
#######################################################
#                                                     #
#                        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    4 (   34),  selected    4 , name T0372TS028_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    4 , name T0372_D1.pdb
# PARAMETERS: T0372TS028_1-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:     4       290 - 293         0.86     0.86
  LCS_AVERAGE:      3.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.86     0.86
  LCS_AVERAGE:      3.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.86     0.86
  LCS_AVERAGE:      3.17

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    4    4     3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     Y     291     Y     291      4    4    4     3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     M     292     M     292      4    4    4     3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     A     293     A     293      4    4    4     3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   3.17  (   3.17    3.17    3.17 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   2.38   2.38   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17
GDT RMS_LOCAL    0.09   0.09   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86
GDT RMS_ALL_CA   1.46   1.46   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86   0.86

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          1.061
LGA    Y     291      Y     291          1.044
LGA    M     292      M     292          0.327
LGA    A     293      A     293          0.802

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  126    4.0      4    0.86     2.976     3.112     0.416

LGA_LOCAL      RMSD =  0.861  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.861  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.861  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.646459 * X  +   0.762590 * Y  +   0.023378 * Z  + -28.135406
  Y_new =  -0.207996 * X  +   0.146675 * Y  +   0.967070 * Z  +  35.039890
  Z_new =   0.734049 * X  +  -0.630034 * Y  +   0.253435 * Z  +  29.818136 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.188347    1.953246  [ DEG:   -68.0872    111.9128 ]
  Theta =  -0.824266   -2.317327  [ DEG:   -47.2269   -132.7731 ]
  Phi   =  -0.311286    2.830307  [ DEG:   -17.8354    162.1646 ]
 
# 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: T0372TS028_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS028_1-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4  126   4.0    4   0.86   3.112     0.86
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS028_1-D1
PFRMAT TS
TARGET T0372
MODEL 1
PARENT 1qsm-A
ATOM   1090  N   LYS   290      27.579  46.706   7.395  1.00  9.00
ATOM   1091  CA  LYS   290      26.605  47.315   6.483  1.00  9.00
ATOM   1092  C   LYS   290      26.286  46.387   5.316  1.00  9.00
ATOM   1093  O   LYS   290      27.065  45.485   4.984  1.00  9.00
ATOM   1094  CB  LYS   290      27.149  48.625   5.929  1.00  9.00
ATOM   1095  CG  LYS   290      27.189  49.727   6.978  1.00  9.00
ATOM   1096  CD  LYS   290      27.629  51.046   6.352  1.00  9.00
ATOM   1097  CE  LYS   290      27.583  52.190   7.360  1.00  9.00
ATOM   1098  NZ  LYS   290      28.466  51.912   8.504  1.00  9.00
ATOM   1099  N   TYR   291      25.124  46.603   4.722  1.00  9.00
ATOM   1100  CA  TYR   291      24.751  45.875   3.502  1.00  9.00
ATOM   1101  C   TYR   291      25.651  46.345   2.359  1.00  9.00
ATOM   1102  O   TYR   291      26.019  47.524   2.293  1.00  9.00
ATOM   1103  CB  TYR   291      23.284  46.172   3.189  1.00  9.00
ATOM   1104  CG  TYR   291      22.730  45.455   1.959  1.00  9.00
ATOM   1105  CD1 TYR   291      22.515  44.083   1.997  1.00  9.00
ATOM   1106  CD2 TYR   291      22.453  46.177   0.802  1.00  9.00
ATOM   1107  CE1 TYR   291      22.022  43.427   0.874  1.00  9.00
ATOM   1108  CE2 TYR   291      21.962  45.522  -0.321  1.00  9.00
ATOM   1109  CZ  TYR   291      21.750  44.150  -0.280  1.00  9.00
ATOM   1110  OH  TYR   291      21.295  43.494  -1.407  1.00  9.00
ATOM   1111  N   MET   292      26.067  45.403   1.531  1.00  9.00
ATOM   1112  CA  MET   292      26.948  45.703   0.400  1.00  9.00
ATOM   1113  C   MET   292      26.349  46.757  -0.533  1.00  9.00
ATOM   1114  O   MET   292      25.156  46.723  -0.855  1.00  9.00
ATOM   1115  CB  MET   292      27.200  44.397  -0.352  1.00  9.00
ATOM   1116  CG  MET   292      28.181  44.551  -1.514  1.00  9.00
ATOM   1117  SD  MET   292      28.559  43.025  -2.411  1.00  9.00
ATOM   1118  CE  MET   292      29.325  42.085  -1.069  1.00  9.00
ATOM   1119  N   ALA   293      27.170  47.761  -0.815  1.00  9.00
ATOM   1120  CA  ALA   293      26.845  48.883  -1.715  1.00  9.00
ATOM   1121  C   ALA   293      25.921  49.892  -1.027  1.00  9.00
ATOM   1122  O   ALA   293      24.957  50.307  -1.668  1.00  9.00
ATOM   1123  CB  ALA   293      26.214  48.396  -3.024  1.00  9.00
TER
END
