
#######################################################
#                                                     #
#                        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 (   12),  selected    3 , name T0316AL316_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected    3 , name T0316_D3.pdb
# PARAMETERS: T0316AL316_5-D3.T0316_D3.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       367 - 369         0.67     0.67
  LCS_AVERAGE:      3.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       367 - 369         0.67     0.67
  LCS_AVERAGE:      3.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       367 - 369         0.67     0.67
  LCS_AVERAGE:      3.33

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:   90
LCS_GDT     G     367     G     367      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     Q     368     Q     368      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     V     369     V     369      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   3.33  (   3.33    3.33    3.33 )

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      0      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   0.00   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33   3.33
GDT RMS_LOCAL  1000.00   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67
GDT RMS_ALL_CA 1000.00   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67

#      Molecule1      Molecule2       DISTANCE
LGA    G     367      G     367          0.707
LGA    Q     368      Q     368          0.610
LGA    V     369      V     369          0.702

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3   90    4.0      3    0.67     3.333     3.333     0.387

LGA_LOCAL      RMSD =  0.675  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.675  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.675  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.551232 * X  +  -0.832928 * Y  +   0.048735 * Z  +  80.674194
  Y_new =   0.672562 * X  +  -0.478150 * Y  +  -0.564830 * Z  +  11.585428
  Z_new =   0.493765 * X  +  -0.278574 * Y  +   0.823767 * Z  + -10.507587 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.326098    2.815494  [ DEG:   -18.6841    161.3159 ]
  Theta =  -0.516414   -2.625178  [ DEG:   -29.5884   -150.4116 ]
  Phi   =   2.257375   -0.884218  [ DEG:   129.3380    -50.6620 ]
 
# 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: T0316AL316_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL316_5-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3   90   4.0    3   0.67   3.333     0.67
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL316_5-D3
REMARK Aligment from pdb entry: 1ni5_A
ATOM    869  N   GLY   367      28.170   1.611 -11.788  1.00  0.00              
ATOM    870  CA  GLY   367      28.960   0.385 -11.864  1.00  0.00              
ATOM    871  C   GLY   367      30.325   0.722 -12.462  1.00  0.00              
ATOM    872  O   GLY   367      31.381   0.334 -11.945  1.00  0.00              
ATOM    873  N   GLN   368      30.290   1.460 -13.559  1.00  0.00              
ATOM    874  CA  GLN   368      31.500   1.868 -14.233  1.00  0.00              
ATOM    875  C   GLN   368      32.300   2.716 -13.262  1.00  0.00              
ATOM    876  O   GLN   368      33.406   2.364 -12.876  1.00  0.00              
ATOM    877  N   VAL   369      31.707   3.819 -12.836  1.00  0.00              
ATOM    878  CA  VAL   369      32.354   4.752 -11.930  1.00  0.00              
ATOM    879  C   VAL   369      32.909   4.200 -10.637  1.00  0.00              
ATOM    880  O   VAL   369      33.855   4.769 -10.088  1.00  0.00              
END
