
#######################################################
#                                                     #
#                        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   22 (   88),  selected   22 , name T0363AL381_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   22 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_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:    22        28 - 49          3.28     3.28
  LCS_AVERAGE:     47.83

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        28 - 45          1.84     3.87
  LCS_AVERAGE:     36.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        34 - 44          0.76     3.95
  LCS_AVERAGE:     18.58

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     K      28     K      28      6   18   22     5    6    7   10   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     S      29     S      29      6   18   22     5    6    7   10   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     F      30     F      30      6   18   22     5    6   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     Q      31     Q      31      6   18   22     5    9   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     V      32     V      32      6   18   22     5    6   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     D      33     D      33      8   18   22     3    9   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     E      34     E      34     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     G      35     G      35     11   18   22     3   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     I      36     I      36     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     T      37     T      37     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     V      38     V      38     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     Q      39     Q      39     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     T      40     T      40     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     A      41     A      41     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     I      42     I      42     11   18   22     6   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     T      43     T      43     11   18   22     4   10   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     Q      44     Q      44     11   18   22     6    9   13   15   17   17   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     S      45     S      45      9   18   22     3    5    8    9   13   16   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     G      46     G      46      6   17   22     3    5    7    9   13   16   17   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     I      47     I      47      6   12   22     3    5    6    8   10   13   14   18   19   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     L      48     L      48      5    9   22     3    5    5    6    7    8   11   12   13   21   21   21   21   22   22   22   22   22   22   22 
LCS_GDT     S      49     S      49      3    3   22     3    3    3    3    3    4    6    7    8    9   12   12   18   22   22   22   22   22   22   22 
LCS_AVERAGE  LCS_A:  34.16  (  18.58   36.07   47.83 )

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      6     10     13     15     17     17     17     18     19     21     21     21     21     22     22     22     22     22     22     22 
GDT PERCENT_CA  13.04  21.74  28.26  32.61  36.96  36.96  36.96  39.13  41.30  45.65  45.65  45.65  45.65  47.83  47.83  47.83  47.83  47.83  47.83  47.83
GDT RMS_LOCAL    0.29   0.66   0.99   1.19   1.56   1.56   1.56   1.84   2.19   2.81   2.81   2.81   2.81   3.28   3.28   3.28   3.28   3.28   3.28   3.28
GDT RMS_ALL_CA   3.66   4.02   3.87   3.93   4.05   4.05   4.05   3.87   3.64   3.36   3.36   3.36   3.36   3.28   3.28   3.28   3.28   3.28   3.28   3.28

#      Molecule1      Molecule2       DISTANCE
LGA    K      28      K      28          3.222
LGA    S      29      S      29          2.893
LGA    F      30      F      30          1.906
LGA    Q      31      Q      31          1.633
LGA    V      32      V      32          2.811
LGA    D      33      D      33          1.786
LGA    E      34      E      34          2.005
LGA    G      35      G      35          2.286
LGA    I      36      I      36          1.441
LGA    T      37      T      37          0.405
LGA    V      38      V      38          0.706
LGA    Q      39      Q      39          0.358
LGA    T      40      T      40          0.596
LGA    A      41      A      41          0.661
LGA    I      42      I      42          0.485
LGA    T      43      T      43          0.812
LGA    Q      44      Q      44          1.385
LGA    S      45      S      45          3.668
LGA    G      46      G      46          5.089
LGA    I      47      I      47          6.341
LGA    L      48      L      48          7.377
LGA    S      49      S      49         10.263

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22   46    4.0     18    1.84    35.326    37.201     0.930

LGA_LOCAL      RMSD =  1.836  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.638  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  3.275  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.654963 * X  +  -0.005728 * Y  +  -0.755639 * Z  +  22.445810
  Y_new =   0.739641 * X  +   0.199951 * Y  +  -0.642612 * Z  +   5.122771
  Z_new =   0.154772 * X  +  -0.979789 * Y  +  -0.126724 * Z  +   3.839168 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.699420    1.442172  [ DEG:   -97.3696     82.6304 ]
  Theta =  -0.155397   -2.986196  [ DEG:    -8.9036   -171.0964 ]
  Phi   =   2.295551   -0.846042  [ DEG:   131.5254    -48.4746 ]
 
# 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: T0363AL381_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_2-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22   46   4.0   18   1.84  37.201     3.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_2-D1
REMARK Aligment from pdb entry: 1rwsA
ATOM      1  N   LYS    28      21.630  14.392  -2.759  1.00  0.00              
ATOM      2  CA  LYS    28      21.588  12.973  -3.188  1.00  0.00              
ATOM      3  C   LYS    28      20.821  12.222  -2.096  1.00  0.00              
ATOM      4  O   LYS    28      21.392  11.987  -1.050  1.00  0.00              
ATOM      5  N   SER    29      19.530  12.039  -2.179  1.00  0.00              
ATOM      6  CA  SER    29      18.825  11.503  -0.966  1.00  0.00              
ATOM      7  C   SER    29      19.698  10.443  -0.289  1.00  0.00              
ATOM      8  O   SER    29      20.753  10.095  -0.779  1.00  0.00              
ATOM      9  N   PHE    30      19.357  10.030   0.917  1.00  0.00              
ATOM     10  CA  PHE    30      20.365   9.195   1.671  1.00  0.00              
ATOM     11  C   PHE    30      19.703   8.384   2.808  1.00  0.00              
ATOM     12  O   PHE    30      19.120   9.011   3.669  1.00  0.00              
ATOM     13  N   GLN    31      19.642   7.066   2.871  1.00  0.00              
ATOM     14  CA  GLN    31      18.872   6.381   3.965  1.00  0.00              
ATOM     15  C   GLN    31      19.378   6.866   5.333  1.00  0.00              
ATOM     16  O   GLN    31      19.617   8.038   5.547  1.00  0.00              
ATOM     17  N   VAL    32      19.539   5.961   6.260  1.00  0.00              
ATOM     18  CA  VAL    32      20.023   6.307   7.634  1.00  0.00              
ATOM     19  C   VAL    32      20.073   4.975   8.394  1.00  0.00              
ATOM     20  O   VAL    32      20.126   3.947   7.747  1.00  0.00              
ATOM     21  N   ASP    33      20.279   4.904   9.692  1.00  0.00              
ATOM     22  CA  ASP    33      20.609   3.534  10.203  1.00  0.00              
ATOM     23  C   ASP    33      20.410   3.318  11.722  1.00  0.00              
ATOM     24  O   ASP    33      19.288   3.419  12.181  1.00  0.00              
ATOM     25  N   GLU    34      21.398   2.959  12.536  1.00  0.00              
ATOM     26  CA  GLU    34      21.065   2.685  13.974  1.00  0.00              
ATOM     27  C   GLU    34      22.348   2.350  14.757  1.00  0.00              
ATOM     28  O   GLU    34      23.001   1.357  14.504  1.00  0.00              
ATOM     29  N   GLY    35      22.738   3.208  15.673  1.00  0.00              
ATOM     30  CA  GLY    35      24.009   2.973  16.431  1.00  0.00              
ATOM     31  C   GLY    35      25.102   3.938  15.938  1.00  0.00              
ATOM     32  O   GLY    35      26.035   4.274  16.642  1.00  0.00              
ATOM     33  N   ILE    36      24.981   4.344  14.710  1.00  0.00              
ATOM     34  CA  ILE    36      26.010   5.268  14.099  1.00  0.00              
ATOM     35  C   ILE    36      25.665   6.652  14.641  1.00  0.00              
ATOM     36  O   ILE    36      25.215   6.851  15.753  1.00  0.00              
ATOM     37  N   THR    37      26.370   7.495  14.013  1.00  0.00              
ATOM     38  CA  THR    37      26.700   8.869  14.456  1.00  0.00              
ATOM     39  C   THR    37      26.793   9.820  13.245  1.00  0.00              
ATOM     40  O   THR    37      27.245   9.403  12.197  1.00  0.00              
ATOM     41  N   VAL    38      26.695  11.125  13.432  1.00  0.00              
ATOM     42  CA  VAL    38      27.183  12.074  12.376  1.00  0.00              
ATOM     43  C   VAL    38      28.571  11.671  11.891  1.00  0.00              
ATOM     44  O   VAL    38      28.808  11.527  10.708  1.00  0.00              
ATOM     45  N   GLN    39      29.527  11.678  12.779  1.00  0.00              
ATOM     46  CA  GLN    39      30.940  11.507  12.368  1.00  0.00              
ATOM     47  C   GLN    39      31.018  10.440  11.281  1.00  0.00              
ATOM     48  O   GLN    39      31.363  10.712  10.148  1.00  0.00              
ATOM     49  N   THR    40      30.647   9.230  11.607  1.00  0.00              
ATOM     50  CA  THR    40      30.659   8.172  10.534  1.00  0.00              
ATOM     51  C   THR    40      30.095   8.707   9.215  1.00  0.00              
ATOM     52  O   THR    40      30.794   8.710   8.221  1.00  0.00              
ATOM     53  N   ALA    41      28.837   9.044   9.121  1.00  0.00              
ATOM     54  CA  ALA    41      28.324   9.429   7.772  1.00  0.00              
ATOM     55  C   ALA    41      29.378  10.310   7.093  1.00  0.00              
ATOM     56  O   ALA    41      29.684  10.175   5.925  1.00  0.00              
ATOM     57  N   ILE    42      29.974  11.149   7.871  1.00  0.00              
ATOM     58  CA  ILE    42      31.083  12.021   7.378  1.00  0.00              
ATOM     59  C   ILE    42      32.298  11.142   7.059  1.00  0.00              
ATOM     60  O   ILE    42      32.936  11.288   6.036  1.00  0.00              
ATOM     61  N   THR    43      32.491  10.120   7.843  1.00  0.00              
ATOM     62  CA  THR    43      33.515   9.083   7.514  1.00  0.00              
ATOM     63  C   THR    43      33.248   8.493   6.127  1.00  0.00              
ATOM     64  O   THR    43      34.169   8.151   5.413  1.00  0.00              
ATOM     65  N   GLN    44      32.009   8.387   5.714  1.00  0.00              
ATOM     66  CA  GLN    44      31.770   7.831   4.331  1.00  0.00              
ATOM     67  C   GLN    44      32.407   8.802   3.336  1.00  0.00              
ATOM     68  O   GLN    44      32.735   8.470   2.215  1.00  0.00              
ATOM     69  N   SER    45      32.711   9.955   3.837  1.00  0.00              
ATOM     70  CA  SER    45      33.480  10.911   3.004  1.00  0.00              
ATOM     71  C   SER    45      34.964  10.639   3.250  1.00  0.00              
ATOM     72  O   SER    45      35.819  11.242   2.634  1.00  0.00              
ATOM     73  N   GLY    46      35.280   9.859   4.253  1.00  0.00              
ATOM     74  CA  GLY    46      36.707   9.712   4.640  1.00  0.00              
ATOM     75  C   GLY    46      37.047  11.010   5.358  1.00  0.00              
ATOM     76  O   GLY    46      38.124  11.558   5.225  1.00  0.00              
ATOM     77  N   ILE    47      36.040  11.588   5.968  1.00  0.00              
ATOM     78  CA  ILE    47      36.153  12.961   6.551  1.00  0.00              
ATOM     79  C   ILE    47      35.184  13.034   7.745  1.00  0.00              
ATOM     80  O   ILE    47      34.059  13.455   7.573  1.00  0.00              
ATOM     81  N   LEU    48      35.658  12.924   8.957  1.00  0.00              
ATOM     82  CA  LEU    48      34.827  13.403  10.108  1.00  0.00              
ATOM     83  C   LEU    48      34.576  14.907   9.932  1.00  0.00              
ATOM     84  O   LEU    48      34.911  15.715  10.775  1.00  0.00              
ATOM     85  N   SER    49      34.195  15.275   8.740  1.00  0.00              
ATOM     86  CA  SER    49      34.167  16.742   8.413  1.00  0.00              
ATOM     87  C   SER    49      35.520  17.362   8.771  1.00  0.00              
ATOM     88  O   SER    49      35.622  17.890   9.861  1.00  0.00              
END
