
#######################################################
#                                                     #
#                        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   11 (   55),  selected   11 , name T0356TS245_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected   11 , name T0356_D1.pdb
# PARAMETERS: T0356TS245_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    24.91
  LCS_AVERAGE:      5.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       342 - 346         1.87    27.38
  LCS_AVERAGE:      3.30

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       314 - 316         0.03    39.72
  LONGEST_CONTINUOUS_SEGMENT:     3       340 - 342         0.62    21.30
  LONGEST_CONTINUOUS_SEGMENT:     3       341 - 343         0.50    17.35
  LONGEST_CONTINUOUS_SEGMENT:     3       342 - 344         0.13    20.63
  LONGEST_CONTINUOUS_SEGMENT:     3       343 - 345         0.01    29.00
  LONGEST_CONTINUOUS_SEGMENT:     3       344 - 346         0.74    26.63
  LONGEST_CONTINUOUS_SEGMENT:     3       345 - 347         0.42    23.99
  LCS_AVERAGE:      2.42

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      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     A     315     A     315      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     I     316     I     316      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    5 
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    6    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:   3.69  (   2.42    3.30    5.35 )

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   2.75   2.75   2.75   3.77   3.77   4.27   4.27   4.27   4.27   4.27   4.27   4.27   4.27
GDT RMS_ALL_CA  29.00  21.02  21.02  21.02  21.02  27.38  27.38  20.55  20.55  20.55  25.60  25.60  24.91  24.91  24.91  24.91  24.91  24.91  24.91  24.91

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         39.023
LGA    A     315      A     315         38.038
LGA    I     316      I     316         38.493
LGA    F     340      F     340          2.395
LGA    V     341      V     341          2.179
LGA    P     342      P     342          2.543
LGA    I     343      I     343          8.434
LGA    L     344      L     344          3.928
LGA    Q     345      Q     345          1.198
LGA    K     346      K     346          3.424
LGA    Q     347      Q     347          8.900

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  124    4.0      6    2.75     4.435     4.150     0.210

LGA_LOCAL      RMSD =  2.755  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 20.554  Number of atoms =   11 
Std_ALL_ATOMS  RMSD = 13.191  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.317367 * X  +  -0.331480 * Y  +   0.888482 * Z  +  52.174969
  Y_new =   0.930265 * X  +   0.290694 * Y  +  -0.223838 * Z  +  33.440773
  Z_new =  -0.184079 * X  +   0.897562 * Y  +   0.400621 * Z  +  11.421363 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.150988   -1.990605  [ DEG:    65.9467   -114.0533 ]
  Theta =   0.185134    2.956458  [ DEG:    10.6074    169.3926 ]
  Phi   =   1.242021   -1.899572  [ DEG:    71.1626   -108.8374 ]
 
# 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: T0356TS245_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS245_1-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  124   4.0    6   2.75   4.150    13.19
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS245_1-D1
PFRMAT TS
TARGET t0356
MODEL 1
PARENT 1ejeA
ATOM    751  N   ASP   314      70.134  76.225  59.382  1.00  0.00
ATOM    752  CA  ASP   314      70.635  77.390  58.662  1.00  0.00
ATOM    753  C   ASP   314      71.621  77.063  57.584  1.00  0.00
ATOM    754  O   ASP   314      72.351  77.792  56.878  1.00  0.00
ATOM    755  CB  ASP   314      71.279  78.309  59.703  1.00  0.00
ATOM    756  N   ALA   315      71.386  75.582  57.288  1.00  0.00
ATOM    757  CA  ALA   315      71.790  74.580  56.305  1.00  0.00
ATOM    758  C   ALA   315      73.020  74.973  55.513  1.00  0.00
ATOM    759  O   ALA   315      72.940  74.145  56.446  1.00  0.00
ATOM    760  CB  ALA   315      70.603  74.369  55.364  1.00  0.00
ATOM    761  N   ILE   316      75.840  75.623  53.925  1.00  0.00
ATOM    762  CA  ILE   316      75.358  74.764  55.018  1.00  0.00
ATOM    763  C   ILE   316      73.928  75.100  55.470  1.00  0.00
ATOM    764  O   ILE   316      75.093  74.889  55.872  1.00  0.00
ATOM    765  CB  ILE   316      76.332  74.930  56.186  1.00  0.00
ATOM    766  N   PHE   340      64.652  71.989  61.376  1.00  0.00
ATOM    767  CA  PHE   340      63.803  71.437  62.424  1.00  0.00
ATOM    768  C   PHE   340      62.341  71.479  62.111  1.00  0.00
ATOM    769  O   PHE   340      63.315  72.216  61.848  1.00  0.00
ATOM    770  CB  PHE   340      64.092  72.239  63.695  1.00  0.00
ATOM    771  N   VAL   341      61.575  71.348  61.487  1.00  0.00
ATOM    772  CA  VAL   341      60.560  71.293  60.447  1.00  0.00
ATOM    773  C   VAL   341      59.637  72.483  60.617  1.00  0.00
ATOM    774  O   VAL   341      60.284  72.973  61.568  1.00  0.00
ATOM    775  CB  VAL   341      59.767  69.990  60.567  1.00  0.00
ATOM    776  N   PRO   342      59.001  73.064  59.987  1.00  0.00
ATOM    777  CA  PRO   342      58.413  74.316  59.602  1.00  0.00
ATOM    778  C   PRO   342      57.373  73.956  58.645  1.00  0.00
ATOM    779  O   PRO   342      57.961  74.078  57.548  1.00  0.00
ATOM    780  CB  PRO   342      59.437  75.241  58.943  1.00  0.00
ATOM    781  N   ILE   343      56.218  73.734  58.733  1.00  0.00
ATOM    782  CA  ILE   343      55.183  73.544  57.730  1.00  0.00
ATOM    783  C   ILE   343      55.568  72.459  56.737  1.00  0.00
ATOM    784  O   ILE   343      56.605  73.115  56.505  1.00  0.00
ATOM    785  CB  ILE   343      54.974  74.873  57.002  1.00  0.00
ATOM    786  N   LEU   344      55.530  71.264  56.694  1.00  0.00
ATOM    787  CA  LEU   344      56.554  70.278  56.393  1.00  0.00
ATOM    788  C   LEU   344      57.894  70.461  55.725  1.00  0.00
ATOM    789  O   LEU   344      58.199  69.519  54.963  1.00  0.00
ATOM    790  CB  LEU   344      55.693  69.305  55.586  1.00  0.00
ATOM    791  N   GLN   345      58.539  71.486  55.799  1.00  0.00
ATOM    792  CA  GLN   345      59.742  71.910  55.106  1.00  0.00
ATOM    793  C   GLN   345      60.845  72.044  56.134  1.00  0.00
ATOM    794  O   GLN   345      60.173  72.561  57.052  1.00  0.00
ATOM    795  CB  GLN   345      59.502  73.254  54.415  1.00  0.00
ATOM    796  N   LYS   346      61.892  71.986  56.156  1.00  0.00
ATOM    797  CA  LYS   346      63.243  72.106  56.561  1.00  0.00
ATOM    798  C   LYS   346      63.420  73.196  57.512  1.00  0.00
ATOM    799  O   LYS   346      63.630  73.601  56.347  1.00  0.00
ATOM    800  CB  LYS   346      64.094  72.352  55.313  1.00  0.00
ATOM    801  N   GLN   347      63.261  73.807  58.273  1.00  0.00
ATOM    802  CA  GLN   347      63.113  75.116  58.876  1.00  0.00
ATOM    803  C   GLN   347      64.475  75.792  58.743  1.00  0.00
ATOM    804  O   GLN   347      65.288  75.849  59.690  1.00  0.00
ATOM    805  CB  GLN   347      62.726  74.999  60.352  1.00  0.00
TER
END
