
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected    8 , name T0386_D1.pdb
# PARAMETERS: T0386TS599_3-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         2.27     2.27
  LCS_AVERAGE:      3.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       212 - 218         1.82     2.55
  LCS_AVERAGE:      3.28

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       213 - 218         0.25     3.42
  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    2    3    4    5    8    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    4    5    8    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    8    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    8    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    8    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    8    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    8    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    8    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      8      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   3.88   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   3.88
GDT RMS_LOCAL    0.25   0.25   0.25   0.25   0.25   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27
GDT RMS_ALL_CA   3.42   3.42   3.42   3.42   3.42   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27

#      Molecule1      Molecule2       DISTANCE
LGA    Q     211      Q     211          3.389
LGA    H     212      H     212          2.529
LGA    L     213      L     213          2.291
LGA    F     214      F     214          2.746
LGA    E     215      E     215          1.692
LGA    D     216      D     216          0.893
LGA    I     217      I     217          1.780
LGA    S     218      S     218          1.957

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  206    4.0      8    2.27     3.398     3.451     0.337

LGA_LOCAL      RMSD =  2.273  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.273  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.273  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.644183 * X  +  -0.761058 * Y  +  -0.076278 * Z  +  24.157726
  Y_new =  -0.178899 * X  +   0.052959 * Y  +   0.982441 * Z  +  73.394562
  Z_new =  -0.743655 * X  +   0.646518 * Y  +  -0.170267 * Z  +  67.943230 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.828310   -1.313283  [ DEG:   104.7544    -75.2456 ]
  Theta =   0.838521    2.303071  [ DEG:    48.0437    131.9563 ]
  Phi   =  -2.870705    0.270888  [ DEG:  -164.4793     15.5207 ]
 
# 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_3-D1                               
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS599_3-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   2.27   3.451     2.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS599_3-D1
PFRMAT TS                                                                       
TARGET T0386                                                                    
MODEL  3                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLN   211       7.444  50.469  67.720  1.00  0.00              
ATOM    212  CA  HIS   212      10.457  51.752  69.451  1.00  0.00              
ATOM    213  CA  LEU   213      12.541  54.933  71.248  1.00  0.00              
ATOM    214  CA  PHE   214       9.747  52.474  70.033  1.00  0.00              
ATOM    215  CA  GLU   215       7.913  53.209  73.315  1.00  0.00              
ATOM    216  CA  ASP   216       8.308  56.952  72.802  1.00  0.00              
ATOM    217  CA  ILE   217       6.991  56.857  69.183  1.00  0.00              
ATOM    218  CA  SER   218       3.954  54.813  70.263  1.00  0.00              
TER                                                                             
END
