   0.618 -24.912  1.00 25.00           C
ATOM     50  CA  LYS    50       6.061   2.853 -24.247  1.00 25.00           C
ATOM     51  CA  SER    51       3.062   3.681 -22.120  1.00 25.00           C
ATOM     52  CA  VAL    52       2.056   2.398 -18.672  1.00 25.00           C
ATOM     53  CA  LYS    53      -0.656   1.123 -16.340  1.00 25.00           C
ATOM     54  CA  ILE    54      -2.016   4.463 -15.059  1.00 25.00           C
ATOM     55  CA  ILE    55      -2.965   7.240 -12.741  1.00 25.00           C
ATOM     56  CA  ASP    56      -2.349  10.194 -14.973  1.00 25.00           C
ATOM     57  CA  PRO    57      -5.635  12.035 -15.370  1.00 25.00           C
ATOM     58  CA  GLU    58      -4.306  15.494 -14.518  1.00 25.00           C
ATOM     59  CA  GLY    59      -3.160  16.424 -18.035  1.00 25.00           C
ATOM     60  CA  ASN    60       0.554  17.159 -18.133  1.00 25.00           C
ATOM     61  CA  ASP    61       1.865  15.965 -14.769  1.00 25.00           C
ATOM     62  CA  VAL    62       1.919  12.662 -12.957  1.00 25.00           C
ATOM     63  CA  THR    63       4.286  10.694 -15.163  1.00 25.00           C
ATOM     64  CA  PRO    64       7.234  10.267 -17.481  1.00 25.00           C
ATOM     65  CA  GLU    65       9.921  12.805 -16.479  1.00 25.00           C
ATOM     66  CA  LYS    66      10.155  11.222 -12.999  1.00 25.00           C
ATOM     67  CA  LEU    67      10.517   7.751 -14.576  1.00 25.00           C
ATOM     68  CA  LYS    68      13.288   9.056 -16.874  1.00 25.00           C
ATOM     69  CA  ARG    69      15.094  10.591 -13.867  1.00 25.00           C
ATOM     70  CA  GLU    70      14.825   7.270 -11.980  1.00 25.00           C
ATOM     71  CA  GLN    71      16.242   5.405 -15.010  1.00 25.00           C
ATOM     72  CA  ARG    72      19.148   7.892 -15.211  1.00 25.00           C
ATOM     73  CA  ASN    73      19.852   7.409 -11.478  1.00 25.00           C
ATOM     74  CA  ASN    74      19.832   3.607 -11.940  1.00 25.00           C
ATOM     75  CA  LYS    75      22.739   1.106 -11.771  1.00 25.00           C
ATOM     76  CA  LEU    76      22.395   1.376  -7.936  1.00 25.00           C
ATOM     77  CA  HIS    77      20.679  -2.043  -8.304  1.00 25.00           C
ATOM     78  CA  LEU    78      22.508  -2.928  -5.054  1.00 25.00           C
ATOM     79  CA  GLU    79      22.374   0.337  -3.148  1.00 25.00           C
ATOM     80  CA  HIS    80      19.100  -0.775  -1.547  1.00 25.00           C
ATOM     81  CA  HIS    81      17.695  -4.320  -1.211  1.00 25.00           C
ATOM     82  CA  HIS    82      15.712  -3.286   1.859  1.00 25.00           C
ATOM     83  CA  HIS    83      16.019  -3.350   5.687  1.00 25.00           C
ATOM     84  CA  HIS    84      12.967  -5.044   7.235  1.00 25.00           C
ATOM     85  CA  HIS    85      10.538  -7.398   8.927  1.00 25.00           C
TER
END
