
#######################################################
#                                                     #
#                        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    8 (    8),  selected    8 , name T0386TS599_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected    8 , name T0386_D1.pdb
# PARAMETERS: T0386TS599_2-D1.T0386_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:     8       211 - 218         2.30     2.30
  LCS_AVERAGE:      3.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       212 - 218         1.85     2.58
  LCS_AVERAGE:      3.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       213 - 218         0.25     3.44
  LCS_AVERAGE:      2.18

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:  206
LCS_GDT     Q     211     Q     211      0    5    8     0    0    3    3    5    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     H     212     H     212      0    7    8     0    0    3    3    5    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     213     L     213      6    7    8     6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     F     214     F     214      6    7    8     6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     215     E     215      6    7    8     6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     216     D     216      6    7    8     6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     I     217     I     217      6    7    8     6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     S     218     S     218      6    7    8     6    6    6    6    6    7    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   3.11  (   2.18    3.28    3.88 )

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      6      6      6      6      6      7      8      8      8      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   2.91   2.91   2.91   2.91   2.91   3.40   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88
GDT RMS_LOCAL    0.25   0.25   0.25   0.25   0.25   1.85   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30
GDT RMS_ALL_CA   3.44   3.44   3.44   3.44   3.44   2.58   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30

#      Molecule1      Molecule2       DISTANCE
LGA    Q     211      Q     211          3.363
LGA    H     212      H     212          2.745
LGA    L     213      L     213          2.411
LGA    F     214      F     214          2.713
LGA    E     215      E     215          1.641
LGA    D     216      D     216          0.801
LGA    I     217      I     217          1.632
LGA    S     218      S     218          2.065

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  206    4.0      8    2.30     3.398     3.421     0.333

LGA_LOCAL      RMSD =  2.299  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.299  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.299  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.004672 * X  +   0.992552 * Y  +  -0.121731 * Z  +  18.980795
  Y_new =   0.735728 * X  +  -0.079034 * Y  +  -0.672650 * Z  +  61.844868
  Z_new =  -0.677261 * X  +  -0.092704 * Y  +  -0.729879 * Z  +  71.001213 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.015257    0.126336  [ DEG:  -172.7615      7.2385 ]
  Theta =   0.744034    2.397559  [ DEG:    42.6300    137.3700 ]
  Phi   =   1.577146   -1.564446  [ DEG:    90.3638    -89.6362 ]
 
# 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: T0386TS599_2-D1                               
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS599_2-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  206   4.0    8   2.30   3.421     2.30
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS599_2-D1
PFRMAT TS                                                                       
TARGET T0386                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLN   211       7.173  49.922  67.924  1.00  0.00              
ATOM    212  CA  HIS   212      10.558  52.026  69.240  1.00  0.00              
ATOM    213  CA  LEU   213      12.533  55.137  71.301  1.00  0.00              
ATOM    214  CA  PHE   214       9.907  52.684  69.947  1.00  0.00              
ATOM    215  CA  GLU   215       7.983  53.119  73.224  1.00  0.00              
ATOM    216  CA  ASP   216       8.220  56.865  72.896  1.00  0.00              
ATOM    217  CA  ILE   217       6.963  56.974  69.274  1.00  0.00              
ATOM    218  CA  SER   218       4.016  54.733  70.210  1.00  0.00              
TER                                                                             
END
