
#######################################################
#                                                     #
#                        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    3 (   29),  selected    3 , name T0372TS389_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    3 , name T0372_D1.pdb
# PARAMETERS: T0372TS389_3-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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         0.71     0.71
  LCS_AVERAGE:      2.38

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         0.71     0.71
  LCS_AVERAGE:      2.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         0.71     0.71
  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    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     Y     291     Y     291      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     M     292     M     292      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   2.38  (   2.38    2.38    2.38 )

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      0      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   0.00   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38   2.38
GDT RMS_LOCAL  1000.00   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71
GDT RMS_ALL_CA 1000.00   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71   0.71

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          0.724
LGA    Y     291      Y     291          0.689
LGA    M     292      M     292          0.724

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  126    4.0      3    0.71     2.381     2.381     0.369

LGA_LOCAL      RMSD =  0.713  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.713  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.713  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.043259 * X  +   0.092133 * Y  +   0.994807 * Z  +   9.985260
  Y_new =   0.050464 * X  +  -0.994669 * Y  +   0.089926 * Z  +  53.227467
  Z_new =   0.997789 * X  +   0.046311 * Y  +  -0.047678 * Z  +   0.223095 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.370731   -0.770862  [ DEG:   135.8329    -44.1671 ]
  Theta =  -1.504280   -1.637313  [ DEG:   -86.1889    -93.8111 ]
  Phi   =   0.862119   -2.279474  [ DEG:    49.3958   -130.6042 ]
 
# 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: T0372TS389_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS389_3-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  126   4.0    3   0.71   2.381     0.71
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS389_3-D1
PFRMAT TS
TARGET T0372
MODEL  3
PARENT N/A
ATOM    900  N   LYS   290      27.786  47.203   6.266  1.00  0.00
ATOM    901  CA  LYS   290      26.608  46.393   6.550  1.00  0.00
ATOM    902  CB  LYS   290      25.701  47.099   7.558  1.00  0.00
ATOM    903  CG  LYS   290      26.269  47.165   8.967  1.00  0.00
ATOM    904  CD  LYS   290      25.305  47.853   9.920  1.00  0.00
ATOM    905  CE  LYS   290      25.863  47.896  11.332  1.00  0.00
ATOM    906  NZ  LYS   290      24.955  48.617  12.267  1.00  0.00
ATOM    907  O   LYS   290      25.437  44.972   4.995  1.00  0.00
ATOM    908  C   LYS   290      25.776  46.120   5.295  1.00  0.00
ATOM    909  N   TYR   291      25.448  47.176   4.559  1.00  0.00
ATOM    910  CA  TYR   291      24.634  47.018   3.363  1.00  0.00
ATOM    911  CB  TYR   291      24.209  48.383   2.821  1.00  0.00
ATOM    912  CG  TYR   291      23.356  48.310   1.574  1.00  0.00
ATOM    913  CD1 TYR   291      22.010  47.977   1.651  1.00  0.00
ATOM    914  CD2 TYR   291      23.902  48.572   0.323  1.00  0.00
ATOM    915  CE1 TYR   291      21.224  47.906   0.516  1.00  0.00
ATOM    916  CE2 TYR   291      23.131  48.506  -0.822  1.00  0.00
ATOM    917  CZ  TYR   291      21.782  48.170  -0.715  1.00  0.00
ATOM    918  OH  TYR   291      21.001  48.101  -1.847  1.00  0.00
ATOM    919  O   TYR   291      24.762  45.527   1.495  1.00  0.00
ATOM    920  C   TYR   291      25.361  46.299   2.240  1.00  0.00
ATOM    921  N   MET   292      26.660  46.536   2.122  1.00  0.00
ATOM    922  CA  MET   292      27.418  45.865   1.080  1.00  0.00
ATOM    923  CB  MET   292      28.848  46.403   1.029  1.00  0.00
ATOM    924  CG  MET   292      28.956  47.839   0.542  1.00  0.00
ATOM    925  SD  MET   292      28.437  48.032  -1.174  1.00  0.00
ATOM    926  CE  MET   292      29.790  47.232  -2.030  1.00  0.00
ATOM    927  O   MET   292      27.310  43.539   0.471  1.00  0.00
ATOM    928  C   MET   292      27.455  44.363   1.379  1.00  0.00
TER
END
