
#######################################################
#                                                     #
#                        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    5 (    5),  selected    5 , name T0301TS464_4_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected    5 , name T0301_D2.pdb
# PARAMETERS: T0301TS464_4_2-D2.T0301_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
  LONGEST_CONTINUOUS_SEGMENT:     5       353 - 357         1.59     1.59
  LCS_AVERAGE:      2.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       353 - 357         1.59     1.59
  LCS_AVERAGE:      2.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       354 - 357         0.58     2.77
  LCS_AVERAGE:      1.99

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:  191
LCS_GDT     S     353     S     353      3    5    5     0    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     354     G     354      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     355     T     355      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     356     L     356      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     R     357     R     357      4    5    5     3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.41  (   1.99    2.62    2.62 )

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      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.57   2.09   2.09   2.09   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62   2.62
GDT RMS_LOCAL    0.11   0.58   0.58   0.58   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59
GDT RMS_ALL_CA   2.46   2.77   2.77   2.77   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59   1.59

#      Molecule1      Molecule2       DISTANCE
LGA    S     353      S     353          2.210
LGA    G     354      G     354          0.917
LGA    T     355      T     355          0.493
LGA    L     356      L     356          1.706
LGA    R     357      R     357          1.959

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  191    4.0      5    1.59     2.356     2.501     0.295

LGA_LOCAL      RMSD =  1.595  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.595  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.595  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.830279 * X  +   0.045002 * Y  +   0.555528 * Z  +  82.923920
  Y_new =  -0.543005 * X  +  -0.289975 * Y  +  -0.788074 * Z  +  19.182941
  Z_new =   0.125624 * X  +  -0.955976 * Y  +   0.265196 * Z  +  66.728218 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.300192    1.841401  [ DEG:   -74.4955    105.5045 ]
  Theta =  -0.125957   -3.015635  [ DEG:    -7.2168   -172.7832 ]
  Phi   =  -2.562409    0.579184  [ DEG:  -146.8152     33.1848 ]
 
# 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: T0301TS464_4_2-D2                             
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_4_2-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  191   4.0    5   1.59   2.501     1.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM     32  CA  SER   353      91.993  14.919  26.079  1.00  0.00
ATOM     33  CA  GLY   354      90.940  11.991  28.252  1.00  0.00
ATOM     34  CA  THR   355      88.569  10.063  26.019  1.00  0.00
ATOM     35  CA  LEU   356      88.127   8.941  22.432  1.00  0.00
ATOM     36  CA  ARG   357      84.638   9.635  21.082  1.00  0.00
TER
END
