
#######################################################
#                                                     #
#                        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    3 (   42),  selected    3 , name T0316TS020_2_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected    3 , name T0316_D2.pdb
# PARAMETERS: T0316TS020_2_3-D2.T0316_D2.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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       281 - 283         0.02     0.01
  LCS_AVERAGE:      5.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       281 - 283         0.02     0.01
  LCS_AVERAGE:      5.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       281 - 283         0.02     0.01
  LCS_AVERAGE:      5.00

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:   60
LCS_GDT     D     281     D     281      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     S     282     S     282      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     L     283     L     283      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   5.00  (   5.00    5.00    5.00 )

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      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00   5.00
GDT RMS_LOCAL    0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02   0.02
GDT RMS_ALL_CA   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01   0.01

#      Molecule1      Molecule2       DISTANCE
LGA    D     281      D     281          0.016
LGA    S     282      S     282          0.004
LGA    L     283      L     283          0.012

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3   60    4.0      3    0.02     5.000     5.000     2.586

LGA_LOCAL      RMSD =  0.016  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.012  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.016  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.436431 * X  +   0.521959 * Y  +  -0.732862 * Z  + -17.661324
  Y_new =  -0.053403 * X  +  -0.828120 * Y  +  -0.558001 * Z  +  69.350357
  Z_new =  -0.898152 * X  +  -0.204392 * Y  +   0.389291 * Z  + -20.619856 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.483475    2.658118  [ DEG:   -27.7011    152.2989 ]
  Theta =   1.115547    2.026045  [ DEG:    63.9162    116.0838 ]
  Phi   =  -3.019835    0.121758  [ DEG:  -173.0238      6.9762 ]
 
# 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: T0316TS020_2_3-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS020_2_3-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3   60   4.0    3   0.02   5.000     0.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS020_2_3-D2
REMARK PARENT number 3
PFRMAT    TS
TARGET    T0316
PARENT    N/A
ATOM   4316  N   ASP   281      23.881  13.128 -21.001  1.00  1.00
ATOM   4317  CA  ASP   281      23.848  11.800 -20.400  1.00  1.00
ATOM   4318  C   ASP   281      25.017  11.598 -19.445  1.00  1.00
ATOM   4319  O   ASP   281      24.912  10.855 -18.469  1.00  1.00
ATOM   4320  CB  ASP   281      23.863  10.720 -21.486  1.00  1.00
ATOM   4321  CG  ASP   281      22.566  10.605 -22.276  1.00  1.00
ATOM   4322  OD1 ASP   281      21.588  11.181 -21.863  1.00  1.00
ATOM   4323  OD2 ASP   281      22.602  10.078 -23.362  1.00  1.00
ATOM   4324  H   ASP   281      23.944  13.213 -22.005  1.00  1.00
ATOM   4325  HA  ASP   281      22.940  11.685 -19.807  1.00  1.00
ATOM   4326 1HB  ASP   281      24.702  10.809 -22.175  1.00  1.00
ATOM   4327 2HB  ASP   281      23.991   9.831 -20.868  1.00  1.00
ATOM   4328  N   SER   282      26.130  12.263 -19.732  1.00  1.00
ATOM   4329  CA  SER   282      27.335  12.125 -18.923  1.00  1.00
ATOM   4330  C   SER   282      27.172  12.809 -17.571  1.00  1.00
ATOM   4331  O   SER   282      27.959  12.583 -16.651  1.00  1.00
ATOM   4332  CB  SER   282      28.529  12.697 -19.663  1.00  1.00
ATOM   4333  OG  SER   282      28.424  14.082 -19.844  1.00  1.00
ATOM   4334  H   SER   282      26.143  12.881 -20.532  1.00  1.00
ATOM   4335  HG  SER   282      27.635  14.278 -20.353  1.00  1.00
ATOM   4336  HA  SER   282      27.645  11.089 -18.780  1.00  1.00
ATOM   4337 1HB  SER   282      29.431  12.482 -19.088  1.00  1.00
ATOM   4338 2HB  SER   282      28.599  12.216 -20.638  1.00  1.00
ATOM   4339  N   LEU   283      26.147  13.646 -17.457  1.00  1.00
ATOM   4340  CA  LEU   283      25.867  14.350 -16.211  1.00  1.00
ATOM   4341  C   LEU   283      24.591  13.833 -15.560  1.00  1.00
ATOM   4342  O   LEU   283      24.094  14.417 -14.597  1.00  1.00
ATOM   4343  CB  LEU   283      25.763  15.858 -16.467  1.00  1.00
ATOM   4344  CG  LEU   283      27.084  16.633 -16.360  1.00  1.00
ATOM   4345  CD1 LEU   283      27.822  16.231 -15.089  1.00  1.00
ATOM   4346  CD2 LEU   283      27.936  16.356 -17.588  1.00  1.00
ATOM   4347  H   LEU   283      25.545  13.798 -18.254  1.00  1.00
ATOM   4348  HA  LEU   283      26.673  14.168 -15.500  1.00  1.00
ATOM   4349 1HB  LEU   283      25.424  15.840 -17.502  1.00  1.00
ATOM   4350 2HB  LEU   283      24.999  16.323 -15.844  1.00  1.00
ATOM   4351  HG  LEU   283      26.837  17.694 -16.355  1.00  1.00
ATOM   4352 1HD1 LEU   283      28.757  16.786 -15.021  1.00  1.00
ATOM   4353 2HD1 LEU   283      27.203  16.459 -14.222  1.00  1.00
ATOM   4354 3HD1 LEU   283      28.033  15.163 -15.114  1.00  1.00
ATOM   4355 1HD2 LEU   283      28.874  16.908 -17.511  1.00  1.00
ATOM   4356 2HD2 LEU   283      28.146  15.289 -17.655  1.00  1.00
ATOM   4357 3HD2 LEU   283      27.402  16.676 -18.483  1.00  1.00
TER
END
