
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0349AL242_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   17 , name T0349_D1.pdb
# PARAMETERS: T0349AL242_5-D1.T0349_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:    17        23 - 54          3.23     3.23
  LCS_AVERAGE:     29.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        46 - 53          1.51     9.55
  LCS_AVERAGE:     11.66

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        24 - 27          0.91     6.16
  LONGEST_CONTINUOUS_SEGMENT:     4        46 - 49          0.22     9.76
  LONGEST_CONTINUOUS_SEGMENT:     4        48 - 51          0.63     8.96
  LONGEST_CONTINUOUS_SEGMENT:     4        50 - 53          0.77     9.49
  LCS_AVERAGE:      6.50

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:   57
LCS_GDT     A      23     A      23      3    6   17     3    4    6    7    7   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     D      24     D      24      4    6   17     3    3    5    6    8   11   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     I      25     I      25      4    6   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     G      26     G      26      4    6   17     3    3    5    6    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     H      27     H      27      4    6   17     3    3    5    6    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     L      28     L      28      3    6   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V      29     V      29      3    5   17     3    3    5    6    8    9   12   13   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     P      45     P      45      3    5   17     0    3    3    4    5    6    6    9   11   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     R      46     R      46      4    8   17     4    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     R      47     R      47      4    8   17     4    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V      48     V      48      4    8   17     4    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     L      49     L      49      4    8   17     4    4    5    6    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     V      50     V      50      4    8   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     H      51     H      51      4    8   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     E      52     E      52      4    8   17     3    4    6    7    8   10   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     D      53     D      53      4    8   17     3    4    6    7    8   12   13   14   15   16   17   17   17   17   17   17   17   17   17   17 
LCS_GDT     D      54     D      54      3    3   17     3    3    3    3    3    4    4    9   10   16   17   17   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  16.00  (   6.50   11.66   29.82 )

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      4      4      6      7      8     12     13     14     15     16     17     17     17     17     17     17     17     17     17     17 
GDT PERCENT_CA   7.02   7.02  10.53  12.28  14.04  21.05  22.81  24.56  26.32  28.07  29.82  29.82  29.82  29.82  29.82  29.82  29.82  29.82  29.82  29.82
GDT RMS_LOCAL    0.22   0.22   1.07   1.27   1.51   2.24   2.37   2.56   2.73   3.00   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23
GDT RMS_ALL_CA   9.76   9.76   3.44   3.43   9.55   3.44   3.43   3.35   3.39   3.29   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23

#      Molecule1      Molecule2       DISTANCE
LGA    A      23      A      23          2.845
LGA    D      24      D      24          3.921
LGA    I      25      I      25          2.001
LGA    G      26      G      26          2.731
LGA    H      27      H      27          2.877
LGA    L      28      L      28          1.205
LGA    V      29      V      29          4.425
LGA    P      45      P      45          6.392
LGA    R      46      R      46          1.087
LGA    R      47      R      47          2.835
LGA    V      48      V      48          1.137
LGA    L      49      L      49          3.403
LGA    V      50      V      50          0.584
LGA    H      51      H      51          3.162
LGA    E      52      E      52          3.394
LGA    D      53      D      53          2.784
LGA    D      54      D      54          5.718

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17   57    4.0     14    2.56    18.421    18.312     0.525

LGA_LOCAL      RMSD =  2.564  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.339  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  3.230  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.479156 * X  +   0.179704 * Y  +   0.859137 * Z  +  -0.724721
  Y_new =  -0.247971 * X  +   0.966658 * Y  +  -0.063896 * Z  +   7.331098
  Z_new =  -0.841974 * X  +  -0.182424 * Y  +   0.507741 * Z  +  -1.589193 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.344923    2.796669  [ DEG:   -19.7627    160.2374 ]
  Theta =   1.000932    2.140661  [ DEG:    57.3492    122.6508 ]
  Phi   =  -0.477561    2.664031  [ DEG:   -27.3623    152.6377 ]
 
# 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: T0349AL242_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349AL242_5-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17   57   4.0   14   2.56  18.312     3.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL242_5-D1
REMARK Aligment from pdb entry: 1ews_A
ATOM      1  N   ALA    23      -6.015  14.066   7.126  1.00  0.00              
ATOM      2  CA  ALA    23      -4.678  13.478   6.839  1.00  0.00              
ATOM      3  C   ALA    23      -3.983  14.371   5.784  1.00  0.00              
ATOM      4  O   ALA    23      -4.572  14.626   4.749  1.00  0.00              
ATOM      5  N   ASP    24      -2.773  14.827   6.042  1.00  0.00              
ATOM      6  CA  ASP    24      -1.988  15.622   5.048  1.00  0.00              
ATOM      7  C   ASP    24      -1.707  14.757   3.809  1.00  0.00              
ATOM      8  O   ASP    24      -1.746  15.232   2.691  1.00  0.00              
ATOM      9  N   ILE    25      -1.432  13.505   4.075  1.00  0.00              
ATOM     10  CA  ILE    25      -1.136  12.516   2.993  1.00  0.00              
ATOM     11  C   ILE    25      -2.472  11.872   2.560  1.00  0.00              
ATOM     12  O   ILE    25      -3.524  12.351   2.940  1.00  0.00              
ATOM     13  N   GLY    26      -2.410  10.814   1.786  1.00  0.00              
ATOM     14  CA  GLY    26      -3.665  10.132   1.322  1.00  0.00              
ATOM     15  C   GLY    26      -3.386   8.752   0.707  1.00  0.00              
ATOM     16  O   GLY    26      -2.467   8.599  -0.075  1.00  0.00              
ATOM     17  N   HIS    27      -4.195   7.790   1.079  1.00  0.00              
ATOM     18  CA  HIS    27      -4.035   6.400   0.552  1.00  0.00              
ATOM     19  C   HIS    27      -4.829   6.194  -0.749  1.00  0.00              
ATOM     20  O   HIS    27      -6.036   6.340  -0.770  1.00  0.00              
ATOM     21  N   LEU    28      -4.111   5.860  -1.793  1.00  0.00              
ATOM     22  CA  LEU    28      -4.721   5.619  -3.142  1.00  0.00              
ATOM     23  C   LEU    28      -3.907   4.540  -3.880  1.00  0.00              
ATOM     24  O   LEU    28      -2.751   4.329  -3.573  1.00  0.00              
ATOM     25  N   VAL    29      -4.536   3.889  -4.831  1.00  0.00              
ATOM     26  CA  VAL    29      -3.834   2.822  -5.623  1.00  0.00              
ATOM     27  C   VAL    29      -2.741   3.509  -6.457  1.00  0.00              
ATOM     28  O   VAL    29      -1.672   2.974  -6.672  1.00  0.00              
ATOM     89  N   PRO    45      -0.576  -4.285   1.747  1.00  0.00              
ATOM     90  CA  PRO    45       0.170  -3.142   1.121  1.00  0.00              
ATOM     91  C   PRO    45      -0.240  -2.926  -0.351  1.00  0.00              
ATOM     92  O   PRO    45       0.479  -2.313  -1.120  1.00  0.00              
ATOM     93  N   ARG    46      -1.397  -3.441  -0.684  1.00  0.00              
ATOM     94  CA  ARG    46      -1.948  -3.326  -2.070  1.00  0.00              
ATOM     95  C   ARG    46      -2.112  -1.855  -2.486  1.00  0.00              
ATOM     96  O   ARG    46      -1.858  -1.500  -3.619  1.00  0.00              
ATOM     97  N   ARG    47      -2.533  -1.055  -1.541  1.00  0.00              
ATOM     98  CA  ARG    47      -2.737   0.403  -1.802  1.00  0.00              
ATOM     99  C   ARG    47      -1.416   1.131  -1.501  1.00  0.00              
ATOM    100  O   ARG    47      -0.511   0.553  -0.927  1.00  0.00              
ATOM    101  N   VAL    48      -1.351   2.378  -1.897  1.00  0.00              
ATOM    102  CA  VAL    48      -0.119   3.203  -1.671  1.00  0.00              
ATOM    103  C   VAL    48      -0.389   4.462  -0.856  1.00  0.00              
ATOM    104  O   VAL    48      -1.405   5.105  -1.032  1.00  0.00              
ATOM    105  N   LEU    49       0.542   4.777   0.010  1.00  0.00              
ATOM    106  CA  LEU    49       0.412   5.988   0.874  1.00  0.00              
ATOM    107  C   LEU    49       1.031   7.103   0.046  1.00  0.00              
ATOM    108  O   LEU    49       2.223   7.330   0.076  1.00  0.00              
ATOM    109  N   VAL    50       0.171   7.761  -0.678  1.00  0.00              
ATOM    110  CA  VAL    50       0.632   8.879  -1.543  1.00  0.00              
ATOM    111  C   VAL    50       0.483  10.227  -0.830  1.00  0.00              
ATOM    112  O   VAL    50      -0.607  10.603  -0.444  1.00  0.00              
ATOM    113  N   HIS    51       1.592  10.909  -0.679  1.00  0.00              
ATOM    114  CA  HIS    51       1.596  12.243   0.001  1.00  0.00              
ATOM    115  C   HIS    51       1.900  13.375  -0.991  1.00  0.00              
ATOM    116  O   HIS    51       2.560  13.170  -1.993  1.00  0.00              
ATOM    117  N   GLU    52       1.400  14.541  -0.660  1.00  0.00              
ATOM    118  CA  GLU    52       1.590  15.768  -1.505  1.00  0.00              
ATOM    119  C   GLU    52       3.052  16.055  -1.891  1.00  0.00              
ATOM    120  O   GLU    52       3.970  15.727  -1.164  1.00  0.00              
ATOM    121  N   ASP    53       3.201  16.666  -3.039  1.00  0.00              
ATOM    122  CA  ASP    53       4.554  17.025  -3.562  1.00  0.00              
ATOM    123  C   ASP    53       4.933  18.410  -3.013  1.00  0.00              
ATOM    124  O   ASP    53       4.722  19.421  -3.655  1.00  0.00              
ATOM    125  N   ASP    54       5.483  18.398  -1.823  1.00  0.00              
ATOM    126  CA  ASP    54       5.908  19.667  -1.146  1.00  0.00              
ATOM    127  C   ASP    54       7.404  19.617  -0.780  1.00  0.00              
ATOM    128  O   ASP    54       7.905  18.512  -0.628  1.00  0.00              
END
