
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0316AL316_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   27 , name T0316_D3.pdb
# PARAMETERS: T0316AL316_4-D3.T0316_D3.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:    16       304 - 319         4.95     9.84
  LONGEST_CONTINUOUS_SEGMENT:    16       309 - 351         4.91    13.25
  LCS_AVERAGE:     16.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       313 - 317         0.42    18.82
  LCS_AVERAGE:      4.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       313 - 317         0.42    18.82
  LCS_AVERAGE:      4.28

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:   90
LCS_GDT     E     298     E     298      4    4   11     3    4    4    4    4    4    8   10   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     M     299     M     299      4    4   11     3    4    4    6    6    7    8   10   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     P     300     P     300      4    4   11     3    4    4    6    6    7    8   10   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     E     301     E     301      4    4   11     3    4    4    4    4    4    6    6    7    9   11   15   17   19   21   22   24   25   25   26 
LCS_GDT     E     302     E     302      4    4   11     3    3    4    4    4    4    6    6    7    8   10   10   13   15   20   22   23   25   25   26 
LCS_GDT     F     303     F     303      4    4   11     0    3    4    4    4    4    8   10   10   12   13   14   16   19   21   22   24   25   25   26 
LCS_GDT     T     304     T     304      3    3   16     0    3    3    6    6    7    8   10   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     L     305     L     305      3    4   16     3    3    4    6    6    7    8   10   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     E     306     E     306      3    4   16     3    3    3    3    4    4    6    8    8   12   13   14   17   19   21   22   24   25   25   26 
LCS_GDT     C     307     C     307      3    4   16     3    3    3    3    4    4    5    5    7   10   12   13   15   17   18   19   24   25   25   26 
LCS_GDT     T     308     T     308      3    4   16     0    3    3    3    4    4    5    6    7   10   12   13   15   16   16   20   24   25   25   26 
LCS_GDT     A     309     A     309      3    3   16     0    3    3    3    6    7    7    8   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     K     310     K     310      4    4   16     3    3    4    5    6    7    7    8   10   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     F     311     F     311      4    4   16     3    3    4    5    6    7    7    8   10   13   14   15   16   19   21   22   24   25   25   26 
LCS_GDT     R     312     R     312      4    4   16     3    3    4    4    5    6    9   10   11   11   12   13   15   17   21   22   24   25   25   26 
LCS_GDT     Y     313     Y     313      5    5   16     4    6    7    8    8    9    9   10   11   11   11   13   15   17   18   20   24   25   25   26 
LCS_GDT     R     314     R     314      5    5   16     4    6    7    8    8    9    9   10   11   11   12   13   15   17   21   22   24   25   25   26 
LCS_GDT     Q     315     Q     315      5    5   16     4    6    7    8    8    9    9   10   11   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     P     316     P     316      5    5   16     4    6    7    8    8    9    9   10   11   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     D     317     D     317      5    5   16     4    5    5    8    8    9    9   10   11   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     S     318     S     318      3    3   16     1    3    4    6    6    7    8   10   11   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     K     319     K     319      3    3   16     0    3    3    3    4    5    6    7    9   12   13   14   17   19   21   22   24   25   25   26 
LCS_GDT     V     320     V     320      3    3   16     0    3    3    3    4    4    6    7    9   10   11   13   14   16   18   20   21   22   24   26 
LCS_GDT     F     348     F     348      4    4   16     0    3    5    5    5    9    9    9   11   11   11   12   13   15   16   17   20   22   22   24 
LCS_GDT     Y     349     Y     349      4    4   16     3    6    7    8    8    9    9   10   11   11   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     D     350     D     350      4    4   16     3    6    7    8    8    9    9   10   11   13   14   15   17   19   21   22   24   25   25   26 
LCS_GDT     G     351     G     351      4    4   16     3    3    7    8    8    9    9   10   11   13   14   15   17   19   21   22   24   25   25   26 
LCS_AVERAGE  LCS_A:   8.42  (   4.28    4.44   16.54 )

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      6      7      8      8      9      9     10     11     13     14     15     17     19     21     22     24     25     25     26 
GDT PERCENT_CA   4.44   6.67   7.78   8.89   8.89  10.00  10.00  11.11  12.22  14.44  15.56  16.67  18.89  21.11  23.33  24.44  26.67  27.78  27.78  28.89
GDT RMS_LOCAL    0.28   0.56   0.76   1.03   1.03   1.49   1.49   2.38   2.75   4.04   4.19   4.34   4.74   5.03   5.61   5.75   6.16   6.29   6.29   6.60
GDT RMS_ALL_CA  17.28  16.78  16.97  17.08  17.08  17.61  17.61  15.22  16.15   6.97   6.99   7.00   7.27   7.07   6.83   6.82   6.90   6.85   6.85   6.82

#      Molecule1      Molecule2       DISTANCE
LGA    E     298      E     298         20.978
LGA    M     299      M     299         22.191
LGA    P     300      P     300         27.378
LGA    E     301      E     301         25.935
LGA    E     302      E     302         25.454
LGA    F     303      F     303         26.784
LGA    T     304      T     304         26.582
LGA    L     305      L     305         20.271
LGA    E     306      E     306         19.359
LGA    C     307      C     307         18.936
LGA    T     308      T     308         16.204
LGA    A     309      A     309          9.483
LGA    K     310      K     310          6.803
LGA    F     311      F     311          9.053
LGA    R     312      R     312          3.191
LGA    Y     313      Y     313          3.450
LGA    R     314      R     314          2.333
LGA    Q     315      Q     315          1.886
LGA    P     316      P     316          0.858
LGA    D     317      D     317          2.559
LGA    S     318      S     318          3.977
LGA    K     319      K     319          8.841
LGA    V     320      V     320          8.649
LGA    F     348      F     348          5.152
LGA    Y     349      Y     349          0.786
LGA    D     350      D     350          0.821
LGA    G     351      G     351          2.779

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   90    4.0     10    2.38    12.778    10.409     0.403

LGA_LOCAL      RMSD =  2.381  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.268  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  6.805  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.414139 * X  +  -0.738804 * Y  +   0.531655 * Z  +  16.166580
  Y_new =  -0.424042 * X  +  -0.360240 * Y  +  -0.830913 * Z  + 126.202057
  Z_new =   0.805405 * X  +  -0.569557 * Y  +  -0.164094 * Z  +  53.905846 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.851308    1.290284  [ DEG:  -106.0722     73.9278 ]
  Theta =  -0.936359   -2.205234  [ DEG:   -53.6494   -126.3506 ]
  Phi   =  -2.344380    0.797212  [ DEG:  -134.3231     45.6769 ]
 
# 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: T0316AL316_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL316_4-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   90   4.0   10   2.38  10.409     6.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL316_4-D3
REMARK Aligment from pdb entry: 1ct9_A
ATOM    965  N   GLU   298      15.688  23.679  14.095  1.00  0.00              
ATOM    966  CA  GLU   298      15.116  24.208  15.344  1.00  0.00              
ATOM    967  C   GLU   298      16.138  24.880  16.285  1.00  0.00              
ATOM    968  O   GLU   298      15.807  25.376  17.364  1.00  0.00              
ATOM    969  N   MET   299      17.400  24.847  15.894  1.00  0.00              
ATOM    970  CA  MET   299      18.477  25.412  16.677  1.00  0.00              
ATOM    971  C   MET   299      19.451  26.021  15.709  1.00  0.00              
ATOM    972  O   MET   299      19.451  25.684  14.502  1.00  0.00              
ATOM    973  N   PRO   300      20.260  26.914  16.284  1.00  0.00              
ATOM    974  CA  PRO   300      21.270  27.657  15.555  1.00  0.00              
ATOM    975  C   PRO   300      22.325  26.759  14.911  1.00  0.00              
ATOM    976  O   PRO   300      22.736  27.052  13.772  1.00  0.00              
ATOM    977  N   GLU   301      22.714  25.677  15.644  1.00  0.00              
ATOM    978  CA  GLU   301      23.667  24.680  15.175  1.00  0.00              
ATOM    979  C   GLU   301      23.066  23.929  13.996  1.00  0.00              
ATOM    980  O   GLU   301      23.694  23.863  12.958  1.00  0.00              
ATOM    981  N   GLU   302      21.821  23.456  14.163  1.00  0.00              
ATOM    982  CA  GLU   302      21.096  22.771  13.092  1.00  0.00              
ATOM    983  C   GLU   302      21.028  23.628  11.874  1.00  0.00              
ATOM    984  O   GLU   302      21.256  23.187  10.750  1.00  0.00              
ATOM    985  N   PHE   303      20.732  24.893  12.120  1.00  0.00              
ATOM    986  CA  PHE   303      20.636  25.852  11.056  1.00  0.00              
ATOM    987  C   PHE   303      21.950  26.042  10.303  1.00  0.00              
ATOM    988  O   PHE   303      21.983  26.130   9.068  1.00  0.00              
ATOM    989  N   THR   304      23.034  26.137  11.063  1.00  0.00              
ATOM    990  CA  THR   304      24.389  26.303  10.527  1.00  0.00              
ATOM    991  C   THR   304      24.728  25.179   9.534  1.00  0.00              
ATOM    992  O   THR   304      25.143  25.385   8.394  1.00  0.00              
ATOM    993  N   LEU   305      24.562  23.955  10.028  1.00  0.00              
ATOM    994  CA  LEU   305      24.823  22.761   9.276  1.00  0.00              
ATOM    995  C   LEU   305      23.877  22.647   8.095  1.00  0.00              
ATOM    996  O   LEU   305      24.285  22.290   6.986  1.00  0.00              
ATOM    997  N   GLU   306      22.606  22.927   8.310  1.00  0.00              
ATOM    998  CA  GLU   306      21.639  22.842   7.217  1.00  0.00              
ATOM    999  C   GLU   306      22.005  23.811   6.085  1.00  0.00              
ATOM   1000  O   GLU   306      21.911  23.529   4.876  1.00  0.00              
ATOM   1001  N   CYS   307      22.410  25.007   6.476  1.00  0.00              
ATOM   1002  CA  CYS   307      22.763  26.021   5.503  1.00  0.00              
ATOM   1003  C   CYS   307      23.913  25.553   4.612  1.00  0.00              
ATOM   1004  O   CYS   307      23.943  25.766   3.398  1.00  0.00              
ATOM   1005  N   THR   308      24.930  24.925   5.199  1.00  0.00              
ATOM   1006  CA  THR   308      26.049  24.434   4.381  1.00  0.00              
ATOM   1007  C   THR   308      25.608  23.306   3.469  1.00  0.00              
ATOM   1008  O   THR   308      25.910  23.294   2.277  1.00  0.00              
ATOM   1009  N   ALA   309      24.855  22.409   4.088  1.00  0.00              
ATOM   1010  CA  ALA   309      24.315  21.271   3.402  1.00  0.00              
ATOM   1011  C   ALA   309      23.618  21.702   2.130  1.00  0.00              
ATOM   1012  O   ALA   309      23.962  21.266   1.017  1.00  0.00              
ATOM   1013  N   LYS   310      22.603  22.548   2.322  1.00  0.00              
ATOM   1014  CA  LYS   310      21.783  23.007   1.192  1.00  0.00              
ATOM   1015  C   LYS   310      22.663  23.656   0.190  1.00  0.00              
ATOM   1016  O   LYS   310      22.559  23.490  -1.026  1.00  0.00              
ATOM   1017  N   PHE   311      23.586  24.361   0.727  1.00  0.00              
ATOM   1018  CA  PHE   311      24.488  25.027  -0.144  1.00  0.00              
ATOM   1019  C   PHE   311      25.265  24.061  -1.017  1.00  0.00              
ATOM   1020  O   PHE   311      25.611  24.351  -2.153  1.00  0.00              
ATOM   1021  N   ARG   312      25.542  22.895  -0.479  1.00  0.00              
ATOM   1022  CA  ARG   312      26.327  21.923  -1.216  1.00  0.00              
ATOM   1023  C   ARG   312      25.496  21.016  -2.075  1.00  0.00              
ATOM   1024  O   ARG   312      25.969  20.526  -3.099  1.00  0.00              
ATOM   1025  N   TYR   313      24.276  20.750  -1.618  1.00  0.00              
ATOM   1026  CA  TYR   313      23.388  19.841  -2.316  1.00  0.00              
ATOM   1027  C   TYR   313      22.052  20.506  -2.531  1.00  0.00              
ATOM   1028  O   TYR   313      21.067  20.212  -1.842  1.00  0.00              
ATOM   1029  N   ARG   314      22.078  21.465  -3.444  1.00  0.00              
ATOM   1030  CA  ARG   314      20.955  22.313  -3.800  1.00  0.00              
ATOM   1031  C   ARG   314      19.667  21.607  -4.262  1.00  0.00              
ATOM   1032  O   ARG   314      18.792  22.203  -4.873  1.00  0.00              
ATOM   1033  N   GLN   315      19.528  20.330  -4.015  1.00  0.00              
ATOM   1034  CA  GLN   315      18.356  19.657  -4.514  1.00  0.00              
ATOM   1035  C   GLN   315      17.419  19.213  -3.431  1.00  0.00              
ATOM   1036  O   GLN   315      17.813  18.550  -2.482  1.00  0.00              
ATOM   1037  N   PRO   316      16.159  19.598  -3.576  1.00  0.00              
ATOM   1038  CA  PRO   316      15.162  19.263  -2.588  1.00  0.00              
ATOM   1039  C   PRO   316      15.151  17.831  -2.083  1.00  0.00              
ATOM   1040  O   PRO   316      15.107  17.615  -0.872  1.00  0.00              
ATOM   1041  N   ASP   317      15.150  16.827  -2.971  1.00  0.00              
ATOM   1042  CA  ASP   317      15.091  15.479  -2.475  1.00  0.00              
ATOM   1043  C   ASP   317      16.357  15.124  -1.634  1.00  0.00              
ATOM   1044  O   ASP   317      16.371  14.182  -0.856  1.00  0.00              
ATOM   1045  N   SER   318      17.469  15.856  -1.835  1.00  0.00              
ATOM   1046  CA  SER   318      18.672  15.568  -1.050  1.00  0.00              
ATOM   1047  C   SER   318      18.352  15.710   0.415  1.00  0.00              
ATOM   1048  O   SER   318      18.627  14.825   1.217  1.00  0.00              
ATOM   1049  N   LYS   319      17.755  16.864   0.752  1.00  0.00              
ATOM   1050  CA  LYS   319      17.397  17.202   2.118  1.00  0.00              
ATOM   1051  C   LYS   319      16.478  16.170   2.689  1.00  0.00              
ATOM   1052  O   LYS   319      16.440  15.904   3.895  1.00  0.00              
ATOM   1053  N   VAL   320      15.724  15.570   1.776  1.00  0.00              
ATOM   1054  CA  VAL   320      14.729  14.574   2.153  1.00  0.00              
ATOM   1055  C   VAL   320      15.249  13.200   2.457  1.00  0.00              
ATOM   1056  O   VAL   320      14.519  12.388   3.039  1.00  0.00              
ATOM   1057  N   PHE   348      16.489  12.946   2.050  1.00  0.00              
ATOM   1058  CA  PHE   348      17.121  11.671   2.331  1.00  0.00              
ATOM   1059  C   PHE   348      17.524  11.645   3.791  1.00  0.00              
ATOM   1060  O   PHE   348      17.721  10.576   4.376  1.00  0.00              
ATOM   1061  N   TYR   349      17.727  12.868   4.325  1.00  0.00              
ATOM   1062  CA  TYR   349      18.126  13.113   5.712  1.00  0.00              
ATOM   1063  C   TYR   349      16.897  12.980   6.596  1.00  0.00              
ATOM   1064  O   TYR   349      15.984  13.784   6.491  1.00  0.00              
ATOM   1065  N   ASP   350      16.888  11.928   7.431  1.00  0.00              
ATOM   1066  CA  ASP   350      15.796  11.596   8.342  1.00  0.00              
ATOM   1067  C   ASP   350      15.356  12.703   9.314  1.00  0.00              
ATOM   1068  O   ASP   350      16.152  13.157  10.155  1.00  0.00              
ATOM   1069  N   GLY   351      14.065  13.097   9.196  1.00  0.00              
ATOM   1070  CA  GLY   351      13.441  14.128  10.020  1.00  0.00              
ATOM   1071  C   GLY   351      13.093  13.614  11.416  1.00  0.00              
ATOM   1072  O   GLY   351      11.963  13.216  11.692  1.00  0.00              
END
