
#######################################################
#                                                     #
#                        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   26 (   26),  selected   26 , name T0289TS599_5-D1
# Molecule2: number of CA atoms  233 ( 1850),  selected   26 , name T0289_D1.pdb
# PARAMETERS: T0289TS599_5-D1.T0289_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:    15       213 - 301         4.99    11.47
  LCS_AVERAGE:      6.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       298 - 305         1.07    14.89
  LCS_AVERAGE:      2.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       298 - 304         0.98    15.19
  LONGEST_CONTINUOUS_SEGMENT:     7       299 - 305         0.74    14.70
  LCS_AVERAGE:      2.18

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:  233
LCS_GDT     G     211     G     211      3    7   13     3    3    4    6    6    7    8    9   10   10   12   14   15   16   17   17   17   18   21   21 
LCS_GDT     K     212     K     212      3    7   13     3    3    4    4    4    7    8    9   10   11   12   14   15   16   17   17   17   18   21   21 
LCS_GDT     E     213     E     213      5    7   15     4    5    5    6    6    7    8    9   10   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     F     214     F     214      5    7   15     4    5    5    6    6    7    8    9   10   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     P     215     P     215      5    7   15     4    5    5    6    6    7    9    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     P     216     P     216      5    7   15     4    5    5    6    7    8    9    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     C     217     C     217      5    7   15     4    5    6    7    7    8    9    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     A     218     A     218      5    7   15     4    4    6    7    7    8    9    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     I     219     I     219      5    7   15     4    4    6    7    7    8    9    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     D     220     D     220      5    7   15     4    4    6    7    7    8    9    9   11   11   12   14   15   16   17   17   18   19   20   22 
LCS_GDT     V     221     V     221      5    7   15     4    4    6    7    7    8    9    9   11   11   12   14   15   16   17   17   18   19   20   22 
LCS_GDT     Y     222     Y     222      5    7   15     4    4    6    7    7    8    9    9   11   11   12   14   15   16   17   17   17   18   18   19 
LCS_GDT     K     223     K     223      5    7   15     3    4    5    7    7    8    9    9   11   11   12   14   15   16   17   17   18   19   20   22 
LCS_GDT     T     298     T     298      7    8   15     3    4    5    8    8    8    8    9   10   11   11   12   12   14   15   18   18   19   20   22 
LCS_GDT     K     299     K     299      7    8   15     3    6    7    8    8    8    8    9   10   11   12   14   14   16   17   18   18   19   21   22 
LCS_GDT     L     300     L     300      7    8   15     4    6    7    8    8    8    8    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     T     301     T     301      7    8   15     4    6    7    8    8    8    8    9   11   11   12   14   15   16   17   18   18   19   21   22 
LCS_GDT     L     302     L     302      7    8   13     4    6    7    8    8    8    8    9   10   11   12   12   13   16   17   18   18   19   21   22 
LCS_GDT     N     303     N     303      7    8   13     4    6    7    8    8    8    8    9   10   11   12   12   13   14   15   18   18   19   21   22 
LCS_GDT     A     304     A     304      7    8   13     3    6    7    8    8    8    8    9   10   11   12   12   13   14   15   18   18   19   21   22 
LCS_GDT     K     305     K     305      7    8   13     2    6    7    8    8    8    8    9   10   11   12   12   13   14   15   16   18   19   21   22 
LCS_GDT     S     306     S     306      3    4   13     2    3    4    4    4    4    5    9   10   11   12   12   13   14   15   18   18   19   21   22 
LCS_GDT     I     307     I     307      3    4   13     0    3    4    4    4    4    4    6   10   11   11   12   12   14   15   18   18   19   21   22 
LCS_GDT     R     308     R     308      3    3   13     0    3    4    4    4    4    4    6   10   11   11   12   12   14   15   18   18   19   21   22 
LCS_GDT     S     309     S     309      3    3   13     0    3    3    3    3    4    4    5    7    7   11   12   12   14   15   18   18   19   21   22 
LCS_GDT     T     310     T     310      3    3   13     0    3    3    3    3    4    4    5    7    7   10   11   12   13   15   16   17   19   21   21 
LCS_AVERAGE  LCS_A:   3.70  (   2.18    2.84    6.07 )

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      8      9      9     11     11     12     14     15     16     17     18     18     19     21     22 
GDT PERCENT_CA   1.72   2.58   3.00   3.43   3.43   3.43   3.86   3.86   4.72   4.72   5.15   6.01   6.44   6.87   7.30   7.73   7.73   8.15   9.01   9.44
GDT RMS_LOCAL    0.18   0.60   0.74   1.07   1.07   1.07   2.45   2.10   3.07   3.07   3.50   4.15   4.38   4.70   4.94   6.22   6.22   6.44   6.97   7.46
GDT RMS_ALL_CA  11.82  14.69  14.70  14.89  14.89  14.89  12.43  13.29  13.85  13.85  12.73  11.90  11.59  11.51  11.42   9.46   9.46   9.47  10.14   9.21

#      Molecule1      Molecule2       DISTANCE
LGA    G     211      G     211         24.950
LGA    K     212      K     212         26.835
LGA    E     213      E     213         22.550
LGA    F     214      F     214         20.532
LGA    P     215      P     215         22.175
LGA    P     216      P     216         21.587
LGA    C     217      C     217         18.682
LGA    A     218      A     218         12.554
LGA    I     219      I     219          9.621
LGA    D     220      D     220          7.451
LGA    V     221      V     221          3.634
LGA    Y     222      Y     222          9.453
LGA    K     223      K     223         12.918
LGA    T     298      T     298          2.074
LGA    K     299      K     299          2.308
LGA    L     300      L     300          1.409
LGA    T     301      T     301          2.078
LGA    L     302      L     302          0.907
LGA    N     303      N     303          1.216
LGA    A     304      A     304          2.458
LGA    K     305      K     305          1.636
LGA    S     306      S     306          7.785
LGA    I     307      I     307          8.397
LGA    R     308      R     308          8.283
LGA    S     309      S     309          8.925
LGA    T     310      T     310         14.098

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  233    4.0      9    2.10     4.399     3.974     0.409

LGA_LOCAL      RMSD =  2.101  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.387  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  8.787  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.454143 * X  +  -0.870819 * Y  +  -0.188227 * Z  +  40.151398
  Y_new =   0.574918 * X  +   0.447839 * Y  +  -0.684769 * Z  +  24.646666
  Z_new =   0.680605 * X  +   0.202768 * Y  +   0.704032 * Z  +  -2.505664 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.280420   -2.861173  [ DEG:    16.0669   -163.9331 ]
  Theta =  -0.748589   -2.393004  [ DEG:   -42.8910   -137.1090 ]
  Phi   =   0.902229   -2.239364  [ DEG:    51.6939   -128.3061 ]
 
# 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: T0289TS599_5-D1                               
REMARK     2: T0289_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289TS599_5-D1.T0289_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  233   4.0    9   2.10   3.974     8.79
REMARK  ---------------------------------------------------------- 
MOLECULE T0289TS599_5-D1
PFRMAT TS                                                                       
TARGET T0289                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLY   211      18.719  18.224   3.661  1.00  0.00              
ATOM    212  CA  LYS   212      19.917  17.074   7.066  1.00  0.00              
ATOM    213  CA  GLU   213      23.711  15.245   7.113  1.00  0.00              
ATOM    214  CA  PHE   214      25.802  16.640   9.804  1.00  0.00              
ATOM    215  CA  PRO   215      26.207  15.343  13.313  1.00  0.00              
ATOM    216  CA  PRO   216      24.525  17.230  16.110  1.00  0.00              
ATOM    217  CA  CYS   217      27.769  18.434  17.766  1.00  0.00              
ATOM    218  CA  ALA   218      29.536  19.798  14.752  1.00  0.00              
ATOM    219  CA  ILE   219      30.531  23.411  14.728  1.00  0.00              
ATOM    220  CA  ASP   220      31.274  25.149  11.387  1.00  0.00              
ATOM    221  CA  VAL   221      32.638  28.705  11.350  1.00  0.00              
ATOM    222  CA  TYR   222      32.495  30.699   8.184  1.00  0.00              
ATOM    223  CA  LYS   223      34.062  34.141   8.219  1.00  0.00              
ATOM    298  CA  THR   298      33.802  27.435  23.513  1.00  0.00              
ATOM    299  CA  LYS   299      36.037  25.505  21.169  1.00  0.00              
ATOM    300  CA  LEU   300      34.868  25.409  17.699  1.00  0.00              
ATOM    301  CA  THR   301      35.582  22.360  15.526  1.00  0.00              
ATOM    302  CA  LEU   302      36.018  22.730  11.821  1.00  0.00              
ATOM    303  CA  ASN   303      36.519  19.619   9.653  1.00  0.00              
ATOM    304  CA  ALA   304      38.835  20.229   6.709  1.00  0.00              
ATOM    305  CA  LYS   305      37.052  17.952   4.220  1.00  0.00              
ATOM    306  CA  SER   306      33.700  19.644   4.961  1.00  0.00              
ATOM    307  CA  ILE   307      35.263  23.088   4.522  1.00  0.00              
ATOM    308  CA  ARG   308      36.873  22.238   1.228  1.00  0.00              
ATOM    309  CA  SER   309      33.595  20.807  -0.137  1.00  0.00              
ATOM    310  CA  THR   310      31.863  24.390   1.172  1.00  0.00              
TER                                                                             
END
