
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0383AL242_2
# Molecule2: number of CA atoms  125 ( 1020),  selected   20 , name T0383.pdb
# PARAMETERS: T0383AL242_2.T0383.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:    11         7 - 17          4.86    18.96
  LONGEST_CONTINUOUS_SEGMENT:    11         8 - 18          4.61    18.57
  LCS_AVERAGE:      8.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6         9 - 14          1.92    20.56
  LONGEST_CONTINUOUS_SEGMENT:     6        11 - 16          1.90    17.45
  LCS_AVERAGE:      3.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4         6 - 9           0.75    29.77
  LONGEST_CONTINUOUS_SEGMENT:     4        10 - 13          0.57    20.16
  LCS_AVERAGE:      2.72

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:  125
LCS_GDT     L       6     L       6      4    5    9     3    3    4    4    5    5    5    6    6    6    7    7    7    7    9    9    9   11   11   11 
LCS_GDT     K       7     K       7      4    5   11     3    3    4    4    5    5    5    6    6    6    7    7    7    8   10   10   10   11   11   11 
LCS_GDT     R       8     R       8      4    5   11     3    3    4    4    5    5    6    7    9    9   10   10   10   10   10   10   10   11   11   11 
LCS_GDT     E       9     E       9      4    6   11     3    3    4    4    5    6    6    7    9    9   10   10   10   10   10   10   10   11   11   11 
LCS_GDT     Q      10     Q      10      4    6   11     3    4    4    5    6    7    8    8    9    9   10   10   10   10   10   10   10   11   11   11 
LCS_GDT     E      11     E      11      4    6   11     3    4    4    5    6    7    8    8    9    9   10   10   10   10   10   10   10   11   11   11 
LCS_GDT     F      12     F      12      4    6   11     3    4    4    5    6    7    8    8    9    9   10   10   10   10   10   10   10   11   11   11 
LCS_GDT     V      13     V      13      4    6   11     3    4    4    5    6    7    8    8    9    9   10   10   10   10   10   10   10   11   11   11 
LCS_GDT     S      14     S      14      3    6   11     3    4    4    5    6    7    8    8    9    9   10   10   10   10   10   10   10   11   11   12 
LCS_GDT     Q      15     Q      15      3    6   11     3    4    4    4    5    7    8    8    9    9   10   10   10   10   10   10   10   11   11   12 
LCS_GDT     Y      16     Y      16      3    6   11     3    3    4    4    6    7    8    8    9    9   10   10   10   10   10   10   10   11   11   12 
LCS_GDT     H      17     H      17      3    4   11     3    3    4    4    5    7    8    8    8    9   10   10   10   10   10   10   10   11   11   12 
LCS_GDT     F      18     F      18      3    4   11     3    3    4    4    4    5    6    6    8    9    9    9   10   10   10   10   10   11   11   12 
LCS_GDT     D      19     D      19      3    4   10     3    3    4    4    4    5    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_GDT     A      20     A      20      3    4   10     0    3    3    3    4    5    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_GDT     R      21     R      21      3    4   10     1    3    3    4    4    5    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_GDT     N      22     N      22      3    4   10     3    3    4    4    4    5    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_GDT     F      23     F      23      3    4   10     3    3    3    4    4    4    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_GDT     E      24     E      24      3    4   10     3    3    3    4    4    4    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_GDT     W      25     W      25      3    3   10     3    3    3    3    3    4    6    6    8    9    9    9   10   10   10   10   10   10   11   12 
LCS_AVERAGE  LCS_A:   5.03  (   2.72    3.92    8.44 )

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      3      4      4      5      6      7      8      8      9      9     10     10     10     10     10     10     10     11     11     12 
GDT PERCENT_CA   2.40   3.20   3.20   4.00   4.80   5.60   6.40   6.40   7.20   7.20   8.00   8.00   8.00   8.00   8.00   8.00   8.00   8.80   8.80   9.60
GDT RMS_LOCAL    0.07   0.57   0.57   1.22   1.70   2.05   2.30   2.30   3.19   3.19   3.62   3.62   3.62   3.62   3.62   3.62   3.62   4.61   4.61   6.64
GDT RMS_ALL_CA  21.13  20.16  20.16  20.84  18.22  18.31  18.29  18.29  18.41  18.41  18.56  18.56  18.56  18.56  18.56  18.56  18.56  18.57  18.57  20.01

#      Molecule1      Molecule2       DISTANCE
LGA    L       6      L       6         18.074
LGA    K       7      K       7         14.915
LGA    R       8      R       8          9.639
LGA    E       9      E       9          8.913
LGA    Q      10      Q      10          2.292
LGA    E      11      E      11          0.379
LGA    F      12      F      12          1.769
LGA    V      13      V      13          2.440
LGA    S      14      S      14          2.027
LGA    Q      15      Q      15          3.041
LGA    Y      16      Y      16          2.682
LGA    H      17      H      17          2.732
LGA    F      18      F      18          8.394
LGA    D      19      D      19         15.131
LGA    A      20      A      20         22.240
LGA    R      21      R      21         26.874
LGA    N      22      N      22         29.396
LGA    F      23      F      23         31.800
LGA    E      24      E      24         35.996
LGA    W      25      W      25         35.202

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  125    4.0      8    2.30     5.400     5.366     0.333

LGA_LOCAL      RMSD =  2.304  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 18.290  Number of atoms =   20 
Std_ALL_ATOMS  RMSD = 14.138  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.659386 * X  +   0.636625 * Y  +  -0.399897 * Z  +  14.255914
  Y_new =   0.432206 * X  +  -0.756230 * Y  +  -0.491237 * Z  +  24.265047
  Z_new =  -0.615148 * X  +   0.151077 * Y  +  -0.773801 * Z  +   8.940662 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.948778   -0.192814  [ DEG:   168.9526    -11.0474 ]
  Theta =   0.662574    2.479019  [ DEG:    37.9627    142.0373 ]
  Phi   =   0.580209   -2.561383  [ DEG:    33.2435   -146.7565 ]
 
# 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: T0383AL242_2                                  
REMARK     2: T0383.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0383AL242_2.T0383.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  125   4.0    8   2.30   5.366    14.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0383AL242_2
REMARK Aligment from pdb entry: 1f3k_A
ATOM      1  N   LEU     6      14.901  32.215   6.677  1.00  0.00              
ATOM      2  CA  LEU     6      15.049  30.764   6.987  1.00  0.00              
ATOM      3  C   LEU     6      15.036  30.545   8.506  1.00  0.00              
ATOM      4  O   LEU     6      14.404  31.286   9.233  1.00  0.00              
ATOM      5  N   LYS     7      15.729  29.547   9.003  1.00  0.00              
ATOM      6  CA  LYS     7      15.743  29.307  10.453  1.00  0.00              
ATOM      7  C   LYS     7      17.100  28.768  10.872  1.00  0.00              
ATOM      8  O   LYS     7      17.712  27.989  10.164  1.00  0.00              
ATOM      9  N   ARG     8      17.577  29.160  12.016  1.00  0.00              
ATOM     10  CA  ARG     8      18.889  28.643  12.465  1.00  0.00              
ATOM     11  C   ARG     8      18.706  27.260  13.072  1.00  0.00              
ATOM     12  O   ARG     8      17.677  26.943  13.638  1.00  0.00              
ATOM     13  N   GLU     9      19.696  26.444  12.942  1.00  0.00              
ATOM     14  CA  GLU     9      19.629  25.064  13.483  1.00  0.00              
ATOM     15  C   GLU     9      18.873  25.029  14.814  1.00  0.00              
ATOM     16  O   GLU     9      19.097  25.849  15.684  1.00  0.00              
ATOM     17  N   GLN    10      17.968  24.085  14.963  1.00  0.00              
ATOM     18  CA  GLN    10      17.162  23.962  16.220  1.00  0.00              
ATOM     19  C   GLN    10      15.987  24.938  16.185  1.00  0.00              
ATOM     20  O   GLN    10      15.397  25.250  17.201  1.00  0.00              
ATOM     21  N   GLU    11      15.638  25.419  15.023  1.00  0.00              
ATOM     22  CA  GLU    11      14.497  26.365  14.930  1.00  0.00              
ATOM     23  C   GLU    11      13.284  25.665  14.309  1.00  0.00              
ATOM     24  O   GLU    11      13.416  24.931  13.350  1.00  0.00              
ATOM     25  N   PHE    12      12.140  25.912  14.887  1.00  0.00              
ATOM     26  CA  PHE    12      10.884  25.294  14.394  1.00  0.00              
ATOM     27  C   PHE    12      10.442  25.930  13.078  1.00  0.00              
ATOM     28  O   PHE    12      10.493  27.132  12.907  1.00  0.00              
ATOM     29  N   VAL    13       9.997  25.130  12.148  1.00  0.00              
ATOM     30  CA  VAL    13       9.542  25.693  10.847  1.00  0.00              
ATOM     31  C   VAL    13       8.638  24.703  10.112  1.00  0.00              
ATOM     32  O   VAL    13       8.406  23.597  10.559  1.00  0.00              
ATOM     33  N   SER    14       8.130  25.100   8.983  1.00  0.00              
ATOM     34  CA  SER    14       7.246  24.196   8.199  1.00  0.00              
ATOM     35  C   SER    14       8.098  23.303   7.296  1.00  0.00              
ATOM     36  O   SER    14       8.977  23.769   6.597  1.00  0.00              
ATOM     37  N   GLN    15       7.849  22.026   7.301  1.00  0.00              
ATOM     38  CA  GLN    15       8.646  21.110   6.441  1.00  0.00              
ATOM     39  C   GLN    15       7.983  20.980   5.070  1.00  0.00              
ATOM     40  O   GLN    15       7.613  19.901   4.652  1.00  0.00              
ATOM     41  N   TYR    16       7.818  22.069   4.369  1.00  0.00              
ATOM     42  CA  TYR    16       7.163  21.984   3.032  1.00  0.00              
ATOM     43  C   TYR    16       7.842  22.930   2.038  1.00  0.00              
ATOM     44  O   TYR    16       7.974  22.624   0.870  1.00  0.00              
ATOM     45  N   HIS    17       8.258  24.080   2.484  1.00  0.00              
ATOM     46  CA  HIS    17       8.912  25.037   1.548  1.00  0.00              
ATOM     47  C   HIS    17      10.158  25.645   2.183  1.00  0.00              
ATOM     48  O   HIS    17      11.274  25.311   1.834  1.00  0.00              
ATOM     49  N   PHE    18       9.978  26.545   3.103  1.00  0.00              
ATOM     50  CA  PHE    18      11.153  27.187   3.749  1.00  0.00              
ATOM     51  C   PHE    18      11.237  26.823   5.232  1.00  0.00              
ATOM     52  O   PHE    18      10.237  26.651   5.902  1.00  0.00              
ATOM     53  N   ASP    19      12.423  26.735   5.753  1.00  0.00              
ATOM     54  CA  ASP    19      12.591  26.422   7.201  1.00  0.00              
ATOM     55  C   ASP    19      13.998  26.798   7.632  1.00  0.00              
ATOM     56  O   ASP    19      14.247  27.885   8.106  1.00  0.00              
ATOM     57  N   ALA    20      12.479  18.867   9.881  1.00  0.00              
ATOM     58  CA  ALA    20      11.867  17.649  10.481  1.00  0.00              
ATOM     59  C   ALA    20      11.714  17.915  11.975  1.00  0.00              
ATOM     60  O   ALA    20      12.362  17.311  12.806  1.00  0.00              
ATOM     61  N   ARG    21      10.896  18.876  12.302  1.00  0.00              
ATOM     62  CA  ARG    21      10.716  19.280  13.718  1.00  0.00              
ATOM     63  C   ARG    21      11.448  20.610  13.874  1.00  0.00              
ATOM     64  O   ARG    21      10.900  21.600  14.315  1.00  0.00              
ATOM     65  N   ASN    22      12.688  20.629  13.464  1.00  0.00              
ATOM     66  CA  ASN    22      13.505  21.869  13.516  1.00  0.00              
ATOM     67  C   ASN    22      14.702  21.689  12.584  1.00  0.00              
ATOM     68  O   ASN    22      15.069  20.580  12.252  1.00  0.00              
ATOM     69  N   PHE    23      15.314  22.753  12.155  1.00  0.00              
ATOM     70  CA  PHE    23      16.485  22.606  11.246  1.00  0.00              
ATOM     71  C   PHE    23      17.403  21.487  11.753  1.00  0.00              
ATOM     72  O   PHE    23      17.978  21.591  12.819  1.00  0.00              
ATOM     73  N   GLU    24      17.545  20.417  11.010  1.00  0.00              
ATOM     74  CA  GLU    24      18.427  19.305  11.480  1.00  0.00              
ATOM     75  C   GLU    24      19.825  19.441  10.890  1.00  0.00              
ATOM     76  O   GLU    24      20.478  18.478  10.541  1.00  0.00              
ATOM     77  N   TRP    25      20.277  20.645  10.802  1.00  0.00              
ATOM     78  CA  TRP    25      21.633  20.926  10.263  1.00  0.00              
ATOM     79  C   TRP    25      22.116  22.295  10.749  1.00  0.00              
ATOM     80  O   TRP    25      21.807  23.277  10.095  1.00  0.00              
END
