
#######################################################
#                                                     #
#                        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 (   40),  selected    8 , name T0372TS103_2_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    8 , name T0372_D1.pdb
# PARAMETERS: T0372TS103_2_2-D1.T0372_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       290 - 298         4.63     4.63
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         0.67    10.96
  LONGEST_CONTINUOUS_SEGMENT:     3       291 - 293         0.39     8.26
  LONGEST_CONTINUOUS_SEGMENT:     3       292 - 294         0.50     7.45
  LONGEST_CONTINUOUS_SEGMENT:     3       293 - 295         0.60     7.35
  LONGEST_CONTINUOUS_SEGMENT:     3       294 - 297         1.50     8.64
  LONGEST_CONTINUOUS_SEGMENT:     3       295 - 298         0.88    10.11
  LCS_AVERAGE:      2.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         0.67    10.96
  LONGEST_CONTINUOUS_SEGMENT:     3       292 - 294         0.50     7.45
  LONGEST_CONTINUOUS_SEGMENT:     3       293 - 295         0.60     7.35
  LONGEST_CONTINUOUS_SEGMENT:     3       295 - 298         0.88    10.11
  LCS_AVERAGE:      2.38

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:  126
LCS_GDT     K     290     K     290      3    3    8     0    3    3    3    3    4    4    5    6    6    6    6    8    8    8    8    8    8    8    8 
LCS_GDT     Y     291     Y     291      3    3    8     3    3    3    3    3    4    4    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     M     292     M     292      3    3    8     3    3    3    3    3    4    4    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     A     293     A     293      3    3    8     3    3    3    3    3    4    4    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     C     294     C     294      3    3    8     0    3    3    3    3    4    4    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     L     295     L     295      3    3    8     0    3    3    3    3    3    4    5    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     D     297     D     297      3    3    8     0    0    3    3    3    3    4    4    5    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     H     298     H     298      3    3    8     1    2    3    3    3    3    4    4    5    6    7    7    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   3.70  (   2.38    2.38    6.35 )

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      3      3      3      3      4      4      5      6      6      7      7      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.38   2.38   2.38   2.38   2.38   3.17   3.17   3.97   4.76   4.76   5.56   5.56   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.39   0.39   0.39   0.39   0.39   2.37   2.37   3.19   3.67   3.67   4.16   4.16   4.63   4.63   4.63   4.63   4.63   4.63   4.63   4.63
GDT RMS_ALL_CA   8.26   8.26   8.26   8.26   8.26   7.08   7.08   5.44   5.46   5.46   4.83   4.83   4.63   4.63   4.63   4.63   4.63   4.63   4.63   4.63

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          3.853
LGA    Y     291      Y     291          2.865
LGA    M     292      M     292          3.103
LGA    A     293      A     293          1.708
LGA    C     294      C     294          3.923
LGA    L     295      L     295          6.970
LGA    D     297      D     297          8.675
LGA    H     298      H     298          7.887

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  126    4.0      5    3.19     3.770     3.502     0.152

LGA_LOCAL      RMSD =  3.193  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.443  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.635  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.026885 * X  +   0.962169 * Y  +  -0.271123 * Z  +  20.794563
  Y_new =  -0.818472 * X  +   0.176902 * Y  +   0.546634 * Z  +  32.233982
  Z_new =   0.573917 * X  +   0.207210 * Y  +   0.792265 * Z  + -17.828300 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.255812   -2.885781  [ DEG:    14.6569   -165.3431 ]
  Theta =  -0.611281   -2.530312  [ DEG:   -35.0238   -144.9762 ]
  Phi   =  -1.537960    1.603632  [ DEG:   -88.1186     91.8814 ]
 
# 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: T0372TS103_2_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS103_2_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  126   4.0    5   3.19   3.502     4.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS103_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1kaf_A
ATOM    451  N   LYS   290      25.734  48.278   4.491  1.00  1.00
ATOM    452  CA  LYS   290      27.030  48.401   3.833  1.00  1.00
ATOM    453  C   LYS   290      27.258  47.299   2.801  1.00  1.00
ATOM    454  O   LYS   290      27.740  47.559   1.696  1.00  1.00
ATOM    455  CB  LYS   290      28.146  48.379   4.878  1.00  1.00
ATOM    456  N   TYR   291      26.905  46.070   3.158  1.00  1.00
ATOM    457  CA  TYR   291      27.095  44.936   2.259  1.00  1.00
ATOM    458  C   TYR   291      26.297  45.046   0.968  1.00  1.00
ATOM    459  O   TYR   291      26.827  44.830  -0.120  1.00  1.00
ATOM    460  CB  TYR   291      26.711  43.612   2.953  1.00  1.00
ATOM    461  N   MET   292      25.017  45.372   1.091  1.00  1.00
ATOM    462  CA  MET   292      24.152  45.492  -0.074  1.00  1.00
ATOM    463  C   MET   292      24.578  46.675  -0.938  1.00  1.00
ATOM    464  O   MET   292      24.516  46.618  -2.165  1.00  1.00
ATOM    465  CB  MET   292      22.680  45.643   0.353  1.00  1.00
ATOM    466  N   ALA   293      25.017  47.746  -0.290  1.00  1.00
ATOM    467  CA  ALA   293      25.477  48.921  -1.015  1.00  1.00
ATOM    468  C   ALA   293      26.652  48.539  -1.910  1.00  1.00
ATOM    469  O   ALA   293      26.701  48.929  -3.071  1.00  1.00
ATOM    470  CB  ALA   293      25.917  50.037  -0.050  1.00  1.00
ATOM    471  N   CYS   294      27.593  47.772  -1.366  1.00  1.00
ATOM    472  CA  CYS   294      28.754  47.348  -2.141  1.00  1.00
ATOM    473  C   CYS   294      28.326  46.428  -3.286  1.00  1.00
ATOM    474  O   CYS   294      28.762  46.596  -4.424  1.00  1.00
ATOM    475  CB  CYS   294      29.793  46.614  -1.246  1.00  1.00
ATOM    476  N   LEU   295      27.464  45.462  -2.987  1.00  1.00
ATOM    477  CA  LEU   295      27.001  44.534  -4.011  1.00  1.00
ATOM    478  C   LEU   295      26.321  45.275  -5.160  1.00  1.00
ATOM    479  O   LEU   295      26.413  44.861  -6.316  1.00  1.00
ATOM    480  CB  LEU   295      26.040  43.518  -3.401  1.00  1.00
ATOM    481  N   ASP   297      25.649  46.377  -4.834  1.00  1.00
ATOM    482  CA  ASP   297      24.934  47.173  -5.831  1.00  1.00
ATOM    483  C   ASP   297      25.828  48.045  -6.710  1.00  1.00
ATOM    484  O   ASP   297      25.441  48.411  -7.821  1.00  1.00
ATOM    485  CB  ASP   297      23.902  48.063  -5.140  1.00  1.00
ATOM    486  N   HIS   298      27.014  48.381  -6.213  1.00  1.00
ATOM    487  CA  HIS   298      27.945  49.223  -6.960  1.00  1.00
ATOM    488  C   HIS   298      28.993  48.428  -7.733  1.00  1.00
ATOM    489  O   HIS   298      29.895  49.008  -8.343  1.00  1.00
ATOM    490  CB  HIS   298      28.645  50.198  -6.010  1.00  1.00
TER
END
