
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0335AL257_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   29 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_5-D1.T0335_D1.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:    29         5 - 40          4.31     4.31
  LCS_AVERAGE:     80.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13         5 - 17          1.65     8.47
  LCS_AVERAGE:     28.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12         5 - 16          0.45     9.24
  LCS_AVERAGE:     24.33

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:   36
LCS_GDT     A       5     A       5     12   13   29     8   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     K       6     K       6     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     I       7     I       7     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     A       8     A       8     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     R       9     R       9     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     I      10     I      10     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     N      11     N      11     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     E      12     E      12     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     L      13     L      13     12   13   29    10   12   12   12   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     A      14     A      14     12   13   29    10   12   12   13   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     A      15     A      15     12   13   29    10   12   12   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     K      16     K      16     12   13   29     8   12   12   12   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     A      17     A      17      4   13   29     3    4    5    5    5   17   20   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     K      18     K      18      4    5   29     3    4    5    5    5    6    8   17   18   19   23   25   26   28   28   28   29   29   29   29 
LCS_GDT     A      19     A      19      4    5   29     0    4    5    5    5    5    5    6    9    9   11   18   18   21   21   25   29   29   29   29 
LCS_GDT     K      27     K      27      7    7   29     4    6    9   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     A      28     A      28      7    7   29     4    6    9   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     E      29     E      29      7    7   29     5    6    9   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     Q      30     Q      30      7    7   29     5    6    9   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     Q      31     Q      31      7    7   29     5    6    9   13   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     K      32     K      32      7    9   29     5    6    9   13   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     L      33     L      33      7    9   29     5    6    9   14   19   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     R      34     R      34      7    9   29     7    7    7    7    8    9   10   12   14   17   21   25   27   28   28   28   29   29   29   29 
LCS_GDT     Q      35     Q      35      7    9   29     7    7    7    7    8    9   10   16   19   22   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     E      36     E      36      7    9   29     7    7    7   10   18   19   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     Y      37     Y      37      7    9   29     7    7    9   13   18   20   21   22   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     L      38     L      38      7    9   29     7    7    7    7   10   13   16   20   22   23   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     K      39     K      39      7    9   29     7    7    7    7    8   11   12   16   19   22   24   25   27   28   28   28   29   29   29   29 
LCS_GDT     G      40     G      40      7    9   29     7    7    7    7    8    9    9   11   14   16   21   25   27   28   28   28   29   29   29   29 
LCS_AVERAGE  LCS_A:  44.38  (  24.33   28.26   80.56 )

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     12     12     14     19     20     21     22     22     23     24     25     27     28     28     28     29     29     29     29 
GDT PERCENT_CA  27.78  33.33  33.33  38.89  52.78  55.56  58.33  61.11  61.11  63.89  66.67  69.44  75.00  77.78  77.78  77.78  80.56  80.56  80.56  80.56
GDT RMS_LOCAL    0.34   0.45   0.45   1.44   1.87   1.98   2.12   2.30   2.30   2.72   3.07   3.25   3.60   3.94   3.94   3.94   4.31   4.31   4.31   4.31
GDT RMS_ALL_CA   9.25   9.24   9.24   6.08   5.32   5.03   4.82   4.88   4.88   4.60   4.53   4.58   4.46   4.36   4.36   4.36   4.31   4.31   4.31   4.31

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.421
LGA    K       6      K       6          2.547
LGA    I       7      I       7          1.720
LGA    A       8      A       8          1.494
LGA    R       9      R       9          2.285
LGA    I      10      I      10          2.313
LGA    N      11      N      11          1.689
LGA    E      12      E      12          2.090
LGA    L      13      L      13          3.140
LGA    A      14      A      14          3.163
LGA    A      15      A      15          2.087
LGA    K      16      K      16          2.286
LGA    A      17      A      17          3.854
LGA    K      18      K      18          7.559
LGA    A      19      A      19         10.353
LGA    K      27      K      27          2.427
LGA    A      28      A      28          2.483
LGA    E      29      E      29          2.095
LGA    Q      30      Q      30          2.166
LGA    Q      31      Q      31          1.059
LGA    K      32      K      32          0.987
LGA    L      33      L      33          1.098
LGA    R      34      R      34          6.863
LGA    Q      35      Q      35          7.644
LGA    E      36      E      36          3.752
LGA    Y      37      Y      37          2.680
LGA    L      38      L      38          8.170
LGA    K      39      K      39         10.354
LGA    G      40      G      40          9.985

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29   36    4.0     22    2.30    52.778    48.694     0.917

LGA_LOCAL      RMSD =  2.300  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.803  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  4.311  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.302013 * X  +  -0.645948 * Y  +   0.701099 * Z  +  13.965701
  Y_new =  -0.788330 * X  +  -0.244299 * Y  +  -0.564672 * Z  +  14.239937
  Z_new =   0.536026 * X  +  -0.723235 * Y  +  -0.435439 * Z  +   0.837574 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.112737    1.028856  [ DEG:  -121.0509     58.9491 ]
  Theta =  -0.565723   -2.575870  [ DEG:   -32.4135   -147.5865 ]
  Phi   =  -1.936654    1.204939  [ DEG:  -110.9621     69.0379 ]
 
# 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: T0335AL257_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_5-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29   36   4.0   22   2.30  48.694     4.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_5-D1
REMARK Aligment from pdb entry: 1yoz_A
ATOM     17  N   ALA     5       0.261  -9.279  -6.504  1.00  0.00              
ATOM     18  CA  ALA     5       0.650  -8.820  -5.148  1.00  0.00              
ATOM     19  C   ALA     5       0.420  -7.350  -5.026  1.00  0.00              
ATOM     20  O   ALA     5      -0.091  -6.861  -4.028  1.00  0.00              
ATOM     21  N   LYS     6       0.764  -6.612  -6.069  1.00  0.00              
ATOM     22  CA  LYS     6       0.503  -5.185  -6.029  1.00  0.00              
ATOM     23  C   LYS     6      -0.976  -4.793  -5.809  1.00  0.00              
ATOM     24  O   LYS     6      -1.270  -3.937  -4.940  1.00  0.00              
ATOM     25  N   ILE     7      -1.840  -5.338  -6.662  1.00  0.00              
ATOM     26  CA  ILE     7      -3.279  -5.168  -6.598  1.00  0.00              
ATOM     27  C   ILE     7      -3.856  -5.543  -5.201  1.00  0.00              
ATOM     28  O   ILE     7      -4.565  -4.752  -4.593  1.00  0.00              
ATOM     29  N   ALA     8      -3.534  -6.731  -4.702  1.00  0.00              
ATOM     30  CA  ALA     8      -4.024  -7.141  -3.376  1.00  0.00              
ATOM     31  C   ALA     8      -3.537  -6.216  -2.237  1.00  0.00              
ATOM     32  O   ALA     8      -4.298  -5.911  -1.327  1.00  0.00              
ATOM     33  N   ARG     9      -2.287  -5.797  -2.280  1.00  0.00              
ATOM     34  CA  ARG     9      -1.750  -4.845  -1.304  1.00  0.00              
ATOM     35  C   ARG     9      -2.365  -3.471  -1.379  1.00  0.00              
ATOM     36  O   ARG     9      -2.488  -2.781  -0.362  1.00  0.00              
ATOM     37  N   ILE    10      -2.681  -3.020  -2.590  1.00  0.00              
ATOM     38  CA  ILE    10      -3.426  -1.772  -2.734  1.00  0.00              
ATOM     39  C   ILE    10      -4.797  -1.890  -2.091  1.00  0.00              
ATOM     40  O   ILE    10      -5.229  -0.980  -1.367  1.00  0.00              
ATOM     41  N   ASN    11      -5.479  -2.997  -2.374  1.00  0.00              
ATOM     42  CA  ASN    11      -6.819  -3.289  -1.808  1.00  0.00              
ATOM     43  C   ASN    11      -6.824  -3.362  -0.267  1.00  0.00              
ATOM     44  O   ASN    11      -7.756  -2.842   0.389  1.00  0.00              
ATOM     45  N   GLU    12      -5.782  -3.955   0.319  1.00  0.00              
ATOM     46  CA  GLU    12      -5.624  -3.984   1.801  1.00  0.00              
ATOM     47  C   GLU    12      -5.615  -2.559   2.396  1.00  0.00              
ATOM     48  O   GLU    12      -6.259  -2.294   3.457  1.00  0.00              
ATOM     49  N   LEU    13      -4.906  -1.655   1.735  1.00  0.00              
ATOM     50  CA  LEU    13      -4.723  -0.280   2.231  1.00  0.00              
ATOM     51  C   LEU    13      -6.018   0.494   2.044  1.00  0.00              
ATOM     52  O   LEU    13      -6.478   1.164   2.960  1.00  0.00              
ATOM     53  N   ALA    14      -6.622   0.368   0.868  1.00  0.00              
ATOM     54  CA  ALA    14      -7.855   1.080   0.563  1.00  0.00              
ATOM     55  C   ALA    14      -9.055   0.621   1.431  1.00  0.00              
ATOM     56  O   ALA    14      -9.934   1.431   1.778  1.00  0.00              
ATOM     57  N   ALA    15      -9.108  -0.671   1.744  1.00  0.00              
ATOM     58  CA  ALA    15     -10.133  -1.206   2.651  1.00  0.00              
ATOM     59  C   ALA    15      -9.860  -0.852   4.134  1.00  0.00              
ATOM     60  O   ALA    15     -10.656  -1.203   5.010  1.00  0.00              
ATOM     61  N   LYS    16      -8.736  -0.189   4.407  1.00  0.00              
ATOM     62  CA  LYS    16      -8.401   0.202   5.772  1.00  0.00              
ATOM     63  C   LYS    16      -8.019  -0.994   6.618  1.00  0.00              
ATOM     64  O   LYS    16      -8.130  -0.935   7.863  1.00  0.00              
ATOM     65  N   ALA    17      -7.562  -2.071   5.957  1.00  0.00              
ATOM     66  CA  ALA    17      -7.052  -3.257   6.671  1.00  0.00              
ATOM     67  C   ALA    17      -5.588  -3.147   7.017  1.00  0.00              
ATOM     68  O   ALA    17      -5.104  -3.876   7.865  1.00  0.00              
ATOM     69  N   LYS    18      -4.871  -2.256   6.346  1.00  0.00              
ATOM     70  CA  LYS    18      -3.460  -2.006   6.660  1.00  0.00              
ATOM     71  C   LYS    18      -3.241  -0.516   6.652  1.00  0.00              
ATOM     72  O   LYS    18      -3.942   0.202   5.959  1.00  0.00              
ATOM     73  N   ALA    19      -2.255  -0.059   7.421  1.00  0.00              
ATOM     74  CA  ALA    19      -1.976   1.353   7.604  1.00  0.00              
ATOM     75  C   ALA    19      -1.697   2.054   6.282  1.00  0.00              
ATOM     76  O   ALA    19      -0.993   1.526   5.448  1.00  0.00              
ATOM     77  N   LYS    27      -2.216   3.259   6.116  1.00  0.00              
ATOM     78  CA  LYS    27      -1.895   4.110   4.959  1.00  0.00              
ATOM     79  C   LYS    27      -0.381   4.446   4.847  1.00  0.00              
ATOM     80  O   LYS    27       0.111   4.819   3.777  1.00  0.00              
ATOM     81  N   ALA    28       0.361   4.237   5.928  1.00  0.00              
ATOM     82  CA  ALA    28       1.805   4.402   5.947  1.00  0.00              
ATOM     83  C   ALA    28       2.476   3.445   4.966  1.00  0.00              
ATOM     84  O   ALA    28       3.497   3.756   4.364  1.00  0.00              
ATOM     85  N   GLU    29       1.866   2.285   4.793  1.00  0.00              
ATOM     86  CA  GLU    29       2.368   1.271   3.899  1.00  0.00              
ATOM     87  C   GLU    29       2.384   1.707   2.432  1.00  0.00              
ATOM     88  O   GLU    29       3.114   1.110   1.640  1.00  0.00              
ATOM     89  N   GLN    30       1.609   2.738   2.079  1.00  0.00              
ATOM     90  CA  GLN    30       1.533   3.231   0.698  1.00  0.00              
ATOM     91  C   GLN    30       2.894   3.685   0.187  1.00  0.00              
ATOM     92  O   GLN    30       3.151   3.626  -1.026  1.00  0.00              
ATOM     93  N   GLN    31       3.760   4.091   1.125  1.00  0.00              
ATOM     94  CA  GLN    31       5.044   4.660   0.814  1.00  0.00              
ATOM     95  C   GLN    31       5.992   3.646   0.153  1.00  0.00              
ATOM     96  O   GLN    31       6.575   3.947  -0.911  1.00  0.00              
ATOM     97  N   LYS    32       6.169   2.479   0.784  1.00  0.00              
ATOM     98  CA  LYS    32       6.974   1.421   0.187  1.00  0.00              
ATOM     99  C   LYS    32       6.300   0.878  -1.065  1.00  0.00              
ATOM    100  O   LYS    32       6.967   0.561  -2.038  1.00  0.00              
ATOM    101  N   LEU    33       4.975   0.775  -1.034  1.00  0.00              
ATOM    102  CA  LEU    33       4.222   0.316  -2.200  1.00  0.00              
ATOM    103  C   LEU    33       4.357   1.265  -3.374  1.00  0.00              
ATOM    104  O   LEU    33       4.410   0.825  -4.497  1.00  0.00              
ATOM    105  N   ARG    34       8.588   2.650  -7.285  1.00  0.00              
ATOM    106  CA  ARG    34       8.617   1.869  -8.536  1.00  0.00              
ATOM    107  C   ARG    34       9.571   0.660  -8.581  1.00  0.00              
ATOM    108  O   ARG    34       9.301  -0.333  -9.271  1.00  0.00              
ATOM    109  N   GLN    35      10.668   0.740  -7.830  1.00  0.00              
ATOM    110  CA  GLN    35      11.611  -0.339  -7.697  1.00  0.00              
ATOM    111  C   GLN    35      10.985  -1.495  -6.942  1.00  0.00              
ATOM    112  O   GLN    35      11.169  -2.646  -7.325  1.00  0.00              
ATOM    113  N   GLU    36      10.275  -1.212  -5.852  1.00  0.00              
ATOM    114  CA  GLU    36       9.562  -2.284  -5.157  1.00  0.00              
ATOM    115  C   GLU    36       8.437  -2.844  -6.039  1.00  0.00              
ATOM    116  O   GLU    36       8.180  -4.027  -6.015  1.00  0.00              
ATOM    117  N   TYR    37       7.748  -1.986  -6.783  1.00  0.00              
ATOM    118  CA  TYR    37       6.668  -2.441  -7.666  1.00  0.00              
ATOM    119  C   TYR    37       7.207  -3.413  -8.730  1.00  0.00              
ATOM    120  O   TYR    37       6.720  -4.532  -8.896  1.00  0.00              
ATOM    121  N   LEU    38       8.257  -2.976  -9.425  1.00  0.00              
ATOM    122  CA  LEU    38       8.948  -3.846 -10.370  1.00  0.00              
ATOM    123  C   LEU    38       9.313  -5.188  -9.707  1.00  0.00              
ATOM    124  O   LEU    38       9.019  -6.259 -10.234  1.00  0.00              
ATOM    125  N   LYS    39       9.906  -5.145  -8.512  1.00  0.00              
ATOM    126  CA  LYS    39      10.214  -6.395  -7.808  1.00  0.00              
ATOM    127  C   LYS    39       9.004  -7.265  -7.454  1.00  0.00              
ATOM    128  O   LYS    39       9.114  -8.498  -7.462  1.00  0.00              
ATOM    129  N   GLY    40       7.881  -6.641  -7.050  1.00  0.00              
ATOM    130  CA  GLY    40       6.679  -7.392  -6.699  1.00  0.00              
ATOM    131  C   GLY    40       6.223  -8.247  -7.857  1.00  0.00              
ATOM    132  O   GLY    40       5.851  -9.393  -7.679  1.00  0.00              
END
