
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0363AL316_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   35 , name T0363_D1.pdb
# PARAMETERS: T0363AL316_2-D1.T0363_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:    35        11 - 56          4.04     4.04
  LCS_AVERAGE:     76.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        29 - 46          1.83     5.33
  LCS_AVERAGE:     29.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        34 - 44          1.00     5.54
  LONGEST_CONTINUOUS_SEGMENT:    11        35 - 45          0.68     6.40
  LCS_AVERAGE:     16.83

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:   46
LCS_GDT     N      11     N      11      0   11   35     0    0    0    4    8   23   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     Q      12     Q      12      9   11   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     I      13     I      13      9   11   35     3   12   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     N      14     N      14      9   11   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     I      15     I      15      9   11   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     E      16     E      16      9   11   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     I      17     I      17      9   11   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     A      18     A      18      9   11   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     Y      19     Y      19      9   11   35     4   12   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     A      20     A      20      9   11   35     4    6   17   21   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     F      21     F      21      4   11   35     3    4    4    7   12   20   26   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     P      22     P      22      4    5   35     3    4    4    5    5    6    8    8   16   20   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     E      23     E      23      4    5   35     3    4    4    5    5    6    6    7    8    8   16   16   18   20   24   35   35   35   35   35 
LCS_GDT     R      24     R      24      4    5   35     3    3    4    5    5    6    6    7   14   14   16   16   19   32   33   35   35   35   35   35 
LCS_GDT     S      29     S      29      5   18   35     3   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     F      30     F      30      5   18   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     Q      31     Q      31      5   18   35     3   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     V      32     V      32      5   18   35     3   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     D      33     D      33      5   18   35     3    6   10   18   22   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     E      34     E      34     11   18   35     3    7   10   12   23   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     G      35     G      35     11   18   35     3   10   11   18   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     I      36     I      36     11   18   35     5   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     T      37     T      37     11   18   35     5   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     V      38     V      38     11   18   35     7   11   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     Q      39     Q      39     11   18   35     7   10   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     T      40     T      40     11   18   35     7   10   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     A      41     A      41     11   18   35     7   10   15   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     I      42     I      42     11   18   35     7   10   15   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     T      43     T      43     11   18   35     7   10   14   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     Q      44     Q      44     11   18   35     7   10   13   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     S      45     S      45     11   18   35     4   10   11   12   18   25   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     G      46     G      46      8   18   35     3    3    5    8   12   15   24   26   28   30   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     I      54     I      54      3    3   35     3    3    3    4    5    6   11   27   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     D      55     D      55      3    3   35     3    3    4   21   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_GDT     L      56     L      56      3    3   35     7   13   17   22   24   26   27   29   30   31   31   32   33   33   33   35   35   35   35   35 
LCS_AVERAGE  LCS_A:  40.68  (  16.83   29.13   76.09 )

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      7     13     17     22     24     26     27     29     30     31     31     32     33     33     33     35     35     35     35     35 
GDT PERCENT_CA  15.22  28.26  36.96  47.83  52.17  56.52  58.70  63.04  65.22  67.39  67.39  69.57  71.74  71.74  71.74  76.09  76.09  76.09  76.09  76.09
GDT RMS_LOCAL    0.32   0.68   0.90   1.31   1.47   1.61   1.73   1.97   2.14   2.35   2.35   2.58   3.01   3.01   3.01   4.04   4.04   4.04   4.04   4.04
GDT RMS_ALL_CA   5.90   4.44   4.36   4.34   4.33   4.33   4.33   4.34   4.33   4.23   4.23   4.26   4.14   4.14   4.14   4.04   4.04   4.04   4.04   4.04

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11          3.888
LGA    Q      12      Q      12          1.045
LGA    I      13      I      13          1.335
LGA    N      14      N      14          0.478
LGA    I      15      I      15          1.160
LGA    E      16      E      16          1.386
LGA    I      17      I      17          1.453
LGA    A      18      A      18          1.773
LGA    Y      19      Y      19          1.756
LGA    A      20      A      20          2.270
LGA    F      21      F      21          6.196
LGA    P      22      P      22         10.005
LGA    E      23      E      23         13.839
LGA    R      24      R      24         12.288
LGA    S      29      S      29          1.050
LGA    F      30      F      30          1.032
LGA    Q      31      Q      31          1.327
LGA    V      32      V      32          0.449
LGA    D      33      D      33          2.743
LGA    E      34      E      34          3.703
LGA    G      35      G      35          2.470
LGA    I      36      I      36          0.470
LGA    T      37      T      37          0.693
LGA    V      38      V      38          0.898
LGA    Q      39      Q      39          1.312
LGA    T      40      T      40          1.005
LGA    A      41      A      41          1.610
LGA    I      42      I      42          1.899
LGA    T      43      T      43          2.316
LGA    Q      44      Q      44          2.376
LGA    S      45      S      45          3.967
LGA    G      46      G      46          6.353
LGA    I      54      I      54          5.102
LGA    D      55      D      55          2.608
LGA    L      56      L      56          1.596

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   35   46    4.0     29    1.97    53.804    49.397     1.399

LGA_LOCAL      RMSD =  1.974  Number of atoms =   29  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.344  Number of atoms =   35 
Std_ALL_ATOMS  RMSD =  4.036  (standard rmsd on all 35 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.535549 * X  +  -0.202063 * Y  +  -0.819975 * Z  +  26.458868
  Y_new =  -0.508971 * X  +  -0.697572 * Y  +   0.504323 * Z  +  15.573690
  Z_new =  -0.673897 * X  +   0.687432 * Y  +   0.270740 * Z  +   8.872012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.195610   -1.945983  [ DEG:    68.5034   -111.4966 ]
  Theta =   0.739470    2.402122  [ DEG:    42.3685    137.6315 ]
  Phi   =  -2.381634    0.759959  [ DEG:  -136.4576     43.5424 ]
 
# 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: T0363AL316_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL316_2-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   35   46   4.0   29   1.97  49.397     4.04
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL316_2-D1
REMARK Aligment from pdb entry: 1ryj_A
ATOM      5  N   ASN    11      12.122  -0.601  13.696  1.00  0.00              
ATOM      6  CA  ASN    11      12.825  -0.805  12.439  1.00  0.00              
ATOM      7  C   ASN    11      13.975   0.189  12.346  1.00  0.00              
ATOM      8  O   ASN    11      13.764   1.399  12.420  1.00  0.00              
ATOM      9  N   GLN    12      16.860   2.244  10.507  1.00  0.00              
ATOM     10  CA  GLN    12      17.082   2.794   9.187  1.00  0.00              
ATOM     11  C   GLN    12      16.846   4.288   9.178  1.00  0.00              
ATOM     12  O   GLN    12      15.702   4.742   9.242  1.00  0.00              
ATOM     13  N   ILE    13      17.922   5.052   9.114  1.00  0.00              
ATOM     14  CA  ILE    13      17.829   6.502   9.212  1.00  0.00              
ATOM     15  C   ILE    13      18.152   7.162   7.878  1.00  0.00              
ATOM     16  O   ILE    13      19.158   6.848   7.246  1.00  0.00              
ATOM     17  N   ASN    14      17.293   8.068   7.449  1.00  0.00              
ATOM     18  CA  ASN    14      17.549   8.845   6.251  1.00  0.00              
ATOM     19  C   ASN    14      17.709  10.312   6.612  1.00  0.00              
ATOM     20  O   ASN    14      16.855  10.898   7.279  1.00  0.00              
ATOM     21  N   ILE    15      18.812  10.895   6.182  1.00  0.00              
ATOM     22  CA  ILE    15      19.140  12.262   6.536  1.00  0.00              
ATOM     23  C   ILE    15      19.705  12.997   5.334  1.00  0.00              
ATOM     24  O   ILE    15      20.029  12.379   4.316  1.00  0.00              
ATOM     25  N   GLU    16      19.815  14.308   5.440  1.00  0.00              
ATOM     26  CA  GLU    16      20.363  15.093   4.357  1.00  0.00              
ATOM     27  C   GLU    16      21.525  15.947   4.839  1.00  0.00              
ATOM     28  O   GLU    16      21.450  16.596   5.885  1.00  0.00              
ATOM     29  N   ILE    17      22.610  15.902   4.091  1.00  0.00              
ATOM     30  CA  ILE    17      23.753  16.753   4.347  1.00  0.00              
ATOM     31  C   ILE    17      23.846  17.799   3.249  1.00  0.00              
ATOM     32  O   ILE    17      23.972  17.459   2.078  1.00  0.00              
ATOM     33  N   ALA    18      23.759  19.065   3.614  1.00  0.00              
ATOM     34  CA  ALA    18      23.793  20.129   2.626  1.00  0.00              
ATOM     35  C   ALA    18      25.187  20.749   2.576  1.00  0.00              
ATOM     36  O   ALA    18      25.778  21.077   3.605  1.00  0.00              
ATOM     37  N   TYR    19      25.727  20.842   1.370  1.00  0.00              
ATOM     38  CA  TYR    19      27.037  21.437   1.141  1.00  0.00              
ATOM     39  C   TYR    19      26.994  22.251  -0.157  1.00  0.00              
ATOM     40  O   TYR    19      25.910  22.580  -0.637  1.00  0.00              
ATOM     41  N   ALA    20      28.156  22.579  -0.723  1.00  0.00              
ATOM     42  CA  ALA    20      28.222  23.293  -2.003  1.00  0.00              
ATOM     43  C   ALA    20      27.567  22.472  -3.108  1.00  0.00              
ATOM     44  O   ALA    20      27.057  23.011  -4.089  1.00  0.00              
ATOM     45  N   PHE    21      27.587  21.156  -2.923  1.00  0.00              
ATOM     46  CA  PHE    21      26.978  20.215  -3.860  1.00  0.00              
ATOM     47  C   PHE    21      25.453  20.242  -3.733  1.00  0.00              
ATOM     48  O   PHE    21      24.731  19.682  -4.558  1.00  0.00              
ATOM     49  N   PRO    22      24.970  20.929  -2.706  1.00  0.00              
ATOM     50  CA  PRO    22      23.549  20.994  -2.447  1.00  0.00              
ATOM     51  C   PRO    22      23.144  20.037  -1.349  1.00  0.00              
ATOM     52  O   PRO    22      23.994  19.561  -0.593  1.00  0.00              
ATOM     53  N   GLU    23      21.853  19.762  -1.250  1.00  0.00              
ATOM     54  CA  GLU    23      21.357  18.786  -0.295  1.00  0.00              
ATOM     55  C   GLU    23      21.620  17.377  -0.794  1.00  0.00              
ATOM     56  O   GLU    23      21.134  16.976  -1.856  1.00  0.00              
ATOM     57  N   ARG    24      22.397  16.635  -0.030  1.00  0.00              
ATOM     58  CA  ARG    24      22.744  15.269  -0.373  1.00  0.00              
ATOM     59  C   ARG    24      21.905  14.313   0.466  1.00  0.00              
ATOM     60  O   ARG    24      21.929  14.375   1.695  1.00  0.00              
ATOM     61  N   SER    29      21.147  13.454  -0.197  1.00  0.00              
ATOM     62  CA  SER    29      20.270  12.521   0.493  1.00  0.00              
ATOM     63  C   SER    29      20.898  11.136   0.566  1.00  0.00              
ATOM     64  O   SER    29      21.228  10.534  -0.458  1.00  0.00              
ATOM     65  N   PHE    30      21.084  10.652   1.783  1.00  0.00              
ATOM     66  CA  PHE    30      21.609   9.316   2.000  1.00  0.00              
ATOM     67  C   PHE    30      20.954   8.690   3.224  1.00  0.00              
ATOM     68  O   PHE    30      20.686   9.373   4.217  1.00  0.00              
ATOM     69  N   GLN    31      20.668   7.400   3.145  1.00  0.00              
ATOM     70  CA  GLN    31      20.068   6.694   4.263  1.00  0.00              
ATOM     71  C   GLN    31      20.950   5.530   4.702  1.00  0.00              
ATOM     72  O   GLN    31      21.528   4.821   3.879  1.00  0.00              
ATOM     73  N   VAL    32      21.059   5.359   6.008  1.00  0.00              
ATOM     74  CA  VAL    32      21.911   4.337   6.591  1.00  0.00              
ATOM     75  C   VAL    32      21.062   3.383   7.425  1.00  0.00              
ATOM     76  O   VAL    32      20.249   3.820   8.244  1.00  0.00              
ATOM     77  N   ASP    33      21.243   2.086   7.206  1.00  0.00              
ATOM     78  CA  ASP    33      20.457   1.087   7.908  1.00  0.00              
ATOM     79  C   ASP    33      20.691   1.100   9.407  1.00  0.00              
ATOM     80  O   ASP    33      19.788   0.787  10.185  1.00  0.00              
ATOM     81  N   GLU    34      21.901   1.444   9.815  1.00  0.00              
ATOM     82  CA  GLU    34      22.233   1.519  11.228  1.00  0.00              
ATOM     83  C   GLU    34      22.361   2.971  11.674  1.00  0.00              
ATOM     84  O   GLU    34      23.125   3.739  11.089  1.00  0.00              
ATOM     85  N   GLY    35      21.589   3.373  12.695  1.00  0.00              
ATOM     86  CA  GLY    35      21.678   4.716  13.280  1.00  0.00              
ATOM     87  C   GLY    35      23.043   4.960  13.920  1.00  0.00              
ATOM     88  O   GLY    35      23.379   4.363  14.945  1.00  0.00              
ATOM     89  N   ILE    36      23.824   5.840  13.310  1.00  0.00              
ATOM     90  CA  ILE    36      25.214   6.034  13.696  1.00  0.00              
ATOM     91  C   ILE    36      25.473   7.456  14.179  1.00  0.00              
ATOM     92  O   ILE    36      24.582   8.308  14.166  1.00  0.00              
ATOM     93  N   THR    37      26.701   7.693  14.604  1.00  0.00              
ATOM     94  CA  THR    37      27.125   8.983  15.111  1.00  0.00              
ATOM     95  C   THR    37      27.658   9.844  13.966  1.00  0.00              
ATOM     96  O   THR    37      28.047   9.314  12.922  1.00  0.00              
ATOM     97  N   VAL    38      27.656  11.168  14.152  1.00  0.00              
ATOM     98  CA  VAL    38      28.187  12.096  13.151  1.00  0.00              
ATOM     99  C   VAL    38      29.582  11.662  12.713  1.00  0.00              
ATOM    100  O   VAL    38      29.870  11.573  11.519  1.00  0.00              
ATOM    101  N   GLN    39      30.423  11.355  13.693  1.00  0.00              
ATOM    102  CA  GLN    39      31.813  10.993  13.450  1.00  0.00              
ATOM    103  C   GLN    39      31.942   9.761  12.560  1.00  0.00              
ATOM    104  O   GLN    39      32.919   9.628  11.830  1.00  0.00              
ATOM    105  N   THR    40      30.965   8.866  12.618  1.00  0.00              
ATOM    106  CA  THR    40      31.014   7.643  11.819  1.00  0.00              
ATOM    107  C   THR    40      30.952   7.978  10.336  1.00  0.00              
ATOM    108  O   THR    40      31.886   7.706   9.585  1.00  0.00              
ATOM    109  N   ALA    41      29.851   8.592   9.925  1.00  0.00              
ATOM    110  CA  ALA    41      29.652   8.955   8.529  1.00  0.00              
ATOM    111  C   ALA    41      30.677   9.997   8.095  1.00  0.00              
ATOM    112  O   ALA    41      31.212   9.936   6.983  1.00  0.00              
ATOM    113  N   ILE    42      30.970  10.933   8.989  1.00  0.00              
ATOM    114  CA  ILE    42      31.950  11.975   8.718  1.00  0.00              
ATOM    115  C   ILE    42      33.331  11.363   8.509  1.00  0.00              
ATOM    116  O   ILE    42      34.075  11.784   7.630  1.00  0.00              
ATOM    117  N   THR    43      33.662  10.371   9.335  1.00  0.00              
ATOM    118  CA  THR    43      34.940   9.694   9.238  1.00  0.00              
ATOM    119  C   THR    43      35.060   8.802   8.011  1.00  0.00              
ATOM    120  O   THR    43      36.140   8.679   7.433  1.00  0.00              
ATOM    121  N   GLN    44      33.958   8.168   7.613  1.00  0.00              
ATOM    122  CA  GLN    44      33.964   7.284   6.445  1.00  0.00              
ATOM    123  C   GLN    44      34.247   8.061   5.164  1.00  0.00              
ATOM    124  O   GLN    44      35.006   7.612   4.307  1.00  0.00              
ATOM    125  N   SER    45      33.636   9.229   5.035  1.00  0.00              
ATOM    126  CA  SER    45      33.911  10.111   3.905  1.00  0.00              
ATOM    127  C   SER    45      35.118  10.986   4.216  1.00  0.00              
ATOM    128  O   SER    45      35.640  11.682   3.345  1.00  0.00              
ATOM    129  N   GLY    46      35.550  10.904   5.472  1.00  0.00              
ATOM    130  CA  GLY    46      36.602  11.747   6.037  1.00  0.00              
ATOM    131  C   GLY    46      36.482  13.189   5.563  1.00  0.00              
ATOM    132  O   GLY    46      37.280  13.668   4.752  1.00  0.00              
ATOM    133  N   ILE    54      35.454  13.866   6.041  1.00  0.00              
ATOM    134  CA  ILE    54      35.288  15.278   5.759  1.00  0.00              
ATOM    135  C   ILE    54      35.937  16.078   6.876  1.00  0.00              
ATOM    136  O   ILE    54      35.481  16.041   8.020  1.00  0.00              
ATOM    137  N   ASP    55      37.027  16.789   6.562  1.00  0.00              
ATOM    138  CA  ASP    55      37.825  17.491   7.563  1.00  0.00              
ATOM    139  C   ASP    55      37.027  18.544   8.320  1.00  0.00              
ATOM    140  O   ASP    55      36.764  19.635   7.805  1.00  0.00              
ATOM    141  N   LEU    56      36.655  18.209   9.552  1.00  0.00              
ATOM    142  CA  LEU    56      35.971  19.142  10.446  1.00  0.00              
ATOM    143  C   LEU    56      36.912  20.301  10.792  1.00  0.00              
ATOM    144  O   LEU    56      36.508  21.322  11.343  1.00  0.00              
END
