
#######################################################
#                                                     #
#                        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_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS349_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         4.51     4.51
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.87     5.33
  LCS_AVERAGE:      4.14

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       292 - 295         0.64     5.39
  LONGEST_CONTINUOUS_SEGMENT:     4       295 - 298         0.50    13.25
  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    3    9     0    3    3    3    3    3    4    4    5    6    6    7    8    8    8    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    6    9     3    3    4    5    5    6    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     M     292     M     292      4    6    9     3    4    4    5    5    6    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    6    9     3    4    4    4    5    6    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     C     294     C     294      4    6    9     3    4    4    5    5    6    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     L     295     L     295      4    6    9     3    4    4    5    5    6    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     K     296     K     296      4    6    9     3    4    4    5    5    6    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     D     297     D     297      4    4    9     3    4    4    4    4    5    6    6    7    7    7    7    8    8    8    9    9    9    9    9 
LCS_GDT     H     298     H     298      4    4    9     3    4    4    4    4    5    5    6    6    7    7    7    8    8    8    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.76  (   3.00    4.14    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      4      5      5      6      6      6      7      7      7      7      8      8      8      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.17   3.97   3.97   4.76   4.76   4.76   5.56   5.56   5.56   5.56   6.35   6.35   6.35   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.13   0.43   0.43   1.37   1.37   1.87   1.87   1.87   2.90   2.86   2.86   2.86   3.74   3.74   3.74   4.51   4.51   4.51   4.51   4.51
GDT RMS_ALL_CA  10.30   5.88   5.88   5.45   5.45   5.33   5.33   5.33   4.78   5.74   5.74   5.74   4.76   4.76   4.76   4.51   4.51   4.51   4.51   4.51

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          7.826
LGA    Y     291      Y     291          1.706
LGA    M     292      M     292          2.613
LGA    A     293      A     293          2.889
LGA    C     294      C     294          1.204
LGA    L     295      L     295          0.994
LGA    K     296      K     296          0.726
LGA    D     297      D     297          7.906
LGA    H     298      H     298         10.540

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      6    1.87     4.762     4.618     0.304

LGA_LOCAL      RMSD =  1.873  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.332  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  4.510  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.356418 * X  +   0.922700 * Y  +   0.146936 * Z  + -17.758343
  Y_new =   0.357887 * X  +   0.280094 * Y  +  -0.890766 * Z  +  40.046227
  Z_new =  -0.863066 * X  +  -0.264899 * Y  +  -0.430053 * Z  +  54.347530 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.589515    0.552078  [ DEG:  -148.3683     31.6317 ]
  Theta =   1.041309    2.100284  [ DEG:    59.6626    120.3374 ]
  Phi   =   2.354138   -0.787455  [ DEG:   134.8822    -45.1178 ]
 
# 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_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS349_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    6   1.87   4.618     4.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS349_5-D1
PFRMAT TS
TARGET T0372
MODEL  5  REFINED
PARENT 1YVO_B
ATOM   1090  N   LYS   290      25.801  41.621   0.189  1.00  0.00
ATOM   1091  CA  LYS   290      26.083  43.052   0.132  1.00  0.00
ATOM   1092  C   LYS   290      24.972  44.009   0.601  1.00  0.00
ATOM   1093  O   LYS   290      24.125  44.422  -0.186  1.00  0.00
ATOM   1094  CB  LYS   290      26.995  43.593  -0.955  1.00  0.00
ATOM   1095  CG  LYS   290      28.230  42.848  -1.224  1.00  0.00
ATOM   1096  CD  LYS   290      29.219  43.120  -0.153  1.00  0.00
ATOM   1097  CE  LYS   290      29.162  42.112   1.045  1.00  0.00
ATOM   1098  NZ  LYS   290      29.900  42.728   2.214  1.00  0.00
ATOM   1099  N   TYR   291      25.324  44.666   1.729  1.00  0.00
ATOM   1100  CA  TYR   291      24.545  45.707   2.367  1.00  0.00
ATOM   1101  C   TYR   291      24.978  47.050   1.646  1.00  0.00
ATOM   1102  O   TYR   291      24.098  47.899   1.397  1.00  0.00
ATOM   1103  CB  TYR   291      24.743  45.808   3.916  1.00  0.00
ATOM   1104  CG  TYR   291      23.926  47.034   4.409  1.00  0.00
ATOM   1105  CD1 TYR   291      24.428  48.330   4.313  1.00  0.00
ATOM   1106  CD2 TYR   291      22.667  46.873   4.936  1.00  0.00
ATOM   1107  CE1 TYR   291      23.693  49.420   4.720  1.00  0.00
ATOM   1108  CE2 TYR   291      21.894  47.956   5.393  1.00  0.00
ATOM   1109  CZ  TYR   291      22.432  49.205   5.276  1.00  0.00
ATOM   1110  OH  TYR   291      21.699  50.269   5.715  1.00  0.00
ATOM   1111  N   MET   292      26.305  47.312   1.518  1.00  0.00
ATOM   1112  CA  MET   292      26.899  48.486   0.823  1.00  0.00
ATOM   1113  C   MET   292      27.693  48.145  -0.486  1.00  0.00
ATOM   1114  O   MET   292      28.154  49.085  -1.118  1.00  0.00
ATOM   1115  CB  MET   292      27.835  49.173   1.830  1.00  0.00
ATOM   1116  CG  MET   292      27.390  49.272   3.275  1.00  0.00
ATOM   1117  SD  MET   292      28.373  50.554   4.317  1.00  0.00
ATOM   1118  CE  MET   292      27.361  50.629   5.751  1.00  0.00
ATOM   1119  N   ALA   293      28.031  46.865  -0.801  1.00  0.00
ATOM   1120  CA  ALA   293      28.681  46.634  -2.075  1.00  0.00
ATOM   1121  C   ALA   293      27.637  46.975  -3.123  1.00  0.00
ATOM   1122  O   ALA   293      26.564  46.359  -3.071  1.00  0.00
ATOM   1123  CB  ALA   293      29.327  45.287  -2.201  1.00  0.00
ATOM   1124  N   CYS   294      27.998  47.799  -4.152  1.00  0.00
ATOM   1125  CA  CYS   294      26.968  48.198  -5.079  1.00  0.00
ATOM   1126  C   CYS   294      27.491  48.658  -6.499  1.00  0.00
ATOM   1127  O   CYS   294      28.433  49.445  -6.616  1.00  0.00
ATOM   1128  CB  CYS   294      26.124  49.386  -4.515  1.00  0.00
ATOM   1129  SG  CYS   294      25.523  48.961  -2.858  1.00  0.00
ATOM   1130  N   LEU   295      26.697  48.236  -7.515  1.00  0.00
ATOM   1131  CA  LEU   295      26.842  48.570  -8.957  1.00  0.00
ATOM   1132  C   LEU   295      25.455  48.273  -9.631  1.00  0.00
ATOM   1133  O   LEU   295      25.027  47.102  -9.490  1.00  0.00
ATOM   1134  CB  LEU   295      28.015  47.737  -9.566  1.00  0.00
ATOM   1135  CG  LEU   295      28.597  48.195 -10.911  1.00  0.00
ATOM   1136  CD1 LEU   295      28.802  47.037 -11.906  1.00  0.00
ATOM   1137  CD2 LEU   295      27.789  49.242 -11.672  1.00  0.00
ATOM   1138  N   LYS   296      25.063  49.026 -10.699  1.00  0.00
ATOM   1139  CA  LYS   296      23.801  48.775 -11.377  1.00  0.00
ATOM   1140  C   LYS   296      22.614  48.688 -10.350  1.00  0.00
ATOM   1141  O   LYS   296      21.654  47.965 -10.627  1.00  0.00
ATOM   1142  CB  LYS   296      23.914  47.511 -12.159  1.00  0.00
ATOM   1143  CG  LYS   296      25.051  47.163 -13.032  1.00  0.00
ATOM   1144  CD  LYS   296      25.308  48.293 -14.021  1.00  0.00
ATOM   1145  CE  LYS   296      26.743  48.524 -14.497  1.00  0.00
ATOM   1146  NZ  LYS   296      26.741  49.481 -15.669  1.00  0.00
ATOM   1147  N   ASP   297      22.521  49.541  -9.311  1.00  0.00
ATOM   1148  CA  ASP   297      21.480  49.406  -8.288  1.00  0.00
ATOM   1149  C   ASP   297      21.475  47.940  -7.681  1.00  0.00
ATOM   1150  O   ASP   297      20.427  47.478  -7.233  1.00  0.00
ATOM   1151  CB  ASP   297      20.113  49.752  -8.878  1.00  0.00
ATOM   1152  CG  ASP   297      19.989  51.229  -9.142  1.00  0.00
ATOM   1153  OD1 ASP   297      20.493  52.059  -8.306  1.00  0.00
ATOM   1154  OD2 ASP   297      19.381  51.627 -10.101  1.00  0.00
ATOM   1155  N   HIS   298      22.681  47.338  -7.441  1.00  0.00
ATOM   1156  CA  HIS   298      23.025  45.935  -6.908  1.00  0.00
ATOM   1157  C   HIS   298      24.522  45.787  -6.255  1.00  0.00
ATOM   1158  O   HIS   298      24.864  46.804  -5.764  1.00  0.00
ATOM   1159  CB  HIS   298      22.953  44.948  -8.072  1.00  0.00
ATOM   1160  CG  HIS   298      21.574  44.868  -8.663  1.00  0.00
ATOM   1161  ND1 HIS   298      20.503  44.221  -8.090  1.00  0.00
ATOM   1162  CD2 HIS   298      21.099  45.422  -9.824  1.00  0.00
ATOM   1163  CE1 HIS   298      19.457  44.391  -8.886  1.00  0.00
ATOM   1164  NE2 HIS   298      19.757  45.126  -9.913  1.00  0.00
TER
END
