
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected    8 , name T0386_D1.pdb
# PARAMETERS: T0386TS599_4-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         2.41     2.41
  LCS_AVERAGE:      3.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       213 - 218         0.15     3.52
  LCS_AVERAGE:      2.67

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       213 - 218         0.15     3.52
  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    4    8     0    0    3    3    5    5    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     H     212     H     212      0    4    8     0    0    3    3    3    5    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L     213     L     213      6    6    8     6    6    6    6    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     F     214     F     214      6    6    8     6    6    6    6    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E     215     E     215      6    6    8     6    6    6    6    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     D     216     D     216      6    6    8     6    6    6    6    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     I     217     I     217      6    6    8     6    6    6    6    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     S     218     S     218      6    6    8     6    6    6    6    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.91  (   2.18    2.67    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      6      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   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
GDT RMS_LOCAL    0.15   0.15   0.15   0.15   0.15   0.15   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41
GDT RMS_ALL_CA   3.52   3.52   3.52   3.52   3.52   3.52   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41   2.41

#      Molecule1      Molecule2       DISTANCE
LGA    Q     211      Q     211          3.124
LGA    H     212      H     212          3.527
LGA    L     213      L     213          2.355
LGA    F     214      F     214          2.867
LGA    E     215      E     215          1.677
LGA    D     216      D     216          0.761
LGA    I     217      I     217          1.706
LGA    S     218      S     218          2.069

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  206    4.0      8    2.41     3.398     3.239     0.318

LGA_LOCAL      RMSD =  2.412  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.412  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.412  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.686338 * X  +   0.727162 * Y  +  -0.013271 * Z  +  16.685268
  Y_new =   0.407352 * X  +   0.369238 * Y  +  -0.835301 * Z  +  70.987679
  Z_new =  -0.602498 * X  +  -0.578705 * Y  +  -0.549633 * Z  +  87.871521 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.330435    0.811157  [ DEG:  -133.5241     46.4759 ]
  Theta =   0.646628    2.494965  [ DEG:    37.0490    142.9510 ]
  Phi   =   2.605954   -0.535638  [ DEG:   149.3102    -30.6898 ]
 
# 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_4-D1                               
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS599_4-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   2.41   3.239     2.41
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS599_4-D1
PFRMAT TS                                                                       
TARGET T0386                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM    211  CA  GLN   211       7.474  50.033  67.935  1.00  0.00              
ATOM    212  CA  HIS   212      10.142  52.575  68.779  1.00  0.00              
ATOM    213  CA  LEU   213      12.720  54.729  71.306  1.00  0.00              
ATOM    214  CA  PHE   214       9.768  52.482  70.203  1.00  0.00              
ATOM    215  CA  GLU   215       7.839  53.135  73.350  1.00  0.00              
ATOM    216  CA  ASP   216       8.269  56.895  73.046  1.00  0.00              
ATOM    217  CA  ILE   217       7.128  56.808  69.383  1.00  0.00              
ATOM    218  CA  SER   218       4.014  54.802  70.014  1.00  0.00              
TER                                                                             
END
