
#######################################################
#                                                     #
#                        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    9 (   86),  selected    9 , name T0372TS277_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS277_5-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:     9       290 - 298         3.91     3.91
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       290 - 295         1.94     6.39
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.89     5.32
  LONGEST_CONTINUOUS_SEGMENT:     6       292 - 297         1.85     5.29
  LONGEST_CONTINUOUS_SEGMENT:     6       293 - 298         1.66     7.04
  LCS_AVERAGE:      4.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       292 - 295         0.62     5.37
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.96    10.63
  LCS_AVERAGE:      3.00

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    6    9     0    3    4    4    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    6    9     3    3    4    5    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      4    6    9     3    4    4    5    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    6    9     3    4    5    5    5    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      4    6    9     3    4    5    5    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      4    6    9     3    4    4    5    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    6    9     3    3    5    5    6    6    7    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      4    6    9     3    4    5    5    5    6    6    7    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      4    6    9     1    4    5    5    5    6    6    7    7    7    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.97  (   3.00    4.76    7.14 )

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      5      5      6      6      7      7      7      8      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.97   3.97   4.76   4.76   5.56   5.56   5.56   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.03   0.59   0.97   0.97   1.75   1.75   2.08   2.08   2.08   3.03   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91
GDT RMS_ALL_CA   5.55   6.65   6.64   6.64   5.22   5.22   5.43   5.43   5.43   4.75   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          2.285
LGA    Y     291      Y     291          1.653
LGA    M     292      M     292          1.874
LGA    A     293      A     293          3.054
LGA    C     294      C     294          1.938
LGA    L     295      L     295          2.037
LGA    K     296      K     296          1.283
LGA    D     297      D     297          8.326
LGA    H     298      H     298         12.863

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      7    2.08     4.960     5.187     0.321

LGA_LOCAL      RMSD =  2.082  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.428  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  3.907  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.679595 * X  +   0.732673 * Y  +  -0.036604 * Z  +  52.366291
  Y_new =   0.367407 * X  +   0.296753 * Y  +  -0.881448 * Z  +  25.960402
  Z_new =  -0.634951 * X  +  -0.612476 * Y  +  -0.470861 * Z  +  32.192520 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.226211    0.915382  [ DEG:  -127.5525     52.4475 ]
  Theta =   0.687945    2.453648  [ DEG:    39.4163    140.5836 ]
  Phi   =   2.645975   -0.495617  [ DEG:   151.6032    -28.3968 ]
 
# 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: T0372TS277_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS277_5-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  126   4.0    7   2.08   5.187     3.91
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS277_5-D1
PFRMAT TS 
TARGET T0372
MODEL 5
PARENT 1S7F_A
ATOM   2979  H   LYS   290      26.282  44.967   6.713  1.00  0.00                              
ATOM   2981  N   LYS   290      25.799  44.820   5.909  1.00  0.00                              
ATOM   2983  CA  LYS   290      24.789  45.790   5.502  1.00  0.00                              
ATOM   2985  CB  LYS   290      24.356  46.646   6.694  1.00  0.00                              
ATOM   2987  C   LYS   290      25.306  46.690   4.386  1.00  0.00                              
ATOM   2989  O   LYS   290      26.458  47.128   4.430  1.00  0.00                              
ATOM   2991  CG  LYS   290      23.300  47.685   6.350  1.00  0.00                              
ATOM   2993  CD  LYS   290      22.808  48.412   7.595  1.00  0.00                              
ATOM   2995  CE  LYS   290      21.715  49.419   7.264  1.00  0.00                              
ATOM   2997  NZ  LYS   290      21.234  50.136   8.481  1.00  0.00                              
ATOM   2999  H   TYR   291      23.626  46.493   3.375  1.00  0.00                              
ATOM   3001  N   TYR   291      24.466  46.924   3.381  1.00  0.00                              
ATOM   3003  CA  TYR   291      24.798  47.817   2.280  1.00  0.00                              
ATOM   3005  CB  TYR   291      24.182  49.195   2.523  1.00  0.00                              
ATOM   3007  C   TYR   291      26.303  47.965   2.102  1.00  0.00                              
ATOM   3009  O   TYR   291      26.870  49.023   2.387  1.00  0.00                              
ATOM   3011  CG  TYR   291      24.251  50.086   1.308  1.00  0.00                              
ATOM   3013  CD1 TYR   291      24.574  49.570   0.054  1.00  0.00                              
ATOM   3015  CE1 TYR   291      24.596  50.387  -1.073  1.00  0.00                              
ATOM   3017  CZ  TYR   291      24.230  51.716  -0.954  1.00  0.00                              
ATOM   3019  CD2 TYR   291      24.012  51.455   1.417  1.00  0.00                              
ATOM   3021  CE2 TYR   291      24.017  52.274   0.295  1.00  0.00                              
ATOM   3023  OH  TYR   291      24.208  52.521  -2.072  1.00  0.00                              
ATOM   3025  H   MET   292      26.442  46.173   1.304  1.00  0.00                              
ATOM   3027  N   MET   292      26.946  46.925   1.576  1.00  0.00                              
ATOM   3029  CA  MET   292      28.401  46.899   1.443  1.00  0.00                              
ATOM   3031  CB  MET   292      28.930  45.515   1.832  1.00  0.00                              
ATOM   3033  C   MET   292      28.916  47.246   0.046  1.00  0.00                              
ATOM   3035  O   MET   292      29.759  48.136  -0.098  1.00  0.00                              
ATOM   3037  CG  MET   292      28.360  44.394   0.975  1.00  0.00                              
ATOM   3039  SD  MET   292      26.612  44.102   1.330  1.00  0.00                              
ATOM   3041  CE  MET   292      26.217  42.920   0.055  1.00  0.00                              
ATOM   3043  H   ALA   293      27.820  45.864  -0.829  1.00  0.00                              
ATOM   3045  N   ALA   293      28.478  46.511  -0.976  1.00  0.00                              
ATOM   3047  CA  ALA   293      28.976  46.726  -2.337  1.00  0.00                              
ATOM   3049  CB  ALA   293      29.040  45.413  -3.119  1.00  0.00                              
ATOM   3051  C   ALA   293      28.106  47.742  -3.080  1.00  0.00                              
ATOM   3053  O   ALA   293      27.118  48.237  -2.530  1.00  0.00                              
ATOM   3055  H   CYS   294      29.245  47.753  -4.688  1.00  0.00                              
ATOM   3057  N   CYS   294      28.468  48.103  -4.312  1.00  0.00                              
ATOM   3059  CA  CYS   294      27.681  49.082  -5.062  1.00  0.00                              
ATOM   3061  CB  CYS   294      28.290  50.478  -4.920  1.00  0.00                              
ATOM   3063  C   CYS   294      27.530  48.725  -6.540  1.00  0.00                              
ATOM   3065  O   CYS   294      28.467  48.887  -7.327  1.00  0.00                              
ATOM   3067  SG  CYS   294      28.762  51.225  -6.499  1.00  0.00                              
ATOM   3069  H   LEU   295      25.621  48.276  -6.302  1.00  0.00                              
ATOM   3071  N   LEU   295      26.331  48.293  -6.928  1.00  0.00                              
ATOM   3073  CA  LEU   295      26.075  47.862  -8.305  1.00  0.00                              
ATOM   3075  CB  LEU   295      26.372  46.364  -8.468  1.00  0.00                              
ATOM   3077  C   LEU   295      24.645  48.144  -8.780  1.00  0.00                              
ATOM   3079  O   LEU   295      23.689  48.026  -8.010  1.00  0.00                              
ATOM   3081  CG  LEU   295      26.035  45.760  -9.836  1.00  0.00                              
ATOM   3083  CD1 LEU   295      26.924  46.375 -10.910  1.00  0.00                              
ATOM   3085  CD2 LEU   295      26.170  44.240  -9.825  1.00  0.00                              
ATOM   3087  H   LYS   296      25.302  48.749 -10.532  1.00  0.00                              
ATOM   3089  N   LYS   296      24.511  48.555 -10.041  1.00  0.00                              
ATOM   3091  CA  LYS   296      23.215  48.765 -10.696  1.00  0.00                              
ATOM   3093  CB  LYS   296      22.253  47.596 -10.462  1.00  0.00                              
ATOM   3095  C   LYS   296      22.565  50.113 -10.371  1.00  0.00                              
ATOM   3097  O   LYS   296      22.684  51.047 -11.169  1.00  0.00                              
ATOM   3099  CG  LYS   296      22.688  46.291 -11.115  1.00  0.00                              
ATOM   3101  CD  LYS   296      22.329  46.246 -12.595  1.00  0.00                              
ATOM   3103  CE  LYS   296      23.287  45.356 -13.376  1.00  0.00                              
ATOM   3105  NZ  LYS   296      23.349  45.742 -14.817  1.00  0.00                              
ATOM   3107  H   ASP   297      21.746  49.518  -8.660  1.00  0.00                              
ATOM   3109  N   ASP   297      21.846  50.244  -9.254  1.00  0.00                              
ATOM   3111  CA  ASP   297      21.242  51.540  -8.943  1.00  0.00                              
ATOM   3113  CB  ASP   297      20.309  51.987 -10.074  1.00  0.00                              
ATOM   3115  C   ASP   297      20.521  51.634  -7.594  1.00  0.00                              
ATOM   3117  O   ASP   297      20.991  52.364  -6.714  1.00  0.00                              
ATOM   3119  CG  ASP   297      20.305  53.493 -10.272  1.00  0.00                              
ATOM   3121  OD1 ASP   297      20.082  54.228  -9.284  1.00  0.00                              
ATOM   3123  OD2 ASP   297      20.536  53.950 -11.413  1.00  0.00                              
ATOM   3125  H   HIS   298      19.085  50.351  -8.089  1.00  0.00                              
ATOM   3127  N   HIS   298      19.387  50.946  -7.418  1.00  0.00                              
ATOM   3129  CA  HIS   298      18.603  51.123  -6.193  1.00  0.00                              
ATOM   3131  CB  HIS   298      17.564  52.228  -6.442  1.00  0.00                              
ATOM   3133  C   HIS   298      17.885  49.885  -5.637  1.00  0.00                              
ATOM   3135  O   HIS   298      18.421  49.193  -4.767  1.00  0.00                              
ATOM   3137  CG  HIS   298      16.748  52.587  -5.239  1.00  0.00                              
ATOM   3139  ND1 HIS   298      17.192  53.477  -4.289  1.00  0.00                              
ATOM   3141  HD1 HIS   298      18.038  53.911  -4.280  1.00  0.00                              
ATOM   3143  CE1 HIS   298      16.284  53.574  -3.334  1.00  0.00                              
ATOM   3145  NE2 HIS   298      15.203  52.919  -3.721  1.00  0.00                              
ATOM   3147  HE2 HIS   298      14.368  52.933  -3.265  1.00  0.00                              
ATOM   3149  CD2 HIS   298      15.453  52.322  -4.929  1.00  0.00                              
TER 
END
