
#######################################################
#                                                     #
#                        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 T0372TS261_1_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    8 , name T0372_D1.pdb
# PARAMETERS: T0372TS261_1_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
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 298         4.60     4.60
  LCS_AVERAGE:      6.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 296         1.28     5.58
  LCS_AVERAGE:      3.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       291 - 294         0.73     5.70
  LCS_AVERAGE:      2.78

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    4    8     0    3    3    3    4    5    5    6    6    6    6    6    6    7    7    8    8    8    8    8 
LCS_GDT     Y     291     Y     291      4    5    8     0    4    4    5    5    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     M     292     M     292      4    5    8     3    4    4    5    5    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     A     293     A     293      4    5    8     3    4    4    5    5    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     C     294     C     294      4    5    8     3    4    4    5    5    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     K     296     K     296      3    5    8     3    3    3    5    5    5    5    6    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     D     297     D     297      3    4    8     3    3    3    3    3    4    4    5    6    6    6    7    7    7    7    8    8    8    8    8 
LCS_GDT     H     298     H     298      3    4    8     3    3    3    3    3    4    4    4    4    6    6    7    7    7    7    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   4.27  (   2.78    3.67    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      4      4      5      5      5      5      6      6      6      6      7      7      7      7      8      8      8      8      8 
GDT PERCENT_CA   2.38   3.17   3.17   3.97   3.97   3.97   3.97   4.76   4.76   4.76   4.76   5.56   5.56   5.56   5.56   6.35   6.35   6.35   6.35   6.35
GDT RMS_LOCAL    0.17   0.73   0.73   1.28   1.28   1.28   1.28   2.32   2.32   2.32   2.32   3.87   3.87   3.66   3.66   4.60   4.60   4.60   4.60   4.60
GDT RMS_ALL_CA  12.54   5.70   5.70   5.58   5.58   5.58   5.58   5.86   5.86   5.86   5.86   4.95   4.95   5.18   5.18   4.60   4.60   4.60   4.60   4.60

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          3.915
LGA    Y     291      Y     291          2.330
LGA    M     292      M     292          1.468
LGA    A     293      A     293          0.557
LGA    C     294      C     294          1.665
LGA    K     296      K     296          2.492
LGA    D     297      D     297          9.210
LGA    H     298      H     298         12.565

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  126    4.0      6    2.32     4.563     4.204     0.248

LGA_LOCAL      RMSD =  2.317  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.862  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.605  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.674180 * X  +  -0.637412 * Y  +   0.373078 * Z  +  78.693382
  Y_new =  -0.108891 * X  +   0.585401 * Y  +   0.803398 * Z  +   8.078721
  Z_new =  -0.730496 * X  +   0.501010 * Y  +  -0.464074 * Z  +  10.019140 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.317940   -0.823653  [ DEG:   132.8082    -47.1918 ]
  Theta =   0.819048    2.322545  [ DEG:    46.9280    133.0720 ]
  Phi   =  -2.981460    0.160133  [ DEG:  -170.8251      9.1749 ]
 
# 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: T0372TS261_1_3-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS261_1_3-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    6   2.32   4.204     4.60
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS261_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0372
PARENT 2fck_A
ATOM   1019  N   LYS   290      23.277  45.743   4.876  1.00  1.00
ATOM   1020  CA  LYS   290      23.693  46.940   4.136  1.00  1.00
ATOM   1021  C   LYS   290      25.197  47.179   4.120  1.00  1.00
ATOM   1022  O   LYS   290      25.699  48.311   4.116  1.00  1.00
ATOM   1023  CB  LYS   290      22.953  48.185   4.717  1.00  1.00
ATOM   1024  N   TYR   291      25.980  46.094   4.094  1.00  1.00
ATOM   1025  CA  TYR   291      27.411  46.251   4.230  1.00  1.00
ATOM   1026  C   TYR   291      28.185  46.655   2.937  1.00  1.00
ATOM   1027  O   TYR   291      29.299  47.161   2.991  1.00  1.00
ATOM   1028  CB  TYR   291      27.989  44.972   4.887  1.00  1.00
ATOM   1029  N   MET   292      27.615  46.410   1.749  1.00  3.25
ATOM   1030  CA  MET   292      28.324  46.845   0.532  1.00  3.25
ATOM   1031  C   MET   292      27.316  47.269  -0.534  1.00  3.25
ATOM   1032  O   MET   292      26.146  46.983  -0.404  1.00  3.25
ATOM   1033  CB  MET   292      29.313  45.763  -0.010  1.00  3.25
ATOM   1034  N   ALA   293      27.791  47.966  -1.570  1.00  4.83
ATOM   1035  CA  ALA   293      26.902  48.358  -2.670  1.00  4.83
ATOM   1036  C   ALA   293      27.084  47.451  -3.899  1.00  4.83
ATOM   1037  O   ALA   293      28.216  47.171  -4.288  1.00  4.83
ATOM   1038  CB  ALA   293      27.169  49.810  -3.073  1.00  4.83
ATOM   1039  N   CYS   294      25.964  47.007  -4.474  1.00  5.25
ATOM   1040  CA  CYS   294      25.944  46.443  -5.833  1.00  5.25
ATOM   1041  C   CYS   294      24.917  47.156  -6.701  1.00  5.25
ATOM   1042  O   CYS   294      23.711  47.119  -6.401  1.00  5.25
ATOM   1043  CB  CYS   294      25.672  44.944  -5.834  1.00  5.25
ATOM   1044  N   LYS   296      25.404  47.800  -7.771  1.00  4.72
ATOM   1045  CA  LYS   296      24.558  48.577  -8.696  1.00  4.72
ATOM   1046  C   LYS   296      23.907  49.774  -7.982  1.00  4.72
ATOM   1047  O   LYS   296      22.723  50.066  -8.189  1.00  4.72
ATOM   1048  CB  LYS   296      23.484  47.678  -9.355  1.00  4.72
ATOM   1049  N   ASP   297      24.704  50.454  -7.148  1.00  4.58
ATOM   1050  CA  ASP   297      24.239  51.554  -6.299  1.00  4.58
ATOM   1051  C   ASP   297      23.226  51.230  -5.193  1.00  4.58
ATOM   1052  O   ASP   297      22.734  52.146  -4.548  1.00  4.58
ATOM   1053  CB  ASP   297      23.659  52.633  -7.230  1.00  4.58
ATOM   1054  N   HIS   298      22.899  49.951  -4.971  1.00  4.16
ATOM   1055  CA  HIS   298      21.976  49.525  -3.876  1.00  4.16
ATOM   1056  C   HIS   298      22.680  48.684  -2.800  1.00  4.16
ATOM   1057  O   HIS   298      23.616  47.947  -3.122  1.00  4.16
ATOM   1058  CB  HIS   298      20.840  48.698  -4.421  1.00  4.16
TER
END
