
#######################################################
#                                                     #
#                        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   28 (  112),  selected   28 , name T0283AL381_5-D1
# Molecule2: number of CA atoms   97 (  768),  selected   28 , name T0283_D1.pdb
# PARAMETERS: T0283AL381_5-D1.T0283_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:    28        58 - 87          4.85     4.85
  LCS_AVERAGE:     28.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        58 - 71          2.00    13.52
  LCS_AVERAGE:     11.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        58 - 70          0.45    13.47
  LCS_AVERAGE:      8.69

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:   97
LCS_GDT     F      58     F      58     13   14   28     9   13   13   13   13   13   13   13   17   19   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     G      59     G      59     13   14   28    10   13   13   13   13   13   13   13   13   14   16   22   23   25   27   27   28   28   28   28 
LCS_GDT     G      60     G      60     13   14   28    10   13   13   13   13   13   13   13   17   19   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     I      61     I      61     13   14   28    10   13   13   13   13   13   14   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     L      62     L      62     13   14   28    10   13   13   13   13   13   13   13   17   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     D      63     D      63     13   14   28     9   13   13   13   13   13   13   13   17   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     L      64     L      64     13   14   28    10   13   13   13   13   13   13   15   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     F      65     F      65     13   14   28    10   13   13   13   13   13   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     E      66     E      66     13   14   28    10   13   13   13   13   13   13   15   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     E      67     E      67     13   14   28    10   13   13   13   13   13   14   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     G      68     G      68     13   14   28    10   13   13   13   13   13   13   13   13   17   21   24   25   25   27   27   28   28   28   28 
LCS_GDT     A      69     A      69     13   14   28    10   13   13   13   13   13   13   17   18   18   20   21   22   25   27   27   28   28   28   28 
LCS_GDT     A      70     A      70     13   14   28     9   13   13   13   13   13   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     E      71     E      71      4   14   28     3    4    5    6    8   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     G      72     G      72      4    6   28     3    5    5    7    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     K      73     K      73      4    9   28     3    4    4    8    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     K      74     K      74      4    9   28     4    4    5    8    9   12   15   17   18   20   21   23   25   25   27   27   28   28   28   28 
LCS_GDT     V      75     V      75      4    9   28     3    5    5    7    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     T      76     T      76      4    9   28     3    4    4    6    7   10   14   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     T      79     T      79      5    9   28     4    5    5    8    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     G      80     G      80      5    9   28     4    5    5    8    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     E      81     E      81      5    9   28     4    5    5    8    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     D      82     D      82      5    9   28     3    5    5    8    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     V      83     V      83      5    9   28     4    5    5    8    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     A      84     A      84      5    8   28     4    4    5    6    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     A      85     A      85      5    7   28     4    5    5    7    9   12   14   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     F      86     F      86      5    7   28     4    4    5    6    9   12   15   17   19   20   23   24   25   25   27   27   28   28   28   28 
LCS_GDT     C      87     C      87      3    7   28     0    3    3    6    8   12   15   17   18   19   21   23   23   25   26   27   28   28   28   28 
LCS_AVERAGE  LCS_A:  16.35  (   8.69   11.49   28.87 )

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     13     13     13     13     13     15     17     19     20     23     24     25     25     27     27     28     28     28     28 
GDT PERCENT_CA  10.31  13.40  13.40  13.40  13.40  13.40  15.46  17.53  19.59  20.62  23.71  24.74  25.77  25.77  27.84  27.84  28.87  28.87  28.87  28.87
GDT RMS_LOCAL    0.29   0.45   0.45   0.45   0.45   0.45   2.48   2.72   3.19   3.29   3.92   4.06   4.18   4.18   4.62   4.62   4.85   4.85   4.85   4.85
GDT RMS_ALL_CA  13.65  13.47  13.47  13.47  13.47  13.47   7.31   7.12   5.26   5.37   4.92   4.88   4.90   4.90   4.89   4.89   4.85   4.85   4.85   4.85

#      Molecule1      Molecule2       DISTANCE
LGA    F      58      F      58         13.462
LGA    G      59      G      59         17.349
LGA    G      60      G      60         15.665
LGA    I      61      I      61          8.389
LGA    L      62      L      62          8.920
LGA    D      63      D      63         11.690
LGA    L      64      L      64          9.256
LGA    F      65      F      65          2.379
LGA    E      66      E      66          4.954
LGA    E      67      E      67          6.096
LGA    G      68      G      68          6.468
LGA    A      69      A      69          5.784
LGA    A      70      A      70          2.525
LGA    E      71      E      71          3.448
LGA    G      72      G      72          1.916
LGA    K      73      K      73          2.567
LGA    K      74      K      74          3.271
LGA    V      75      V      75          1.930
LGA    T      76      T      76          3.893
LGA    T      79      T      79          3.428
LGA    G      80      G      80          2.973
LGA    E      81      E      81          0.833
LGA    D      82      D      82          1.440
LGA    V      83      V      83          2.414
LGA    A      84      A      84          2.476
LGA    A      85      A      85          3.534
LGA    F      86      F      86          2.207
LGA    C      87      C      87          3.354

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28   97    4.0     17    2.72    18.041    16.360     0.603

LGA_LOCAL      RMSD =  2.721  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.981  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  4.850  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.576555 * X  +   0.816671 * Y  +  -0.025150 * Z  +  63.576927
  Y_new =   0.228634 * X  +   0.131707 * Y  +  -0.964562 * Z  +  12.020983
  Z_new =  -0.784418 * X  +  -0.561873 * Y  +  -0.262655 * Z  +  50.840332 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.008077    1.133515  [ DEG:  -115.0544     64.9456 ]
  Theta =   0.901757    2.239836  [ DEG:    51.6669    128.3331 ]
  Phi   =   2.764063   -0.377530  [ DEG:   158.3691    -21.6309 ]
 
# 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: T0283AL381_5-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0283AL381_5-D1.T0283_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28   97   4.0   17   2.72  16.360     4.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL381_5-D1
REMARK Aligment from pdb entry: 1nq4A
ATOM      1  N   PHE    58      26.179  33.614  -7.522  1.00  0.00              
ATOM      2  CA  PHE    58      24.728  33.772  -7.444  1.00  0.00              
ATOM      3  C   PHE    58      24.065  33.181  -8.681  1.00  0.00              
ATOM      4  O   PHE    58      23.038  32.507  -8.596  1.00  0.00              
ATOM      5  N   GLY    59      24.668  33.445  -9.834  1.00  0.00              
ATOM      6  CA  GLY    59      24.136  32.941 -11.099  1.00  0.00              
ATOM      7  C   GLY    59      24.087  31.415 -11.095  1.00  0.00              
ATOM      8  O   GLY    59      23.236  30.806 -11.743  1.00  0.00              
ATOM      9  N   GLY    60      25.011  30.804 -10.357  1.00  0.00              
ATOM     10  CA  GLY    60      25.067  29.352 -10.274  1.00  0.00              
ATOM     11  C   GLY    60      23.887  28.816  -9.472  1.00  0.00              
ATOM     12  O   GLY    60      23.022  28.120 -10.000  1.00  0.00              
ATOM     13  N   ILE    61      23.873  29.148  -8.182  1.00  0.00              
ATOM     14  CA  ILE    61      22.810  28.696  -7.278  1.00  0.00              
ATOM     15  C   ILE    61      21.423  29.009  -7.836  1.00  0.00              
ATOM     16  O   ILE    61      20.463  28.282  -7.585  1.00  0.00              
ATOM     17  N   LEU    62      21.326  30.103  -8.581  1.00  0.00              
ATOM     18  CA  LEU    62      20.047  30.512  -9.156  1.00  0.00              
ATOM     19  C   LEU    62      19.591  29.544 -10.246  1.00  0.00              
ATOM     20  O   LEU    62      18.475  29.026 -10.207  1.00  0.00              
ATOM     21  N   ASP    63      20.464  29.305 -11.219  1.00  0.00              
ATOM     22  CA  ASP    63      20.161  28.404 -12.317  1.00  0.00              
ATOM     23  C   ASP    63      19.809  27.013 -11.798  1.00  0.00              
ATOM     24  O   ASP    63      18.749  26.471 -12.110  1.00  0.00              
ATOM     25  N   LEU    64      20.703  26.434 -10.997  1.00  0.00              
ATOM     26  CA  LEU    64      20.449  25.096 -10.445  1.00  0.00              
ATOM     27  C   LEU    64      19.106  25.077  -9.718  1.00  0.00              
ATOM     28  O   LEU    64      18.378  24.086  -9.758  1.00  0.00              
ATOM     29  N   PHE    65      18.769  26.202  -9.090  1.00  0.00              
ATOM     30  CA  PHE    65      17.491  26.313  -8.406  1.00  0.00              
ATOM     31  C   PHE    65      16.394  26.399  -9.460  1.00  0.00              
ATOM     32  O   PHE    65      15.330  25.793  -9.335  1.00  0.00              
ATOM     33  N   GLU    66      16.691  27.154 -10.518  1.00  0.00              
ATOM     34  CA  GLU    66      15.759  27.319 -11.623  1.00  0.00              
ATOM     35  C   GLU    66      15.471  25.961 -12.271  1.00  0.00              
ATOM     36  O   GLU    66      14.322  25.627 -12.564  1.00  0.00              
ATOM     37  N   GLU    67      16.530  25.186 -12.489  1.00  0.00              
ATOM     38  CA  GLU    67      16.388  23.863 -13.102  1.00  0.00              
ATOM     39  C   GLU    67      15.514  22.985 -12.222  1.00  0.00              
ATOM     40  O   GLU    67      14.652  22.246 -12.702  1.00  0.00              
ATOM     41  N   GLY    68      15.756  23.083 -10.922  1.00  0.00              
ATOM     42  CA  GLY    68      14.994  22.303  -9.946  1.00  0.00              
ATOM     43  C   GLY    68      13.509  22.631 -10.038  1.00  0.00              
ATOM     44  O   GLY    68      12.674  21.756 -10.267  1.00  0.00              
ATOM     45  N   ALA    69      13.193  23.909  -9.858  1.00  0.00              
ATOM     46  CA  ALA    69      11.804  24.361  -9.920  1.00  0.00              
ATOM     47  C   ALA    69      11.210  24.075 -11.297  1.00  0.00              
ATOM     48  O   ALA    69      10.042  23.710 -11.422  1.00  0.00              
ATOM     49  N   ALA    70      12.032  24.243 -12.329  1.00  0.00              
ATOM     50  CA  ALA    70      11.582  23.999 -13.697  1.00  0.00              
ATOM     51  C   ALA    70      11.198  25.305 -14.389  1.00  0.00              
ATOM     52  O   ALA    70      10.344  25.324 -15.276  1.00  0.00              
ATOM     53  N   GLU    71      11.838  26.396 -13.976  1.00  0.00              
ATOM     54  CA  GLU    71      11.556  27.699 -14.564  1.00  0.00              
ATOM     55  C   GLU    71      12.267  27.842 -15.906  1.00  0.00              
ATOM     56  O   GLU    71      12.943  26.922 -16.367  1.00  0.00              
ATOM     57  N   GLY    72      12.108  29.006 -16.526  1.00  0.00              
ATOM     58  CA  GLY    72      12.739  29.263 -17.817  1.00  0.00              
ATOM     59  C   GLY    72      13.685  30.456 -17.721  1.00  0.00              
ATOM     60  O   GLY    72      13.820  31.242 -18.658  1.00  0.00              
ATOM     61  N   LYS    73      14.338  30.576 -16.571  1.00  0.00              
ATOM     62  CA  LYS    73      15.274  31.668 -16.342  1.00  0.00              
ATOM     63  C   LYS    73      15.902  31.538 -14.956  1.00  0.00              
ATOM     64  O   LYS    73      15.210  31.600 -13.940  1.00  0.00              
ATOM     65  N   LYS    74      17.230  31.364 -14.930  1.00  0.00              
ATOM     66  CA  LYS    74      17.980  31.224 -13.668  1.00  0.00              
ATOM     67  C   LYS    74      17.496  32.217 -12.611  1.00  0.00              
ATOM     68  O   LYS    74      17.375  31.886 -11.432  1.00  0.00              
ATOM     69  N   VAL    75      17.219  33.437 -13.055  1.00  0.00              
ATOM     70  CA  VAL    75      16.749  34.479 -12.151  1.00  0.00              
ATOM     71  C   VAL    75      15.413  35.025 -12.651  1.00  0.00              
ATOM     72  O   VAL    75      15.342  36.102 -13.242  1.00  0.00              
ATOM     73  N   THR    76      14.363  34.260 -12.396  1.00  0.00              
ATOM     74  CA  THR    76      13.020  34.655 -12.812  1.00  0.00              
ATOM     75  C   THR    76      12.471  35.731 -11.878  1.00  0.00              
ATOM     76  O   THR    76      11.705  36.601 -12.292  1.00  0.00              
ATOM     77  N   THR    79      12.873  35.660 -10.609  1.00  0.00              
ATOM     78  CA  THR    79      12.419  36.631  -9.612  1.00  0.00              
ATOM     79  C   THR    79      12.755  38.056 -10.050  1.00  0.00              
ATOM     80  O   THR    79      12.047  39.005  -9.714  1.00  0.00              
ATOM     81  N   GLY    80      13.843  38.194 -10.802  1.00  0.00              
ATOM     82  CA  GLY    80      14.261  39.508 -11.281  1.00  0.00              
ATOM     83  C   GLY    80      15.730  39.757 -10.964  1.00  0.00              
ATOM     84  O   GLY    80      16.542  39.997 -11.859  1.00  0.00              
ATOM     85  N   GLU    81      16.065  39.699  -9.678  1.00  0.00              
ATOM     86  CA  GLU    81      17.441  39.922  -9.251  1.00  0.00              
ATOM     87  C   GLU    81      17.504  40.300  -7.774  1.00  0.00              
ATOM     88  O   GLU    81      18.492  40.026  -7.092  1.00  0.00              
ATOM     89  N   ASP    82      16.442  40.938  -7.288  1.00  0.00              
ATOM     90  CA  ASP    82      16.388  41.353  -5.893  1.00  0.00              
ATOM     91  C   ASP    82      15.922  40.198  -5.007  1.00  0.00              
ATOM     92  O   ASP    82      14.907  40.287  -4.314  1.00  0.00              
ATOM     93  N   VAL    83      16.681  39.107  -5.037  1.00  0.00              
ATOM     94  CA  VAL    83      16.345  37.934  -4.236  1.00  0.00              
ATOM     95  C   VAL    83      17.619  37.243  -3.739  1.00  0.00              
ATOM     96  O   VAL    83      17.649  36.033  -3.513  1.00  0.00              
ATOM     97  N   ALA    84      18.676  38.032  -3.563  1.00  0.00              
ATOM     98  CA  ALA    84      19.940  37.498  -3.085  1.00  0.00              
ATOM     99  C   ALA    84      19.970  37.470  -1.555  1.00  0.00              
ATOM    100  O   ALA    84      20.670  36.661  -0.946  1.00  0.00              
ATOM    101  N   ALA    85      19.199  38.369  -0.944  1.00  0.00              
ATOM    102  CA  ALA    85      19.136  38.448   0.510  1.00  0.00              
ATOM    103  C   ALA    85      17.704  38.230   0.998  1.00  0.00              
ATOM    104  O   ALA    85      17.321  38.695   2.072  1.00  0.00              
ATOM    105  N   PHE    86      16.923  37.497   0.205  1.00  0.00              
ATOM    106  CA  PHE    86      15.543  37.198   0.568  1.00  0.00              
ATOM    107  C   PHE    86      15.413  35.707   0.864  1.00  0.00              
ATOM    108  O   PHE    86      15.908  34.867   0.112  1.00  0.00              
ATOM    109  N   CYS    87      14.756  35.383   1.976  1.00  0.00              
ATOM    110  CA  CYS    87      14.587  33.982   2.373  1.00  0.00              
ATOM    111  C   CYS    87      13.955  33.158   1.254  1.00  0.00              
ATOM    112  O   CYS    87      13.156  33.659   0.461  1.00  0.00              
END
