
#######################################################
#                                                     #
#                        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 T0372TS249_3_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_3_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         2.85     2.85
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       291 - 296         1.46     3.45
  LCS_AVERAGE:      4.32

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       292 - 295         0.93     4.02
  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      3    3    9     0    2    3    3    3    3    6    6    7    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      3    6    9     0    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      4    6    9     1    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      4    6    9     3    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      4    6    9     3    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      4    6    9     3    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      3    6    9     3    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      3    5    9     3    3    3    4    5    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    5    9     3    3    5    6    7    7    8    8    8    8    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.73  (   2.73    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      3      3      5      6      7      7      8      8      8      8      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   2.38   3.97   4.76   5.56   5.56   6.35   6.35   6.35   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    0.25   0.25   1.02   1.23   1.54   1.54   2.08   2.08   2.08   2.08   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85
GDT RMS_ALL_CA   7.77   7.77   3.20   3.09   3.18   3.18   3.09   3.09   3.09   3.09   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85   2.85

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          7.176
LGA    Y     291      Y     291          1.879
LGA    M     292      M     292          0.682
LGA    A     293      A     293          2.097
LGA    C     294      C     294          1.724
LGA    L     295      L     295          2.858
LGA    K     296      K     296          1.596
LGA    D     297      D     297          3.313
LGA    H     298      H     298          1.181

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      8    2.08     5.159     5.296     0.368

LGA_LOCAL      RMSD =  2.075  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.090  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  2.854  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.983312 * X  +  -0.017735 * Y  +   0.181060 * Z  +  15.424225
  Y_new =  -0.161680 * X  +  -0.371094 * Y  +  -0.914412 * Z  +  54.893108
  Z_new =   0.083407 * X  +  -0.928426 * Y  +   0.362034 * Z  +   8.119495 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.198989    1.942603  [ DEG:   -68.6970    111.3030 ]
  Theta =  -0.083504   -3.058089  [ DEG:    -4.7844   -175.2156 ]
  Phi   =  -2.978627    0.162966  [ DEG:  -170.6628      9.3372 ]
 
# 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: T0372TS249_3_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_3_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    8   2.08   5.296     2.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      22.933  44.264   2.368  1.00  0.00
ATOM   1036  CA  LYS   290      22.889  44.760   1.018  1.00  0.00
ATOM   1037  C   LYS   290      23.589  46.075   0.939  1.00  0.00
ATOM   1038  O   LYS   290      23.693  46.659  -0.138  1.00  0.00
ATOM   1039  CB  LYS   290      21.473  44.951   0.437  1.00  0.00
ATOM   1040  CG  LYS   290      20.861  43.676  -0.150  1.00  0.00
ATOM   1041  CD  LYS   290      20.509  42.614   0.884  1.00  0.00
ATOM   1042  CE  LYS   290      19.988  41.317   0.269  1.00  0.00
ATOM   1043  NZ  LYS   290      18.733  41.570  -0.471  1.00  0.00
ATOM   1044  N   TYR   291      24.027  46.621   2.085  1.00  0.00
ATOM   1045  CA  TYR   291      24.710  47.877   2.057  1.00  0.00
ATOM   1046  C   TYR   291      25.867  47.740   1.127  1.00  0.00
ATOM   1047  O   TYR   291      26.233  48.698   0.449  1.00  0.00
ATOM   1048  CB  TYR   291      25.177  48.378   3.444  1.00  0.00
ATOM   1049  CG  TYR   291      26.121  47.416   4.084  1.00  0.00
ATOM   1050  CD1 TYR   291      27.461  47.431   3.771  1.00  0.00
ATOM   1051  CD2 TYR   291      25.668  46.512   5.018  1.00  0.00
ATOM   1052  CE1 TYR   291      28.330  46.549   4.370  1.00  0.00
ATOM   1053  CE2 TYR   291      26.532  45.628   5.620  1.00  0.00
ATOM   1054  CZ  TYR   291      27.867  45.645   5.295  1.00  0.00
ATOM   1055  OH  TYR   291      28.755  44.738   5.913  1.00  0.00
ATOM   1056  N   MET   292      26.504  46.557   1.081  1.00  0.00
ATOM   1057  CA  MET   292      27.513  46.434   0.078  1.00  0.00
ATOM   1058  C   MET   292      26.795  46.115  -1.193  1.00  0.00
ATOM   1059  O   MET   292      26.958  45.031  -1.749  1.00  0.00
ATOM   1060  CB  MET   292      28.485  45.274   0.346  1.00  0.00
ATOM   1061  CG  MET   292      29.325  45.474   1.606  1.00  0.00
ATOM   1062  SD  MET   292      30.572  46.787   1.471  1.00  0.00
ATOM   1063  CE  MET   292      31.682  45.815   0.411  1.00  0.00
ATOM   1064  N   ALA   293      25.959  47.055  -1.681  1.00  0.00
ATOM   1065  CA  ALA   293      25.354  46.859  -2.968  1.00  0.00
ATOM   1066  C   ALA   293      26.080  47.840  -3.832  1.00  0.00
ATOM   1067  O   ALA   293      25.538  48.879  -4.208  1.00  0.00
ATOM   1068  CB  ALA   293      23.864  47.233  -3.012  1.00  0.00
ATOM   1069  N   CYS   294      27.360  47.526  -4.110  1.00  0.00
ATOM   1070  CA  CYS   294      28.269  48.390  -4.806  1.00  0.00
ATOM   1071  C   CYS   294      28.165  48.483  -6.316  1.00  0.00
ATOM   1072  O   CYS   294      28.152  49.584  -6.861  1.00  0.00
ATOM   1073  CB  CYS   294      29.725  48.024  -4.480  1.00  0.00
ATOM   1074  SG  CYS   294      30.043  48.079  -2.691  1.00  0.00
ATOM   1075  N   LEU   295      28.103  47.312  -6.986  1.00  0.00
ATOM   1076  CA  LEU   295      28.393  47.022  -8.383  1.00  0.00
ATOM   1077  C   LEU   295      27.569  47.404  -9.610  1.00  0.00
ATOM   1078  O   LEU   295      28.169  47.756 -10.624  1.00  0.00
ATOM   1079  CB  LEU   295      28.705  45.529  -8.567  1.00  0.00
ATOM   1080  CG  LEU   295      30.012  45.124  -7.872  1.00  0.00
ATOM   1081  CD1 LEU   295      30.317  43.631  -8.064  1.00  0.00
ATOM   1082  CD2 LEU   295      31.166  46.032  -8.324  1.00  0.00
ATOM   1083  N   LYS   296      26.225  47.366  -9.590  1.00  0.00
ATOM   1084  CA  LYS   296      25.394  47.200 -10.778  1.00  0.00
ATOM   1085  C   LYS   296      25.402  48.139 -11.986  1.00  0.00
ATOM   1086  O   LYS   296      25.467  47.642 -13.109  1.00  0.00
ATOM   1087  CB  LYS   296      23.914  47.044 -10.387  1.00  0.00
ATOM   1088  CG  LYS   296      23.021  46.601 -11.543  1.00  0.00
ATOM   1089  CD  LYS   296      23.347  45.196 -12.050  1.00  0.00
ATOM   1090  CE  LYS   296      22.311  44.637 -13.027  1.00  0.00
ATOM   1091  NZ  LYS   296      21.116  44.178 -12.284  1.00  0.00
ATOM   1092  N   ASP   297      25.364  49.477 -11.848  1.00  0.00
ATOM   1093  CA  ASP   297      24.938  50.338 -12.940  1.00  0.00
ATOM   1094  C   ASP   297      25.645  50.235 -14.270  1.00  0.00
ATOM   1095  O   ASP   297      25.038  49.802 -15.247  1.00  0.00
ATOM   1096  CB  ASP   297      24.998  51.819 -12.529  1.00  0.00
ATOM   1097  CG  ASP   297      24.289  52.635 -13.593  1.00  0.00
ATOM   1098  OD1 ASP   297      23.511  52.040 -14.383  1.00  0.00
ATOM   1099  OD2 ASP   297      24.512  53.873 -13.625  1.00  0.00
ATOM   1100  N   HIS   298      26.937  50.598 -14.366  1.00  0.00
ATOM   1101  CA  HIS   298      27.579  50.631 -15.654  1.00  0.00
ATOM   1102  C   HIS   298      28.714  49.672 -15.550  1.00  0.00
ATOM   1103  O   HIS   298      28.924  49.083 -14.493  1.00  0.00
ATOM   1104  CB  HIS   298      28.193  52.008 -15.990  1.00  0.00
ATOM   1105  CG  HIS   298      27.214  53.154 -16.014  1.00  0.00
ATOM   1106  ND1 HIS   298      26.440  53.493 -17.100  1.00  0.00
ATOM   1107  CD2 HIS   298      26.909  54.064 -15.046  1.00  0.00
ATOM   1108  CE1 HIS   298      25.711  54.583 -16.742  1.00  0.00
ATOM   1109  NE2 HIS   298      25.965  54.966 -15.504  1.00  0.00
TER
END
