
#######################################################
#                                                     #
#                        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 (   75),  selected    9 , name T0372TS022_4_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS022_4_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:     9       290 - 298         4.61     4.61
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       293 - 298         1.90     6.95
  LCS_AVERAGE:      4.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.61    11.08
  LCS_AVERAGE:      2.73

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      4    5    9     3    4    4    4    4    5    5    5    5    5    6    7    7    8    8    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      4    5    9     3    4    4    4    4    5    5    5    6    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     M     292     M     292      4    5    9     3    4    4    4    4    5    5    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    6    9     3    4    5    5    5    5    6    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     C     294     C     294      3    6    9     3    4    5    5    5    5    6    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     L     295     L     295      3    6    9     3    3    3    4    4    4    6    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     K     296     K     296      3    6    9     3    4    5    5    5    5    6    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     D     297     D     297      3    6    9     3    4    5    5    5    5    6    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    6    9     3    4    5    5    5    5    6    7    7    8    8    8    8    8    8    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.79  (   2.73    4.50    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      5      5      6      7      7      8      8      8      8      8      8      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.97   3.97   3.97   3.97   4.76   5.56   5.56   6.35   6.35   6.35   6.35   6.35   6.35   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.04   0.61   1.11   1.11   1.11   1.11   1.90   2.67   2.67   3.47   3.47   3.47   3.47   3.47   3.47   4.61   4.61   4.61   4.61   4.61
GDT RMS_ALL_CA  11.64  11.08   7.06   7.06   7.06   7.06   6.95   5.95   5.95   5.04   5.04   5.04   5.04   5.04   5.04   4.61   4.61   4.61   4.61   4.61

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         10.966
LGA    Y     291      Y     291          5.568
LGA    M     292      M     292          3.466
LGA    A     293      A     293          2.238
LGA    C     294      C     294          3.363
LGA    L     295      L     295          3.821
LGA    K     296      K     296          2.490
LGA    D     297      D     297          3.140
LGA    H     298      H     298          3.568

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      7    2.67     4.960     4.852     0.253

LGA_LOCAL      RMSD =  2.668  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.977  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.613  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.976115 * X  +  -0.182794 * Y  +   0.117414 * Z  +   3.536862
  Y_new =  -0.176074 * X  +  -0.349010 * Y  +   0.920429 * Z  +  44.820122
  Z_new =  -0.127270 * X  +  -0.919118 * Y  +  -0.372860 * Z  +  13.791472 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.956182    1.185411  [ DEG:  -112.0810     67.9190 ]
  Theta =   0.127616    3.013977  [ DEG:     7.3118    172.6882 ]
  Phi   =  -0.178463    2.963129  [ DEG:   -10.2252    169.7748 ]
 
# 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: T0372TS022_4_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_4_2-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   2.67   4.852     4.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1qst_A
ATOM   2148  N   LYS   290      21.324  43.750  -3.613  1.00  0.00
ATOM   2149  CA  LYS   290      21.192  43.668  -2.192  1.00  0.00
ATOM   2150  C   LYS   290      22.444  44.195  -1.575  1.00  0.00
ATOM   2151  O   LYS   290      22.388  44.921  -0.584  1.00  0.00
ATOM   2152  CB  LYS   290      20.978  42.216  -1.758  1.00  0.00
ATOM   2153  CG  LYS   290      20.782  42.040  -0.260  1.00  0.00
ATOM   2154  CD  LYS   290      20.497  40.589   0.092  1.00  0.00
ATOM   2155  CE  LYS   290      20.330  40.407   1.591  1.00  0.00
ATOM   2156  NZ  LYS   290      20.066  38.987   1.952  1.00  0.00
ATOM   2157  N   TYR   291      23.616  43.876  -2.150  1.00  0.00
ATOM   2158  CA  TYR   291      24.799  44.388  -1.529  1.00  0.00
ATOM   2159  C   TYR   291      24.928  45.817  -1.935  1.00  0.00
ATOM   2160  O   TYR   291      24.951  46.145  -3.119  1.00  0.00
ATOM   2161  CB  TYR   291      26.028  43.599  -1.985  1.00  0.00
ATOM   2162  CG  TYR   291      27.320  44.056  -1.349  1.00  0.00
ATOM   2163  CD1 TYR   291      27.649  43.673  -0.054  1.00  0.00
ATOM   2164  CD2 TYR   291      28.208  44.867  -2.043  1.00  0.00
ATOM   2165  CE1 TYR   291      28.828  44.086   0.537  1.00  0.00
ATOM   2166  CE2 TYR   291      29.392  45.289  -1.468  1.00  0.00
ATOM   2167  CZ  TYR   291      29.697  44.892  -0.167  1.00  0.00
ATOM   2168  OH  TYR   291      30.872  45.304   0.418  1.00  0.00
ATOM   2169  N   MET   292      25.015  46.714  -0.933  1.00  0.00
ATOM   2170  CA  MET   292      25.036  48.122  -1.200  1.00  0.00
ATOM   2171  C   MET   292      26.411  48.561  -1.574  1.00  0.00
ATOM   2172  O   MET   292      27.405  47.944  -1.197  1.00  0.00
ATOM   2173  CB  MET   292      24.596  48.908   0.037  1.00  0.00
ATOM   2174  CG  MET   292      23.169  48.624   0.476  1.00  0.00
ATOM   2175  SD  MET   292      21.951  49.087  -0.770  1.00  0.00
ATOM   2176  CE  MET   292      22.091  50.872  -0.733  1.00  0.00
ATOM   2177  N   ALA   293      26.455  49.666  -2.345  1.00  0.00
ATOM   2178  CA  ALA   293      27.612  50.372  -2.818  1.00  0.00
ATOM   2179  C   ALA   293      28.551  49.498  -3.584  1.00  0.00
ATOM   2180  O   ALA   293      28.873  48.373  -3.206  1.00  0.00
ATOM   2181  CB  ALA   293      28.392  50.956  -1.650  1.00  0.00
ATOM   2182  N   CYS   294      29.000  50.033  -4.731  1.00  0.00
ATOM   2183  CA  CYS   294      29.983  49.411  -5.563  1.00  0.00
ATOM   2184  C   CYS   294      29.427  48.151  -6.135  1.00  0.00
ATOM   2185  O   CYS   294      30.109  47.454  -6.884  1.00  0.00
ATOM   2186  CB  CYS   294      31.237  49.077  -4.753  1.00  0.00
ATOM   2187  SG  CYS   294      32.021  50.504  -3.967  1.00  0.00
ATOM   2188  N   LEU   295      28.162  47.818  -5.822  1.00  0.00
ATOM   2189  CA  LEU   295      27.631  46.640  -6.426  1.00  0.00
ATOM   2190  C   LEU   295      26.300  47.031  -6.968  1.00  0.00
ATOM   2191  O   LEU   295      25.298  47.020  -6.253  1.00  0.00
ATOM   2192  CB  LEU   295      27.491  45.523  -5.390  1.00  0.00
ATOM   2193  CG  LEU   295      27.045  44.159  -5.920  1.00  0.00
ATOM   2194  CD1 LEU   295      28.062  43.608  -6.909  1.00  0.00
ATOM   2195  CD2 LEU   295      26.901  43.160  -4.781  1.00  0.00
ATOM   2196  N   LYS   296      26.261  47.405  -8.260  1.00  0.00
ATOM   2197  CA  LYS   296      25.010  47.813  -8.825  1.00  0.00
ATOM   2198  C   LYS   296      25.070  47.589 -10.298  1.00  0.00
ATOM   2199  O   LYS   296      26.148  47.522 -10.887  1.00  0.00
ATOM   2200  CB  LYS   296      24.752  49.295  -8.540  1.00  0.00
ATOM   2201  CG  LYS   296      25.740  50.236  -9.210  1.00  0.00
ATOM   2202  CD  LYS   296      25.652  51.636  -8.624  1.00  0.00
ATOM   2203  CE  LYS   296      24.318  52.287  -8.947  1.00  0.00
ATOM   2204  NZ  LYS   296      24.208  53.651  -8.359  1.00  0.00
ATOM   2205  N   ASP   297      23.888  47.436 -10.923  1.00  0.00
ATOM   2206  CA  ASP   297      23.826  47.256 -12.341  1.00  0.00
ATOM   2207  C   ASP   297      23.995  48.603 -12.959  1.00  0.00
ATOM   2208  O   ASP   297      23.583  49.612 -12.390  1.00  0.00
ATOM   2209  CB  ASP   297      22.481  46.653 -12.746  1.00  0.00
ATOM   2210  CG  ASP   297      22.349  45.197 -12.345  1.00  0.00
ATOM   2211  OD1 ASP   297      23.373  44.591 -11.967  1.00  0.00
ATOM   2212  OD2 ASP   297      21.222  44.662 -12.408  1.00  0.00
ATOM   2213  N   HIS   298      24.629  48.659 -14.143  1.00  0.00
ATOM   2214  CA  HIS   298      24.781  49.931 -14.780  1.00  0.00
ATOM   2215  C   HIS   298      24.239  49.788 -16.161  1.00  0.00
ATOM   2216  O   HIS   298      24.337  48.734 -16.785  1.00  0.00
ATOM   2217  CB  HIS   298      26.256  50.335 -14.826  1.00  0.00
ATOM   2218  CG  HIS   298      26.887  50.476 -13.476  1.00  0.00
ATOM   2219  ND1 HIS   298      26.785  51.625 -12.723  1.00  0.00
ATOM   2220  CD2 HIS   298      27.690  49.623 -12.611  1.00  0.00
ATOM   2221  CE1 HIS   298      27.450  51.451 -11.567  1.00  0.00
ATOM   2222  NE2 HIS   298      27.995  50.253 -11.493  1.00  0.00
TER
END
