
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0316AL044_4-D3
# Molecule2: number of CA atoms   90 (  711),  selected   24 , name T0316_D3.pdb
# PARAMETERS: T0316AL044_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:    11       294 - 304         4.83    15.49
  LONGEST_CONTINUOUS_SEGMENT:    11       295 - 305         4.21    12.33
  LONGEST_CONTINUOUS_SEGMENT:    11       296 - 307         4.81    12.46
  LONGEST_CONTINUOUS_SEGMENT:    11       298 - 309         4.90    15.07
  LCS_AVERAGE:     10.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       299 - 304         1.51    15.06
  LCS_AVERAGE:      4.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.97    18.26
  LONGEST_CONTINUOUS_SEGMENT:     4       301 - 304         0.51    12.19
  LCS_AVERAGE:      3.01

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     289     E     289      3    3    7     3    4    4    4    4    4    7    7    8    9    9   10   11   13   15   16   17   19   20   22 
LCS_GDT     A     290     A     290      3    3    7     3    4    4    4    4    4    7    7    8    9    9   10   11   13   15   16   17   19   20   22 
LCS_GDT     S     291     S     291      3    3    7     1    3    3    4    4    5    7    7    8    9    9   10   11   13   15   16   17   19   20   22 
LCS_GDT     Q     292     Q     292      3    3    7     0    3    3    3    4    4    5    7    8    8    9   10   12   13   15   16   17   19   20   22 
LCS_GDT     V     293     V     293      0    0    8     0    0    1    1    2    3    4    5    5    5    6    8    8   11   12   13   15   16   16   18 
LCS_GDT     H     294     H     294      0    0   11     0    0    0    0    0    0    3    4    5    5    5    8    9   11   12   13   17   18   20   22 
LCS_GDT     F     295     F     295      4    4   11     3    4    4    4    4    5    7    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     T     296     T     296      4    4   11     3    3    4    4    4    4    6    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     R     297     R     297      4    4   11     3    3    4    4    4    4    5    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     E     298     E     298      4    4   11     1    3    4    4    4    5    7    7    8    9   10   11   12   13   15   16   17   19   20   22 
LCS_GDT     M     299     M     299      3    6   11     3    4    5    5    6    6    7    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     P     300     P     300      3    6   11     3    4    4    4    6    6    7    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     E     301     E     301      4    6   11     3    4    5    5    6    6    6    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     E     302     E     302      4    6   11     3    4    5    5    6    6    6    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     F     303     F     303      4    6   11     3    4    5    5    6    6    6    9    9    9   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     T     304     T     304      4    6   11     3    4    5    5    6    6    6    9    9    9   11   11   12   13   15   15   15   17   19   22 
LCS_GDT     L     305     L     305      0    5   11     1    1    3    3    4    5    6    7    8    8   11   11   12   13   15   16   17   19   20   22 
LCS_GDT     C     307     C     307      3    5   11     3    3    4    4    4    5    5    6    8    8    9   10   12   13   15   16   17   19   20   22 
LCS_GDT     T     308     T     308      3    5   11     3    3    4    4    4    5    5    6    8    8    9    9   10   12   15   16   17   19   20   22 
LCS_GDT     A     309     A     309      3    5   11     3    3    4    4    4    5    5    6    8    8    9   10   12   13   15   16   17   19   20   22 
LCS_GDT     K     310     K     310      3    4    8     3    3    3    3    4    4    5    6    7    8    9    9   12   13   15   16   16   19   20   22 
LCS_GDT     F     311     F     311      3    4    8     3    3    3    3    4    4    4    5    6    6    6    6    8   10   10   11   13   16   18   22 
LCS_GDT     K     319     K     319      0    0    7     0    0    1    1    4    4    5    5    6    6    8    9   12   13   15   16   17   19   20   22 
LCS_GDT     V     320     V     320      0    0    7     1    2    2    3    4    4    5    7    9    9   11   11   12   13   14   15   17   18   19   19 
LCS_AVERAGE  LCS_A:   5.99  (   3.01    4.26   10.69 )

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      5      5      6      6      7      9      9      9     11     11     12     13     15     16     17     19     20     22 
GDT PERCENT_CA   3.33   4.44   5.56   5.56   6.67   6.67   7.78  10.00  10.00  10.00  12.22  12.22  13.33  14.44  16.67  17.78  18.89  21.11  22.22  24.44
GDT RMS_LOCAL    0.01   0.51   1.18   1.18   1.51   1.51   2.73   3.28   3.28   3.28   4.05   4.10   4.29   4.70   5.77   6.25   6.39   7.13   7.32   7.75
GDT RMS_ALL_CA  18.96  12.19  14.96  14.96  15.06  15.06  11.76  13.76  13.76  13.76  11.55  12.11  11.74  10.88  11.86   9.18   9.00   8.51   8.41   8.29

#      Molecule1      Molecule2       DISTANCE
LGA    E     289      E     289         26.975
LGA    A     290      A     290         22.704
LGA    S     291      S     291         20.915
LGA    Q     292      Q     292         14.217
LGA    V     293      V     293         15.444
LGA    H     294      H     294         14.088
LGA    F     295      F     295          3.146
LGA    T     296      T     296          3.285
LGA    R     297      R     297          3.830
LGA    E     298      E     298          5.366
LGA    M     299      M     299          3.871
LGA    P     300      P     300          3.980
LGA    E     301      E     301          3.914
LGA    E     302      E     302          2.209
LGA    F     303      F     303          1.393
LGA    T     304      T     304          3.414
LGA    L     305      L     305          9.720
LGA    C     307      C     307         17.222
LGA    T     308      T     308         21.905
LGA    A     309      A     309         21.178
LGA    K     310      K     310         19.550
LGA    F     311      F     311         15.366
LGA    K     319      K     319         15.833
LGA    V     320      V     320         11.027

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   90    4.0      9    3.28     9.444     7.868     0.266

LGA_LOCAL      RMSD =  3.278  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.081  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  8.199  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.436722 * X  +  -0.885830 * Y  +  -0.156777 * Z  +  17.370466
  Y_new =   0.667737 * X  +  -0.202418 * Y  +  -0.716348 * Z  +  96.156143
  Z_new =   0.602828 * X  +  -0.417531 * Y  +   0.679902 * Z  +  -5.784862 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.550726    2.590866  [ DEG:   -31.5543    148.4457 ]
  Theta =  -0.647041   -2.494552  [ DEG:   -37.0727   -142.9273 ]
  Phi   =   2.150002   -0.991591  [ DEG:   123.1860    -56.8140 ]
 
# 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: T0316AL044_4-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL044_4-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   90   4.0    9   3.28   7.868     8.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL044_4-D3
REMARK Aligment from pdb entry: 1wy5_A
ATOM    789  N   GLU   289      35.262  13.759  21.935  1.00  0.00              
ATOM    790  CA  GLU   289      34.205  14.392  22.736  1.00  0.00              
ATOM    791  C   GLU   289      32.885  14.535  21.974  1.00  0.00              
ATOM    792  O   GLU   289      32.877  14.850  20.783  1.00  0.00              
ATOM    793  N   ALA   290      31.774  14.319  22.669  1.00  0.00              
ATOM    794  CA  ALA   290      30.449  14.412  22.055  1.00  0.00              
ATOM    795  C   ALA   290      30.270  15.691  21.233  1.00  0.00              
ATOM    796  O   ALA   290      29.786  15.652  20.097  1.00  0.00              
ATOM    797  N   SER   291      30.661  16.824  21.814  1.00  0.00              
ATOM    798  CA  SER   291      30.525  18.117  21.151  1.00  0.00              
ATOM    799  C   SER   291      31.194  18.145  19.786  1.00  0.00              
ATOM    800  O   SER   291      30.595  18.585  18.806  1.00  0.00              
ATOM    801  N   GLN   292      32.434  17.675  19.717  1.00  0.00              
ATOM    802  CA  GLN   292      33.152  17.676  18.450  1.00  0.00              
ATOM    803  C   GLN   292      32.609  16.634  17.471  1.00  0.00              
ATOM    804  O   GLN   292      32.683  16.822  16.256  1.00  0.00              
ATOM    805  N   VAL   293      22.124  21.176  10.184  1.00  0.00              
ATOM    806  CA  VAL   293      22.150  21.572  11.590  1.00  0.00              
ATOM    807  C   VAL   293      21.075  20.879  12.431  1.00  0.00              
ATOM    808  O   VAL   293      21.167  20.860  13.659  1.00  0.00              
ATOM    809  N   HIS   294      20.070  20.306  11.772  1.00  0.00              
ATOM    810  CA  HIS   294      18.975  19.614  12.460  1.00  0.00              
ATOM    811  C   HIS   294      19.453  18.643  13.532  1.00  0.00              
ATOM    812  O   HIS   294      20.116  17.648  13.236  1.00  0.00              
ATOM    813  N   PHE   295      22.659  10.313  12.317  1.00  0.00              
ATOM    814  CA  PHE   295      23.876  10.009  11.582  1.00  0.00              
ATOM    815  C   PHE   295      24.976   9.636  12.577  1.00  0.00              
ATOM    816  O   PHE   295      25.764   8.724  12.339  1.00  0.00              
ATOM    817  N   THR   296      25.017  10.328  13.709  1.00  0.00              
ATOM    818  CA  THR   296      26.032  10.054  14.717  1.00  0.00              
ATOM    819  C   THR   296      25.991   8.607  15.204  1.00  0.00              
ATOM    820  O   THR   296      27.031   8.016  15.498  1.00  0.00              
ATOM    821  N   ARG   297      24.791   8.037  15.283  1.00  0.00              
ATOM    822  CA  ARG   297      24.630   6.664  15.751  1.00  0.00              
ATOM    823  C   ARG   297      25.353   5.635  14.889  1.00  0.00              
ATOM    824  O   ARG   297      25.699   4.554  15.369  1.00  0.00              
ATOM    825  N   GLU   298      25.592   5.962  13.622  1.00  0.00              
ATOM    826  CA  GLU   298      26.283   5.031  12.736  1.00  0.00              
ATOM    827  C   GLU   298      27.756   4.926  13.103  1.00  0.00              
ATOM    828  O   GLU   298      28.526   4.223  12.448  1.00  0.00              
ATOM    829  N   MET   299      28.142   5.628  14.162  1.00  0.00              
ATOM    830  CA  MET   299      29.518   5.598  14.635  1.00  0.00              
ATOM    831  C   MET   299      29.698   4.423  15.597  1.00  0.00              
ATOM    832  O   MET   299      30.825   4.059  15.945  1.00  0.00              
ATOM    833  N   PRO   300      28.584   3.825  16.019  1.00  0.00              
ATOM    834  CA  PRO   300      28.641   2.706  16.954  1.00  0.00              
ATOM    835  C   PRO   300      28.022   1.418  16.413  1.00  0.00              
ATOM    836  O   PRO   300      28.257   0.339  16.962  1.00  0.00              
ATOM    837  N   GLU   301      27.231   1.531  15.346  1.00  0.00              
ATOM    838  CA  GLU   301      26.590   0.367  14.737  1.00  0.00              
ATOM    839  C   GLU   301      26.381   0.576  13.237  1.00  0.00              
ATOM    840  O   GLU   301      25.781   1.566  12.821  1.00  0.00              
ATOM    841  N   GLU   302      26.875  -0.360  12.432  1.00  0.00              
ATOM    842  CA  GLU   302      26.729  -0.257  10.989  1.00  0.00              
ATOM    843  C   GLU   302      25.306   0.018  10.533  1.00  0.00              
ATOM    844  O   GLU   302      24.353  -0.178  11.290  1.00  0.00              
ATOM    845  N   PHE   303      25.158   0.474   9.292  1.00  0.00              
ATOM    846  CA  PHE   303      23.836   0.766   8.766  1.00  0.00              
ATOM    847  C   PHE   303      23.846   1.860   7.715  1.00  0.00              
ATOM    848  O   PHE   303      24.895   2.197   7.168  1.00  0.00              
ATOM    849  N   THR   304      22.672   2.417   7.431  1.00  0.00              
ATOM    850  CA  THR   304      22.549   3.480   6.439  1.00  0.00              
ATOM    851  C   THR   304      21.555   4.546   6.900  1.00  0.00              
ATOM    852  O   THR   304      20.680   4.275   7.721  1.00  0.00              
ATOM    853  N   LEU   305      27.888   2.816   6.564  1.00  0.00              
ATOM    854  CA  LEU   305      29.007   2.503   7.445  1.00  0.00              
ATOM    855  C   LEU   305      29.713   1.289   6.846  1.00  0.00              
ATOM    856  O   LEU   305      29.218   0.164   6.925  1.00  0.00              
ATOM    857  N   CYS   307      30.862   1.532   6.227  1.00  0.00              
ATOM    858  CA  CYS   307      31.642   0.471   5.606  1.00  0.00              
ATOM    859  C   CYS   307      32.856   0.168   6.475  1.00  0.00              
ATOM    860  O   CYS   307      33.975   0.552   6.137  1.00  0.00              
ATOM    861  N   THR   308      32.625  -0.517   7.594  1.00  0.00              
ATOM    862  CA  THR   308      33.686  -0.883   8.531  1.00  0.00              
ATOM    863  C   THR   308      34.768   0.190   8.690  1.00  0.00              
ATOM    864  O   THR   308      35.693   0.278   7.886  1.00  0.00              
ATOM    865  N   ALA   309      34.641   1.006   9.731  1.00  0.00              
ATOM    866  CA  ALA   309      35.610   2.063  10.014  1.00  0.00              
ATOM    867  C   ALA   309      35.452   3.333   9.179  1.00  0.00              
ATOM    868  O   ALA   309      35.812   4.415   9.635  1.00  0.00              
ATOM    869  N   LYS   310      34.925   3.212   7.963  1.00  0.00              
ATOM    870  CA  LYS   310      34.746   4.385   7.109  1.00  0.00              
ATOM    871  C   LYS   310      33.266   4.763   7.026  1.00  0.00              
ATOM    872  O   LYS   310      32.426   4.128   7.660  1.00  0.00              
ATOM    873  N   PHE   311      32.954   5.796   6.244  1.00  0.00              
ATOM    874  CA  PHE   311      31.572   6.255   6.095  1.00  0.00              
ATOM    875  C   PHE   311      31.404   7.294   4.977  1.00  0.00              
ATOM    876  O   PHE   311      32.021   8.354   5.026  1.00  0.00              
ATOM    877  N   LYS   319      30.545   7.004   3.997  1.00  0.00              
ATOM    878  CA  LYS   319      30.333   7.909   2.860  1.00  0.00              
ATOM    879  C   LYS   319      29.150   8.876   2.903  1.00  0.00              
ATOM    880  O   LYS   319      28.186   8.681   3.639  1.00  0.00              
ATOM    881  N   VAL   320      29.269   9.906   2.062  1.00  0.00              
ATOM    882  CA  VAL   320      28.308  10.986   1.827  1.00  0.00              
ATOM    883  C   VAL   320      29.032  12.321   1.811  1.00  0.00              
ATOM    884  O   VAL   320      28.957  13.053   2.820  1.00  0.00              
END
