
#######################################################
#                                                     #
#                        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 T0372TS349_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS349_4-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       291 - 296         1.56     5.45
  LCS_AVERAGE:      4.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 295         0.94     6.00
  LCS_AVERAGE:      3.53

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    9     0    3    3    3    3    4    4    4    6    6    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      5    6    9     4    4    5    5    6    6    6    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     M     292     M     292      5    6    9     4    4    5    5    6    6    6    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     A     293     A     293      5    6    9     4    4    5    5    6    6    6    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     C     294     C     294      5    6    9     3    4    5    5    6    6    6    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     L     295     L     295      5    6    9     3    4    5    5    6    6    6    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    6    9     4    4    4    5    6    6    6    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     D     297     D     297      4    5    9     3    4    4    4    4    5    5    6    6    7    7    8    8    8    8    9    9    9    9    9 
LCS_GDT     H     298     H     298      4    5    9     3    4    4    4    4    5    5    5    5    6    6    7    7    8    8    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   5.00  (   3.53    4.32    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      4      4      5      5      6      6      6      6      6      7      7      8      8      8      8      9      9      9      9      9 
GDT PERCENT_CA   3.17   3.17   3.97   3.97   4.76   4.76   4.76   4.76   4.76   5.56   5.56   6.35   6.35   6.35   6.35   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.32   0.32   0.94   0.94   1.56   1.56   1.56   1.56   1.56   3.00   3.00   3.79   3.79   3.79   3.79   4.61   4.61   4.61   4.61   4.61
GDT RMS_ALL_CA   5.31   5.31   6.00   6.00   5.45   5.45   5.45   5.45   5.45   5.08   5.08   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          8.134
LGA    Y     291      Y     291          1.357
LGA    M     292      M     292          1.779
LGA    A     293      A     293          1.047
LGA    C     294      C     294          0.856
LGA    L     295      L     295          2.291
LGA    K     296      K     296          1.602
LGA    D     297      D     297          8.281
LGA    H     298      H     298         10.858

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    1.56     4.762     4.763     0.361

LGA_LOCAL      RMSD =  1.563  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.450  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.605  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.459474 * X  +  -0.639663 * Y  +   0.616210 * Z  +  43.219791
  Y_new =  -0.539404 * X  +   0.752148 * Y  +   0.378571 * Z  +  -7.519368
  Z_new =  -0.705640 * X  +  -0.158443 * Y  +  -0.690629 * Z  +  59.627419 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.916077    0.225515  [ DEG:  -167.0789     12.9211 ]
  Theta =   0.783326    2.358267  [ DEG:    44.8813    135.1187 ]
  Phi   =  -2.276345    0.865248  [ DEG:  -130.4249     49.5751 ]
 
# 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: T0372TS349_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS349_4-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    6   1.56   4.763     4.61
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS349_4-D1
PFRMAT TS
TARGET T0372
MODEL  4  REFINED
PARENT 1YR0_D
ATOM   1090  N   LYS   290      24.189  41.568   0.655  1.00  0.00
ATOM   1091  CA  LYS   290      24.454  42.902   0.075  1.00  0.00
ATOM   1092  C   LYS   290      25.373  43.680   1.102  1.00  0.00
ATOM   1093  O   LYS   290      26.597  43.524   1.027  1.00  0.00
ATOM   1094  CB  LYS   290      23.036  43.563   0.176  1.00  0.00
ATOM   1095  CG  LYS   290      22.043  42.671  -0.595  1.00  0.00
ATOM   1096  CD  LYS   290      20.705  43.322  -0.208  1.00  0.00
ATOM   1097  CE  LYS   290      19.543  42.772  -0.996  1.00  0.00
ATOM   1098  NZ  LYS   290      19.936  42.706  -2.430  1.00  0.00
ATOM   1099  N   TYR   291      24.797  44.745   1.747  1.00  0.00
ATOM   1100  CA  TYR   291      25.412  45.687   2.684  1.00  0.00
ATOM   1101  C   TYR   291      26.170  46.819   1.907  1.00  0.00
ATOM   1102  O   TYR   291      25.804  47.976   2.137  1.00  0.00
ATOM   1103  CB  TYR   291      26.334  44.993   3.740  1.00  0.00
ATOM   1104  CG  TYR   291      27.130  45.996   4.590  1.00  0.00
ATOM   1105  CD1 TYR   291      26.493  46.652   5.634  1.00  0.00
ATOM   1106  CD2 TYR   291      28.461  46.221   4.239  1.00  0.00
ATOM   1107  CE1 TYR   291      27.230  47.613   6.349  1.00  0.00
ATOM   1108  CE2 TYR   291      29.215  47.169   4.920  1.00  0.00
ATOM   1109  CZ  TYR   291      28.547  47.796   5.966  1.00  0.00
ATOM   1110  OH  TYR   291      29.298  48.768   6.657  1.00  0.00
ATOM   1111  N   MET   292      27.186  46.544   1.090  1.00  0.00
ATOM   1112  CA  MET   292      27.778  47.602   0.319  1.00  0.00
ATOM   1113  C   MET   292      26.875  47.755  -0.935  1.00  0.00
ATOM   1114  O   MET   292      26.465  46.684  -1.473  1.00  0.00
ATOM   1115  CB  MET   292      29.234  47.292  -0.091  1.00  0.00
ATOM   1116  CG  MET   292      29.832  48.464  -0.905  1.00  0.00
ATOM   1117  SD  MET   292      31.535  48.195  -1.249  1.00  0.00
ATOM   1118  CE  MET   292      32.254  48.729   0.308  1.00  0.00
ATOM   1119  N   ALA   293      26.396  48.981  -1.274  1.00  0.00
ATOM   1120  CA  ALA   293      25.591  49.004  -2.503  1.00  0.00
ATOM   1121  C   ALA   293      26.603  48.510  -3.536  1.00  0.00
ATOM   1122  O   ALA   293      27.432  49.355  -3.931  1.00  0.00
ATOM   1123  CB  ALA   293      25.026  50.396  -2.793  1.00  0.00
ATOM   1124  N   CYS   294      26.431  47.338  -4.179  1.00  0.00
ATOM   1125  CA  CYS   294      27.567  46.950  -5.064  1.00  0.00
ATOM   1126  C   CYS   294      27.224  46.538  -6.514  1.00  0.00
ATOM   1127  O   CYS   294      27.762  45.514  -6.916  1.00  0.00
ATOM   1128  CB  CYS   294      28.375  45.962  -4.282  1.00  0.00
ATOM   1129  SG  CYS   294      27.563  44.361  -3.949  1.00  0.00
ATOM   1130  N   LEU   295      26.882  47.474  -7.366  1.00  0.00
ATOM   1131  CA  LEU   295      26.672  47.276  -8.818  1.00  0.00
ATOM   1132  C   LEU   295      25.676  48.324  -9.258  1.00  0.00
ATOM   1133  O   LEU   295      24.641  48.329  -8.665  1.00  0.00
ATOM   1134  CB  LEU   295      26.189  45.831  -9.037  1.00  0.00
ATOM   1135  CG  LEU   295      26.221  45.068 -10.308  1.00  0.00
ATOM   1136  CD1 LEU   295      25.933  45.913 -11.560  1.00  0.00
ATOM   1137  CD2 LEU   295      27.578  44.364 -10.598  1.00  0.00
ATOM   1138  N   LYS   296      25.757  48.881 -10.457  1.00  0.00
ATOM   1139  CA  LYS   296      24.716  49.851 -10.915  1.00  0.00
ATOM   1140  C   LYS   296      23.906  50.479  -9.720  1.00  0.00
ATOM   1141  O   LYS   296      22.713  50.662  -9.919  1.00  0.00
ATOM   1142  CB  LYS   296      23.807  49.150 -11.947  1.00  0.00
ATOM   1143  CG  LYS   296      24.548  48.539 -13.093  1.00  0.00
ATOM   1144  CD  LYS   296      23.561  47.801 -13.971  1.00  0.00
ATOM   1145  CE  LYS   296      24.260  47.433 -15.274  1.00  0.00
ATOM   1146  NZ  LYS   296      23.200  47.706 -16.341  1.00  0.00
ATOM   1147  N   ASP   297      24.541  51.049  -8.661  1.00  0.00
ATOM   1148  CA  ASP   297      23.908  51.565  -7.476  1.00  0.00
ATOM   1149  C   ASP   297      23.071  50.468  -6.637  1.00  0.00
ATOM   1150  O   ASP   297      22.153  50.943  -5.930  1.00  0.00
ATOM   1151  CB  ASP   297      23.041  52.718  -7.874  1.00  0.00
ATOM   1152  CG  ASP   297      23.561  53.941  -8.507  1.00  0.00
ATOM   1153  OD1 ASP   297      22.752  54.784  -8.982  1.00  0.00
ATOM   1154  OD2 ASP   297      24.800  54.095  -8.521  1.00  0.00
ATOM   1155  N   HIS   298      23.563  49.206  -6.413  1.00  0.00
ATOM   1156  CA  HIS   298      22.812  48.146  -5.663  1.00  0.00
ATOM   1157  C   HIS   298      23.653  46.911  -5.034  1.00  0.00
ATOM   1158  O   HIS   298      24.557  46.509  -5.782  1.00  0.00
ATOM   1159  CB  HIS   298      21.658  47.601  -6.539  1.00  0.00
ATOM   1160  CG  HIS   298      22.059  47.118  -7.903  1.00  0.00
ATOM   1161  ND1 HIS   298      22.084  48.044  -8.917  1.00  0.00
ATOM   1162  CD2 HIS   298      22.453  45.949  -8.415  1.00  0.00
ATOM   1163  CE1 HIS   298      22.448  47.413 -10.026  1.00  0.00
ATOM   1164  NE2 HIS   298      22.656  46.144  -9.746  1.00  0.00
TER
END
