
#######################################################
#                                                     #
#                        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 T0381AL333_3-D2
# Molecule2: number of CA atoms  176 ( 1314),  selected    3 , name T0381_D2.pdb
# PARAMETERS: T0381AL333_3-D2.T0381_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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       219 - 221         0.47     0.47
  LCS_AVERAGE:      1.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       219 - 221         0.47     0.47
  LCS_AVERAGE:      1.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       219 - 221         0.47     0.47
  LCS_AVERAGE:      1.70

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:  176
LCS_GDT     A     219     A     219      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     S     220     S     220      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     G     221     G     221      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   1.70  (   1.70    1.70    1.70 )

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      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70   1.70
GDT RMS_LOCAL    0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47
GDT RMS_ALL_CA   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47

#      Molecule1      Molecule2       DISTANCE
LGA    A     219      A     219          0.474
LGA    S     220      S     220          0.450
LGA    G     221      G     221          0.493

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  176    4.0      3    0.47     1.705     1.705     0.524

LGA_LOCAL      RMSD =  0.473  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.473  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.473  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.613660 * X  +  -0.747760 * Y  +   0.253526 * Z  +  35.274826
  Y_new =  -0.586415 * X  +   0.216621 * Y  +  -0.780508 * Z  +  64.184113
  Z_new =   0.528714 * X  +  -0.627638 * Y  +  -0.571430 * Z  +   6.614535 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.309352    0.832241  [ DEG:  -132.3161     47.6839 ]
  Theta =  -0.557084   -2.584508  [ DEG:   -31.9186   -148.0814 ]
  Phi   =  -2.378893    0.762699  [ DEG:  -136.3005     43.6995 ]
 
# 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: T0381AL333_3-D2                               
REMARK     2: T0381_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381AL333_3-D2.T0381_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  176   4.0    3   0.47   1.705     0.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL333_3-D2
REMARK Aligment from pdb entry: 1j5y_A
ATOM    237  N   ALA   219       7.863  30.063  16.015  1.00  0.00              
ATOM    238  CA  ALA   219       7.652  28.677  16.443  1.00  0.00              
ATOM    239  C   ALA   219       6.667  27.879  15.614  1.00  0.00              
ATOM    240  O   ALA   219       5.528  28.302  15.392  1.00  0.00              
ATOM    241  N   SER   220       7.096  26.724  15.129  1.00  0.00              
ATOM    242  CA  SER   220       6.156  25.899  14.401  1.00  0.00              
ATOM    243  C   SER   220       5.284  25.303  15.497  1.00  0.00              
ATOM    244  O   SER   220       5.005  25.962  16.503  1.00  0.00              
ATOM    245  N   GLY   221       4.867  24.055  15.329  1.00  0.00              
ATOM    246  CA  GLY   221       4.052  23.413  16.349  1.00  0.00              
ATOM    247  C   GLY   221       2.809  24.165  16.803  1.00  0.00              
ATOM    248  O   GLY   221       2.526  24.207  18.005  1.00  0.00              
END
