
#######################################################
#                                                     #
#                        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_5
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335TS393_5.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          3.81     3.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    38         4 - 41          1.93     4.05
  LCS_AVERAGE:     85.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        20 - 41          0.89     4.00
  LCS_AVERAGE:     43.20

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    5    5    5    8   16   18   19   19   21   21   21   21   22   23   24   27   31   39   39 
LCS_GDT     I       2     I       2      5    5   42     3    5    5    5    5   10   18   19   19   21   21   21   21   24   28   40   40   40   41   41 
LCS_GDT     S       3     S       3      5   20   42     3    5    5    5   15   17   19   34   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     N       4     N       4     16   38   42     4   12   16   24   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A       5     A       5     16   38   42     6   12   19   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     K       6     K       6     16   38   42     7   13   16   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     I       7     I       7     16   38   42     7   13   16   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A       8     A       8     16   38   42     7   13   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     R       9     R       9     16   38   42     7   13   17   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     I      10     I      10     16   38   42     7   13   16   25   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     N      11     N      11     16   38   42     7   13   21   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     E      12     E      12     16   38   42     7   13   19   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     L      13     L      13     16   38   42     7   13   16   16   28   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A      14     A      14     16   38   42     7   13   16   23   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A      15     A      15     16   38   42     7   13   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     K      16     K      16     16   38   42     7   13   16   16   26   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A      17     A      17     16   38   42     7   13   16   16   17   18   27   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     K      18     K      18     16   38   42     7   13   19   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A      19     A      19     20   38   42     7   13   16   16   32   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     G      20     G      20     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     V      21     V      21     22   38   42     3   10   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     I      22     I      22     22   38   42     3    6   21   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     T      23     T      23     22   38   42     8   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     E      24     E      24     22   38   42     5   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     E      25     E      25     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     E      26     E      26     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     K      27     K      27     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     A      28     A      28     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     E      29     E      29     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     Q      30     Q      30     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     Q      31     Q      31     22   38   42     8   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     K      32     K      32     22   38   42     4   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     L      33     L      33     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     R      34     R      34     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     Q      35     Q      35     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     E      36     E      36     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     Y      37     Y      37     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     L      38     L      38     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     K      39     K      39     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     G      40     G      40     22   38   42     8   15   21   24   30   35   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     F      41     F      41     22   38   42     9   19   22   28   33   36   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_GDT     R      42     R      42      3   36   42     3    3    3    3   25   35   38   39   39   39   39   40   40   40   40   40   40   40   41   41 
LCS_AVERAGE  LCS_A:  76.27  (  43.20   85.60  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     19     22     28     33     36     38     39     39     39     39     40     40     40     40     40     40     40     41     41 
GDT PERCENT_CA  21.43  45.24  52.38  66.67  78.57  85.71  90.48  92.86  92.86  92.86  92.86  95.24  95.24  95.24  95.24  95.24  95.24  95.24  97.62  97.62
GDT RMS_LOCAL    0.32   0.64   0.91   1.32   1.57   1.78   1.91   2.01   2.01   2.01   2.01   2.28   2.28   2.28   2.28   2.28   2.28   2.28   2.99   2.99
GDT RMS_ALL_CA   4.01   4.02   3.99   4.01   4.08   4.09   4.11   4.11   4.11   4.11   4.11   4.01   4.01   4.01   4.01   4.01   4.01   4.01   3.88   3.88

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         17.924
LGA    I       2      I       2         13.459
LGA    S       3      S       3          7.427
LGA    N       4      N       4          1.890
LGA    A       5      A       5          1.881
LGA    K       6      K       6          2.200
LGA    I       7      I       7          1.712
LGA    A       8      A       8          1.484
LGA    R       9      R       9          2.387
LGA    I      10      I      10          2.139
LGA    N      11      N      11          1.532
LGA    E      12      E      12          2.518
LGA    L      13      L      13          3.444
LGA    A      14      A      14          1.859
LGA    A      15      A      15          2.172
LGA    K      16      K      16          3.983
LGA    A      17      A      17          3.843
LGA    K      18      K      18          0.792
LGA    A      19      A      19          3.966
LGA    G      20      G      20          2.761
LGA    V      21      V      21          2.118
LGA    I      22      I      22          2.250
LGA    T      23      T      23          0.751
LGA    E      24      E      24          1.306
LGA    E      25      E      25          1.505
LGA    E      26      E      26          1.459
LGA    K      27      K      27          1.179
LGA    A      28      A      28          0.817
LGA    E      29      E      29          0.965
LGA    Q      30      Q      30          1.357
LGA    Q      31      Q      31          1.211
LGA    K      32      K      32          1.319
LGA    L      33      L      33          1.153
LGA    R      34      R      34          1.164
LGA    Q      35      Q      35          0.607
LGA    E      36      E      36          1.407
LGA    Y      37      Y      37          2.002
LGA    L      38      L      38          1.395
LGA    K      39      K      39          2.037
LGA    G      40      G      40          3.077
LGA    F      41      F      41          1.610
LGA    R      42      R      42          3.537

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   85   42    4.0     39    2.01    75.000    81.300     1.851

LGA_LOCAL      RMSD =  2.007  Number of atoms =   39  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.175  Number of atoms =   42 
Std_ALL_ATOMS  RMSD =  3.808  (standard rmsd on all 42 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.612732 * X  +   0.466265 * Y  +   0.638089 * Z  +   4.614117
  Y_new =   0.690845 * X  +   0.708118 * Y  +   0.145954 * Z  +   1.707396
  Z_new =  -0.383788 * X  +   0.530251 * Y  +  -0.756003 * Z  +  -6.597661 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.529936   -0.611657  [ DEG:   144.9547    -35.0453 ]
  Theta =   0.393895    2.747697  [ DEG:    22.5685    157.4315 ]
  Phi   =   2.296344   -0.845249  [ DEG:   131.5708    -48.4292 ]
 
# 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_5                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_5.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   2.01  81.300     3.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_5
PFRMAT TS
TARGET T0335
MODEL 5
PARENT N/A
ATOM      1  CA  MET     1      -7.475 -18.458 -12.470  1.00 25.00           C
ATOM      2  CA  ILE     2      -5.991 -15.878 -10.067  1.00 25.00           C
ATOM      3  CA  SER     3      -2.599 -14.314 -10.616  1.00 25.00           C
ATOM      4  CA  ASN     4      -1.525 -10.645 -10.079  1.00 25.00           C
ATOM      5  CA  ALA     5       0.404 -10.918  -6.782  1.00 25.00           C
ATOM      6  CA  LYS     6       1.511  -7.266  -7.100  1.00 25.00           C
ATOM      7  CA  ILE     7      -2.109  -6.199  -7.751  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.266  -8.159  -4.671  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.551  -6.481  -2.554  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.644  -3.041  -3.834  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.286  -3.850  -2.970  1.00 25.00           C
ATOM     12  CA  GLU    12      -4.236  -4.946   0.546  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.265  -1.694   0.998  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.307   0.336  -0.139  1.00 25.00           C
ATOM     15  CA  ALA    15      -7.528  -1.559   2.341  1.00 25.00           C
ATOM     16  CA  LYS    16      -5.021  -0.867   5.152  1.00 25.00           C
ATOM     17  CA  ALA    17      -4.978   2.851   4.233  1.00 25.00           C
ATOM     18  CA  LYS    18      -8.806   2.931   4.277  1.00 25.00           C
ATOM     19  CA  ALA    19      -8.827   1.248   7.717  1.00 25.00           C
ATOM     20  CA  GLY    20      -9.318   1.150  11.520  1.00 25.00           C
ATOM     21  CA  VAL    21      -6.688   3.821  11.525  1.00 25.00           C
ATOM     22  CA  ILE    22      -3.800   2.473   9.370  1.00 25.00           C
ATOM     23  CA  THR    23      -1.717   4.830  11.507  1.00 25.00           C
ATOM     24  CA  GLU    24       1.715   6.456  11.285  1.00 25.00           C
ATOM     25  CA  GLU    25       4.245   3.638  10.714  1.00 25.00           C
ATOM     26  CA  GLU    26       1.568   1.563   8.926  1.00 25.00           C
ATOM     27  CA  LYS    27       0.687   4.563   6.713  1.00 25.00           C
ATOM     28  CA  ALA    28       4.389   5.056   5.866  1.00 25.00           C
ATOM     29  CA  GLU    29       4.703   1.346   4.969  1.00 25.00           C
ATOM     30  CA  GLN    30       1.611   1.601   2.724  1.00 25.00           C
ATOM     31  CA  GLN    31       3.090   4.684   0.996  1.00 25.00           C
ATOM     32  CA  LYS    32       6.388   2.818   0.436  1.00 25.00           C
ATOM     33  CA  LEU    33       4.482  -0.156  -1.046  1.00 25.00           C
ATOM     34  CA  ARG    34       2.565   2.203  -3.376  1.00 25.00           C
ATOM     35  CA  GLN    35       5.855   3.817  -4.488  1.00 25.00           C
ATOM     36  CA  GLU    36       7.348   0.359  -5.176  1.00 25.00           C
ATOM     37  CA  TYR    37       4.259  -0.594  -7.229  1.00 25.00           C
ATOM     38  CA  LEU    38       4.557   2.656  -9.233  1.00 25.00           C
ATOM     39  CA  LYS    39       8.262   1.941  -9.888  1.00 25.00           C
ATOM     40  CA  GLY    40       7.396  -1.601 -11.061  1.00 25.00           C
ATOM     41  CA  PHE    41       4.710  -0.196 -13.402  1.00 25.00           C
ATOM     42  CA  ARG    42       7.228   2.319 -14.821  1.00 25.00           C
ATOM     43  CA  SER    43       9.758  -0.499 -15.391  1.00 25.00           C
ATOM     44  CA  SER    44       7.081  -2.574 -17.180  1.00 25.00           C
ATOM     45  CA  MET    45       6.200   0.425 -19.392  1.00 25.00           C
ATOM     46  CA  LYS    46       9.901   0.919 -20.240  1.00 25.00           C
ATOM     47  CA  ASN    47      10.215  -2.791 -21.137  1.00 25.00           C
ATOM     48  CA  THR    48       7.123  -2.536 -23.382  1.00 25.00           C
ATOM     49  CA  LEU    49       8.602   0.546 -25.110  1.00 25.00           C
ATOM     50  CA  LYS    50       5.427   2.239 -24.064  1.00 25.00           C
ATOM     51  CA  SER    51       2.182   1.995 -22.132  1.00 25.00           C
ATOM     52  CA  VAL    52       1.345   2.759 -18.472  1.00 25.00           C
ATOM     53  CA  LYS    53      -1.768   0.822 -17.395  1.00 25.00           C
ATOM     54  CA  ILE    54      -3.415   3.690 -15.402  1.00 25.00           C
ATOM     55  CA  ILE    55      -5.576   6.004 -13.280  1.00 25.00           C
ATOM     56  CA  ASP    56      -4.123   9.179 -14.797  1.00 25.00           C
ATOM     57  CA  PRO    57      -6.523  11.280 -12.765  1.00 25.00           C
ATOM     58  CA  GLU    58      -5.544  14.443 -14.667  1.00 25.00           C
ATOM     59  CA  GLY    59      -4.906  17.112 -12.054  1.00 25.00           C
ATOM     60  CA  ASN    60      -1.256  16.916 -13.169  1.00 25.00           C
ATOM     61  CA  ASP    61      -0.138  13.553 -14.679  1.00 25.00           C
ATOM     62  CA  VAL    62       1.760  10.256 -14.165  1.00 25.00           C
ATOM     63  CA  THR    63       3.002   8.887 -17.501  1.00 25.00           C
ATOM     64  CA  PRO    64       6.341  10.704 -16.938  1.00 25.00           C
ATOM     65  CA  GLU    65       8.720  13.299 -15.430  1.00 25.00           C
ATOM     66  CA  LYS    66       8.717  11.403 -12.102  1.00 25.00           C
ATOM     67  CA  LEU    67       9.490   8.131 -13.936  1.00 25.00           C
ATOM     68  CA  LYS    68      12.375   9.829 -15.798  1.00 25.00           C
ATOM     69  CA  ARG    69      13.751  11.176 -12.487  1.00 25.00           C
ATOM     70  CA  GLU    70      13.539   7.676 -10.947  1.00 25.00           C
ATOM     71  CA  GLN    71      15.387   6.210 -13.962  1.00 25.00           C
ATOM     72  CA  ARG    72      18.108   8.883 -13.627  1.00 25.00           C
ATOM     73  CA  ASN    73      18.465   8.087  -9.898  1.00 25.00           C
ATOM     74  CA  ASN    74      18.771   4.354 -10.700  1.00 25.00           C
ATOM     75  CA  LYS    75      22.323   4.442 -12.058  1.00 25.00           C
ATOM     76  CA  LEU    76      23.385   3.999  -8.425  1.00 25.00           C
ATOM     77  CA  HIS    77      23.702   0.813  -6.424  1.00 25.00           C
ATOM     78  CA  LEU    78      23.269  -2.870  -7.059  1.00 25.00           C
ATOM     79  CA  GLU    79      21.282  -3.804  -3.969  1.00 25.00           C
ATOM     80  CA  HIS    80      20.727  -1.648  -0.925  1.00 25.00           C
ATOM     81  CA  HIS    81      18.049  -4.036   0.456  1.00 25.00           C
ATOM     82  CA  HIS    82      16.103  -4.041   3.763  1.00 25.00           C
ATOM     83  CA  HIS    83      18.214  -1.101   4.936  1.00 25.00           C
ATOM     84  CA  HIS    84      15.922  -1.206   8.004  1.00 25.00           C
ATOM     85  CA  HIS    85      14.111  -4.099   9.762  1.00 25.00           C
TER
END
