
#######################################################
#                                                     #
#                        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    8 (   61),  selected    8 , name T0385TS009_1_3
# Molecule2: number of CA atoms  142 ( 1050),  selected    8 , name T0385.pdb
# PARAMETERS: T0385TS009_1_3.T0385.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       119 - 126         3.41     3.41
  LCS_AVERAGE:      5.63

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       120 - 124         1.77     5.20
  LONGEST_CONTINUOUS_SEGMENT:     5       121 - 125         1.76     5.52
  LCS_AVERAGE:      3.26

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       119 - 121         0.13     6.45
  LONGEST_CONTINUOUS_SEGMENT:     3       120 - 122         0.51     7.35
  LONGEST_CONTINUOUS_SEGMENT:     3       121 - 123         0.32     6.79
  LONGEST_CONTINUOUS_SEGMENT:     3       123 - 125         0.28     8.35
  LONGEST_CONTINUOUS_SEGMENT:     3       124 - 126         0.44    11.41
  LCS_AVERAGE:      2.11

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:  142
LCS_GDT     E     119     E     119      3    4    8     3    3    4    5    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     H     120     H     120      3    5    8     3    3    4    5    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     121     A     121      3    5    8     3    3    4    5    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     122     E     122      3    5    8     3    3    4    4    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     T     123     T     123      3    5    8     3    3    4    5    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     A     124     A     124      3    5    8     3    3    4    5    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     125     D     125      3    5    8     3    3    3    4    5    5    6    6    6    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     126     D     126      3    3    8     3    3    3    3    3    4    5    5    5    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   3.67  (   2.11    3.26    5.63 )

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      3      4      5      5      5      6      6      6      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.11   2.11   2.82   3.52   3.52   3.52   4.23   4.23   4.23   5.63   5.63   5.63   5.63   5.63   5.63   5.63   5.63   5.63   5.63   5.63
GDT RMS_LOCAL    0.13   0.13   0.77   1.33   1.33   1.33   2.22   2.17   2.17   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41
GDT RMS_ALL_CA   6.45   6.45   5.26   4.92   4.92   4.92   4.77   5.06   5.06   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41   3.41

#      Molecule1      Molecule2       DISTANCE
LGA    E     119      E     119          2.123
LGA    H     120      H     120          1.246
LGA    A     121      A     121          1.104
LGA    E     122      E     122          3.974
LGA    T     123      T     123          1.913
LGA    A     124      A     124          1.265
LGA    D     125      D     125          7.205
LGA    D     126      D     126         11.159

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  142    4.0      6    2.17     3.873     3.912     0.264

LGA_LOCAL      RMSD =  2.173  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.059  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  3.413  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.974664 * X  +  -0.004043 * Y  +   0.223639 * Z  +  22.717564
  Y_new =   0.139146 * X  +  -0.793780 * Y  +   0.592075 * Z  +  48.758080
  Z_new =   0.175126 * X  +   0.608192 * Y  +   0.774231 * Z  +  -8.388805 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.665864   -2.475729  [ DEG:    38.1512   -141.8488 ]
  Theta =  -0.176034   -2.965559  [ DEG:   -10.0860   -169.9140 ]
  Phi   =   2.999788   -0.141805  [ DEG:   171.8752     -8.1248 ]
 
# 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: T0385TS009_1_3                                
REMARK     2: T0385.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS009_1_3.T0385.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  142   4.0    6   2.17   3.912     3.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS009_1_3
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0385                                                                    
PARENT N/A                                                                      
ATOM    858  N   GLU   119      23.207  24.724  40.576  1.00  0.00              
ATOM    859  CA  GLU   119      23.213  23.925  39.356  1.00  0.00              
ATOM    860  C   GLU   119      23.957  22.610  39.562  1.00  0.00              
ATOM    861  O   GLU   119      24.872  22.279  38.807  1.00  0.00              
ATOM    862  CB  GLU   119      21.783  23.652  38.887  1.00  0.00              
ATOM    863  CG  GLU   119      21.233  24.698  37.930  1.00  0.00              
ATOM    864  CD  GLU   119      20.252  24.116  36.932  1.00  0.00              
ATOM    865  OE1 GLU   119      19.787  22.978  37.150  1.00  0.00              
ATOM    866  OE2 GLU   119      19.948  24.799  35.930  1.00  0.00              
ATOM    867  N   HIS   120      23.558  21.863  40.586  1.00  0.00              
ATOM    868  CA  HIS   120      24.186  20.584  40.892  1.00  0.00              
ATOM    869  C   HIS   120      25.706  20.685  40.825  1.00  0.00              
ATOM    870  O   HIS   120      26.363  20.962  41.828  1.00  0.00              
ATOM    871  CB  HIS   120      23.751  20.091  42.274  1.00  0.00              
ATOM    872  CG  HIS   120      24.851  19.445  43.058  1.00  0.00              
ATOM    873  ND1 HIS   120      26.182  19.734  42.851  1.00  0.00              
ATOM    874  CD2 HIS   120      24.817  18.522  44.048  1.00  0.00              
ATOM    875  CE1 HIS   120      26.919  19.019  43.681  1.00  0.00              
ATOM    876  NE2 HIS   120      26.117  18.275  44.418  1.00  0.00              
ATOM    877  N   ALA   121      26.257  20.459  39.638  1.00  0.00              
ATOM    878  CA  ALA   121      27.700  20.525  39.438  1.00  0.00              
ATOM    879  C   ALA   121      28.208  21.958  39.549  1.00  0.00              
ATOM    880  O   ALA   121      29.414  22.202  39.544  1.00  0.00              
ATOM    881  CB  ALA   121      28.415  19.636  40.443  1.00  0.00              
ATOM    882  N   GLU   122      27.279  22.904  39.649  1.00  0.00              
ATOM    883  CA  GLU   122      27.630  24.314  39.762  1.00  0.00              
ATOM    884  C   GLU   122      28.760  24.523  40.765  1.00  0.00              
ATOM    885  O   GLU   122      29.450  25.542  40.735  1.00  0.00              
ATOM    886  CB  GLU   122      28.029  24.878  38.396  1.00  0.00              
ATOM    887  CG  GLU   122      27.601  24.016  37.220  1.00  0.00              
ATOM    888  CD  GLU   122      26.183  24.308  36.769  1.00  0.00              
ATOM    889  OE1 GLU   122      25.291  24.400  37.640  1.00  0.00              
ATOM    890  OE2 GLU   122      25.963  24.444  35.548  1.00  0.00              
ATOM    891  N   THR   123      28.942  23.550  41.653  1.00  0.00              
ATOM    892  CA  THR   123      30.011  23.628  42.690  1.00  0.00              
ATOM    893  C   THR   123      31.161  24.519  42.232  1.00  0.00              
ATOM    894  O   THR   123      32.041  24.866  43.019  1.00  0.00              
ATOM    895  CB  THR   123      29.463  24.160  44.026  1.00  0.00              
ATOM    896  OG1 THR   123      28.365  25.045  43.778  1.00  0.00              
ATOM    897  CG2 THR   123      28.992  23.009  44.904  1.00  0.00              
ATOM    898  N   ALA   124      31.145  24.888  40.955  1.00  0.00              
ATOM    899  CA  ALA   124      32.185  25.739  40.391  1.00  0.00              
ATOM    900  C   ALA   124      32.715  26.724  41.427  1.00  0.00              
ATOM    901  O   ALA   124      33.730  27.384  41.208  1.00  0.00              
ATOM    902  CB  ALA   124      33.323  24.893  39.841  1.00  0.00              
ATOM    903  N   ASP   125      32.021  26.816  42.557  1.00  0.00              
ATOM    904  CA  ASP   125      32.420  27.720  43.629  1.00  0.00              
ATOM    905  C   ASP   125      32.560  29.151  43.121  1.00  0.00              
ATOM    906  O   ASP   125      31.701  29.649  42.394  1.00  0.00              
ATOM    907  CB  ASP   125      31.411  27.666  44.778  1.00  0.00              
ATOM    908  CG  ASP   125      31.592  26.444  45.656  1.00  0.00              
ATOM    909  OD1 ASP   125      32.451  26.485  46.562  1.00  0.00              
ATOM    910  OD2 ASP   125      30.875  25.444  45.438  1.00  0.00              
ATOM    911  N   ASP   126      33.649  29.807  43.508  1.00  0.00              
ATOM    912  CA  ASP   126      33.904  31.181  43.093  1.00  0.00              
ATOM    913  C   ASP   126      35.397  31.437  42.920  1.00  0.00              
ATOM    914  O   ASP   126      36.228  30.670  43.405  1.00  0.00              
ATOM    915  CB  ASP   126      33.163  31.494  41.792  1.00  0.00              
ATOM    916  CG  ASP   126      32.186  32.644  41.940  1.00  0.00              
ATOM    917  OD1 ASP   126      32.170  33.527  41.056  1.00  0.00              
ATOM    918  OD2 ASP   126      31.437  32.663  42.939  1.00  0.00              
TER
END
