
#######################################################
#                                                     #
#                        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    9 (   36),  selected    9 , name T0378AL316_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected    9 , name T0378_D1.pdb
# PARAMETERS: T0378AL316_4-D1.T0378_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:     9         9 - 17          3.81     3.81
  LCS_AVERAGE:     10.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4         9 - 12          1.85     7.58
  LONGEST_CONTINUOUS_SEGMENT:     4        13 - 16          1.82     5.33
  LONGEST_CONTINUOUS_SEGMENT:     4        14 - 17          0.68    11.65
  LCS_AVERAGE:      4.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        14 - 17          0.68    11.65
  LCS_AVERAGE:      3.87

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:   89
LCS_GDT     F       9     F       9      3    4    9     3    3    3    3    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     L      10     L      10      3    4    9     3    3    3    3    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     R      11     R      11      3    4    9     3    3    3    3    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     S      12     S      12      3    4    9     3    3    3    3    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     L      13     L      13      3    4    9     0    3    3    3    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     R      14     R      14      4    4    9     3    4    4    4    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     E      15     E      15      4    4    9     3    4    4    4    4    4    5    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     R      16     R      16      4    4    9     3    4    4    4    4    4    7    7    8    8    8    8    9    9    9    9    9    9    9    9 
LCS_GDT     K      17     K      17      4    4    9     0    4    4    4    4    4    5    5    5    7    8    8    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   6.16  (   3.87    4.49   10.11 )

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      4      4      4      7      7      8      8      8      8      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   3.37   4.49   4.49   4.49   4.49   4.49   7.87   7.87   8.99   8.99   8.99   8.99  10.11  10.11  10.11  10.11  10.11  10.11  10.11  10.11
GDT RMS_LOCAL    0.02   0.68   0.68   0.68   0.68   0.68   2.90   2.90   3.16   3.16   3.16   3.16   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81
GDT RMS_ALL_CA   8.12  11.65  11.65  11.65  11.65  11.65   4.25   4.25   4.02   4.02   4.02   4.02   3.81   3.81   3.81   3.81   3.81   3.81   3.81   3.81

#      Molecule1      Molecule2       DISTANCE
LGA    F       9      F       9          3.236
LGA    L      10      L      10          2.874
LGA    R      11      R      11          2.546
LGA    S      12      S      12          3.393
LGA    L      13      L      13          1.631
LGA    R      14      R      14          2.977
LGA    E      15      E      15          5.194
LGA    R      16      R      16          3.232
LGA    K      17      K      17          8.787

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9   89    4.0      7    2.90     6.742     6.303     0.234

LGA_LOCAL      RMSD =  2.896  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.254  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  3.806  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.917035 * X  +  -0.397379 * Y  +   0.033698 * Z  +  17.283714
  Y_new =  -0.116499 * X  +   0.347739 * Y  +   0.930325 * Z  +   2.355226
  Z_new =  -0.381410 * X  +   0.849216 * Y  +  -0.365184 * Z  +  62.419384 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.976915   -1.164678  [ DEG:   113.2689    -66.7311 ]
  Theta =   0.391321    2.750271  [ DEG:    22.4211    157.5789 ]
  Phi   =  -3.015230    0.126362  [ DEG:  -172.7600      7.2400 ]
 
# 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: T0378AL316_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL316_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9   89   4.0    7   2.90   6.303     3.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL316_4-D1
REMARK Aligment from pdb entry: 1ipa_A
ATOM      1  N   PHE     9       7.728  31.584  55.780  1.00  0.00              
ATOM      2  CA  PHE     9       8.667  32.186  54.836  1.00  0.00              
ATOM      3  C   PHE     9       8.760  31.344  53.561  1.00  0.00              
ATOM      4  O   PHE     9       9.049  30.145  53.609  1.00  0.00              
ATOM      5  N   LEU    10       8.513  31.986  52.423  1.00  0.00              
ATOM      6  CA  LEU    10       8.539  31.314  51.128  1.00  0.00              
ATOM      7  C   LEU    10       9.934  31.253  50.505  1.00  0.00              
ATOM      8  O   LEU    10      10.071  31.304  49.282  1.00  0.00              
ATOM      9  N   ARG    11      10.963  31.150  51.340  1.00  0.00              
ATOM     10  CA  ARG    11      12.330  31.072  50.840  1.00  0.00              
ATOM     11  C   ARG    11      12.548  29.753  50.103  1.00  0.00              
ATOM     12  O   ARG    11      12.064  28.701  50.528  1.00  0.00              
ATOM     13  N   SER    12      13.274  29.813  48.992  1.00  0.00              
ATOM     14  CA  SER    12      13.536  28.619  48.207  1.00  0.00              
ATOM     15  C   SER    12      14.743  27.871  48.742  1.00  0.00              
ATOM     16  O   SER    12      15.563  28.430  49.470  1.00  0.00              
ATOM     17  N   LEU    13      14.848  26.601  48.367  1.00  0.00              
ATOM     18  CA  LEU    13      15.927  25.750  48.838  1.00  0.00              
ATOM     19  C   LEU    13      16.764  25.114  47.737  1.00  0.00              
ATOM     20  O   LEU    13      16.235  24.603  46.752  1.00  0.00              
ATOM     21  N   ARG    14      18.081  25.166  47.921  1.00  0.00              
ATOM     22  CA  ARG    14      19.037  24.562  46.998  1.00  0.00              
ATOM     23  C   ARG    14      20.028  23.759  47.830  1.00  0.00              
ATOM     24  O   ARG    14      20.706  24.295  48.711  1.00  0.00              
ATOM     25  N   GLU    15      20.119  22.451  47.562  1.00  0.00              
ATOM     26  CA  GLU    15      21.025  21.558  48.287  1.00  0.00              
ATOM     27  C   GLU    15      22.477  22.018  48.336  1.00  0.00              
ATOM     28  O   GLU    15      23.049  22.416  47.323  1.00  0.00              
ATOM     29  N   ARG    16      23.071  21.961  49.522  1.00  0.00              
ATOM     30  CA  ARG    16      24.461  22.349  49.687  1.00  0.00              
ATOM     31  C   ARG    16      25.336  21.133  49.361  1.00  0.00              
ATOM     32  O   ARG    16      24.842  20.013  49.289  1.00  0.00              
ATOM     33  N   LYS    17      26.648  21.340  49.162  1.00  0.00              
ATOM     34  CA  LYS    17      27.574  20.247  48.843  1.00  0.00              
ATOM     35  C   LYS    17      27.656  19.118  49.878  1.00  0.00              
ATOM     36  O   LYS    17      28.281  18.078  49.632  1.00  0.00              
END
