
#######################################################
#                                                     #
#                        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 T0356TS383_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected    9 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_1-D1.T0356_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:     8       340 - 347         4.27    12.95
  LCS_AVERAGE:      5.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       342 - 346         1.87    15.27
  LCS_AVERAGE:      3.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       340 - 342         0.62    12.44
  LONGEST_CONTINUOUS_SEGMENT:     3       341 - 343         0.50    16.44
  LONGEST_CONTINUOUS_SEGMENT:     3       342 - 344         0.13    16.83
  LONGEST_CONTINUOUS_SEGMENT:     3       343 - 345         0.01    17.93
  LONGEST_CONTINUOUS_SEGMENT:     3       344 - 346         0.74    14.67
  LONGEST_CONTINUOUS_SEGMENT:     3       345 - 347         0.42    20.18
  LCS_AVERAGE:      2.15

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:  124
LCS_GDT     D     314     D     314      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     F     340     F     340      3    3    8     3    4    4    4    4    4    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     V     341     V     341      3    4    8     3    4    4    4    4    4    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     P     342     P     342      3    5    8     3    4    4    4    4    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     I     343     I     343      3    5    8     3    3    4    4    4    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     L     344     L     344      3    5    8     3    3    4    4    4    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     Q     345     Q     345      3    5    8     3    4    4    4    4    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     K     346     K     346      3    5    8     3    3    3    4    4    5    5    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     Q     347     Q     347      3    4    8     3    3    3    3    4    4    5    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   3.70  (   2.15    3.23    5.73 )

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      5      5      6      6      6      7      7      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.42   3.23   3.23   3.23   3.23   4.03   4.03   4.84   4.84   4.84   5.65   5.65   6.45   6.45   6.45   6.45   6.45   6.45   6.45   6.45
GDT RMS_LOCAL    0.01   0.70   0.70   0.70   0.70   1.87   1.87   3.11   2.97   2.97   3.77   3.77   4.27   4.27   4.27   4.27   4.27   4.27   4.27   4.27
GDT RMS_ALL_CA  17.93  12.43  12.43  12.43  12.43  15.27  15.27  12.54  15.97  15.97  13.21  13.21  12.95  12.95  12.95  12.95  12.95  12.95  12.95  12.95

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         34.391
LGA    F     340      F     340          2.685
LGA    V     341      V     341          1.189
LGA    P     342      P     342          2.615
LGA    I     343      I     343          3.771
LGA    L     344      L     344          3.687
LGA    Q     345      Q     345          3.824
LGA    K     346      K     346          8.952
LGA    Q     347      Q     347          9.761

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  124    4.0      6    3.11     4.435     4.131     0.187

LGA_LOCAL      RMSD =  3.107  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.543  Number of atoms =    9 
Std_ALL_ATOMS  RMSD = 11.838  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.903913 * X  +   0.365901 * Y  +  -0.221489 * Z  +  18.814207
  Y_new =  -0.427712 * X  +   0.775673 * Y  +  -0.464106 * Z  +  52.011818
  Z_new =   0.001987 * X  +   0.514245 * Y  +   0.857641 * Z  +  18.771509 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.540128   -2.601465  [ DEG:    30.9471   -149.0529 ]
  Theta =  -0.001987   -3.139606  [ DEG:    -0.1138   -179.8862 ]
  Phi   =  -0.441961    2.699632  [ DEG:   -25.3225    154.6775 ]
 
# 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: T0356TS383_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_1-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  124   4.0    6   3.11   4.131    11.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_1-D1
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    609  N   ASP   314      59.720  73.824  67.058  1.00  0.00
ATOM    610  CA  ASP   314      61.067  73.406  66.718  1.00  0.00
ATOM    611  C   ASP   314      61.170  72.051  66.040  1.00  0.00
ATOM    612  O   ASP   314      62.269  71.592  65.737  1.00  0.00
ATOM    613  N   PHE   340      60.039  71.404  65.789  1.00  0.00
ATOM    614  CA  PHE   340      60.065  70.087  65.160  1.00  0.00
ATOM    615  C   PHE   340      60.068  70.154  63.639  1.00  0.00
ATOM    616  O   PHE   340      60.231  69.134  62.967  1.00  0.00
ATOM    617  N   VAL   341      59.894  71.355  63.098  1.00  0.00
ATOM    618  CA  VAL   341      59.877  71.543  61.654  1.00  0.00
ATOM    619  C   VAL   341      61.036  72.397  61.144  1.00  0.00
ATOM    620  O   VAL   341      61.253  73.513  61.613  1.00  0.00
ATOM    621  N   PRO   342      61.764  71.866  60.170  1.00  0.00
ATOM    622  CA  PRO   342      62.896  72.568  59.580  1.00  0.00
ATOM    623  C   PRO   342      62.698  72.663  58.069  1.00  0.00
ATOM    624  O   PRO   342      62.863  71.677  57.347  1.00  0.00
ATOM    625  N   ILE   343      62.335  73.856  57.606  1.00  0.00
ATOM    626  CA  ILE   343      62.091  74.119  56.192  1.00  0.00
ATOM    627  C   ILE   343      60.909  73.332  55.646  1.00  0.00
ATOM    628  O   ILE   343      60.924  72.888  54.499  1.00  0.00
ATOM    629  N   LEU   344      59.884  73.168  56.476  1.00  0.00
ATOM    630  CA  LEU   344      58.694  72.451  56.061  1.00  0.00
ATOM    631  C   LEU   344      58.761  70.951  56.259  1.00  0.00
ATOM    632  O   LEU   344      57.759  70.259  56.079  1.00  0.00
ATOM    633  N   GLN   345      59.935  70.447  56.635  1.00  0.00
ATOM    634  CA  GLN   345      60.127  69.014  56.846  1.00  0.00
ATOM    635  C   GLN   345      60.316  68.701  58.325  1.00  0.00
ATOM    636  O   GLN   345      60.615  69.590  59.121  1.00  0.00
ATOM    637  N   LYS   346      60.138  67.437  58.695  1.00  0.00
ATOM    638  CA  LYS   346      60.319  67.038  60.082  1.00  0.00
ATOM    639  C   LYS   346      61.795  67.207  60.399  1.00  0.00
ATOM    640  O   LYS   346      62.641  66.586  59.762  1.00  0.00
ATOM    641  N   GLN   347      62.104  68.061  61.368  1.00  0.00
ATOM    642  CA  GLN   347      63.494  68.301  61.746  1.00  0.00
ATOM    643  C   GLN   347      64.077  67.047  62.390  1.00  0.00
ATOM    644  O   GLN   347      64.284  67.000  63.600  1.00  0.00
TER
END
