
#######################################################
#                                                     #
#                        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_1_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected    3 , name T0316_D2.pdb
# PARAMETERS: T0316TS020_1_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         0.08     0.08
  LCS_AVERAGE:      5.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       281 - 283         0.08     0.08
  LCS_AVERAGE:      5.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       281 - 283         0.08     0.08
  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    0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08
GDT RMS_ALL_CA   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08   0.08

#      Molecule1      Molecule2       DISTANCE
LGA    D     281      D     281          0.090
LGA    S     282      S     282          0.065
LGA    L     283      L     283          0.092

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3   60    4.0      3    0.08     5.000     5.000     1.643

LGA_LOCAL      RMSD =  0.083  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.083  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.083  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.696355 * X  +  -0.543332 * Y  +  -0.468915 * Z  +  70.363251
  Y_new =   0.386945 * X  +  -0.266042 * Y  +   0.882890 * Z  +  24.778164
  Z_new =  -0.604453 * X  +  -0.796249 * Y  +   0.024981 * Z  +  29.354832 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.539434    1.602159  [ DEG:   -88.2031     91.7969 ]
  Theta =   0.649079    2.492513  [ DEG:    37.1895    142.8105 ]
  Phi   =   0.507188   -2.634404  [ DEG:    29.0598   -150.9402 ]
 
# 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_1_3-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS020_1_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   0.08   5.000     0.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS020_1_3-D2
REMARK PARENT number 3
PFRMAT    TS
TARGET    T0316
PARENT    N/A
ATOM   4316  N   ASP   281      23.590  13.176 -20.562  1.00  1.00
ATOM   4317  CA  ASP   281      23.840  11.741 -20.485  1.00  1.00
ATOM   4318  C   ASP   281      25.058  11.440 -19.621  1.00  1.00
ATOM   4319  O   ASP   281      25.078  10.457 -18.881  1.00  1.00
ATOM   4320  CB  ASP   281      24.032  11.154 -21.886  1.00  1.00
ATOM   4321  CG  ASP   281      22.747  11.011 -22.689  1.00  1.00
ATOM   4322  OD1 ASP   281      21.692  11.138 -22.113  1.00  1.00
ATOM   4323  OD2 ASP   281      22.827  10.932 -23.891  1.00  1.00
ATOM   4324  H   ASP   281      23.596  13.629 -21.464  1.00  1.00
ATOM   4325  HA  ASP   281      22.994  11.243 -20.013  1.00  1.00
ATOM   4326 1HB  ASP   281      24.775  11.686 -22.482  1.00  1.00
ATOM   4327 2HB  ASP   281      24.412  10.165 -21.628  1.00  1.00
ATOM   4328  N   SER   282      26.072  12.292 -19.718  1.00  1.00
ATOM   4329  CA  SER   282      27.276  12.148 -18.908  1.00  1.00
ATOM   4330  C   SER   282      27.072  12.727 -17.513  1.00  1.00
ATOM   4331  O   SER   282      27.659  12.251 -16.542  1.00  1.00
ATOM   4332  CB  SER   282      28.450  12.820 -19.592  1.00  1.00
ATOM   4333  OG  SER   282      28.276  14.206 -19.697  1.00  1.00
ATOM   4334  H   SER   282      26.009  13.060 -20.371  1.00  1.00
ATOM   4335  HG  SER   282      28.185  14.584 -18.819  1.00  1.00
ATOM   4336  HA  SER   282      27.628  11.118 -18.835  1.00  1.00
ATOM   4337 1HB  SER   282      29.351  12.618 -19.014  1.00  1.00
ATOM   4338 2HB  SER   282      28.558  12.400 -20.591  1.00  1.00
ATOM   4339  N   LEU   283      26.236  13.756 -17.421  1.00  1.00
ATOM   4340  CA  LEU   283      25.935  14.386 -16.141  1.00  1.00
ATOM   4341  C   LEU   283      25.198  13.426 -15.216  1.00  1.00
ATOM   4342  O   LEU   283      25.491  13.351 -14.022  1.00  1.00
ATOM   4343  CB  LEU   283      25.108  15.659 -16.358  1.00  1.00
ATOM   4344  CG  LEU   283      25.077  16.627 -15.169  1.00  1.00
ATOM   4345  CD1 LEU   283      24.398  17.930 -15.575  1.00  1.00
ATOM   4346  CD2 LEU   283      24.344  15.979 -14.005  1.00  1.00
ATOM   4347  H   LEU   283      25.800  14.112 -18.259  1.00  1.00
ATOM   4348  HA  LEU   283      26.864  14.650 -15.636  1.00  1.00
ATOM   4349 1HB  LEU   283      25.671  16.097 -17.182  1.00  1.00
ATOM   4350 2HB  LEU   283      24.096  15.431 -16.691  1.00  1.00
ATOM   4351  HG  LEU   283      26.108  16.797 -14.861  1.00  1.00
ATOM   4352 1HD1 LEU   283      24.381  18.611 -14.724  1.00  1.00
ATOM   4353 2HD1 LEU   283      24.953  18.388 -16.394  1.00  1.00
ATOM   4354 3HD1 LEU   283      23.379  17.725 -15.896  1.00  1.00
ATOM   4355 1HD2 LEU   283      24.322  16.668 -13.159  1.00  1.00
ATOM   4356 2HD2 LEU   283      23.322  15.739 -14.304  1.00  1.00
ATOM   4357 3HD2 LEU   283      24.860  15.064 -13.712  1.00  1.00
TER
END
