
#######################################################
#                                                     #
#                        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    6 (   24),  selected    6 , name T0386AL333_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected    6 , name T0386_D2.pdb
# PARAMETERS: T0386AL333_2-D2.T0386_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
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         2.86     2.86
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       221 - 224         0.75     4.74
  LCS_AVERAGE:      4.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       221 - 224         0.75     4.74
  LCS_AVERAGE:      4.53

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:   81
LCS_GDT     N     219     N     219      3    3    6     0    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     P     220     P     220      3    3    6     3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     E     221     E     221      4    4    6     3    4    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     K     222     K     222      4    4    6     3    4    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     223     I     223      4    4    6     3    4    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     R     224     R     224      4    4    6     3    4    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   5.49  (   4.53    4.53    7.41 )

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      4      4      4      4      4      5      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   3.70   4.94   4.94   4.94   4.94   4.94   6.17   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41
GDT RMS_LOCAL    0.05   0.75   0.75   0.75   0.75   0.75   2.40   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86
GDT RMS_ALL_CA   4.73   4.74   4.74   4.74   4.74   4.74   3.02   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          3.478
LGA    P     220      P     220          2.921
LGA    E     221      E     221          3.945
LGA    K     222      K     222          1.389
LGA    I     223      I     223          2.575
LGA    R     224      R     224          2.093

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   81    4.0      6    2.86     6.173     5.750     0.203

LGA_LOCAL      RMSD =  2.862  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.862  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.862  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.403819 * X  +  -0.560834 * Y  +  -0.722769 * Z  +  22.771679
  Y_new =   0.229276 * X  +   0.826880 * Y  +  -0.513520 * Z  +  33.799068
  Z_new =   0.885643 * X  +   0.041655 * Y  +   0.462495 * Z  +  40.690296 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.089824   -3.051769  [ DEG:     5.1465   -174.8535 ]
  Theta =  -1.087876   -2.053717  [ DEG:   -62.3307   -117.6693 ]
  Phi   =   0.516383   -2.625210  [ DEG:    29.5866   -150.4134 ]
 
# 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: T0386AL333_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL333_2-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   81   4.0    6   2.86   5.750     2.86
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL333_2-D2
REMARK Aligment from pdb entry: 1oe0_A
ATOM    705  N   ASN   219      -0.291  52.154  75.470  1.00  0.00              
ATOM    706  CA  ASN   219       0.622  53.195  75.015  1.00  0.00              
ATOM    707  C   ASN   219       0.453  54.484  75.813  1.00  0.00              
ATOM    708  O   ASN   219      -0.659  54.944  76.029  1.00  0.00              
ATOM    709  N   PRO   220       1.567  55.055  76.252  1.00  0.00              
ATOM    710  CA  PRO   220       1.556  56.295  77.018  1.00  0.00              
ATOM    711  C   PRO   220       2.482  57.314  76.372  1.00  0.00              
ATOM    712  O   PRO   220       3.613  56.989  76.008  1.00  0.00              
ATOM    713  N   GLU   221       2.006  58.544  76.219  1.00  0.00              
ATOM    714  CA  GLU   221       2.829  59.590  75.629  1.00  0.00              
ATOM    715  C   GLU   221       3.843  60.010  76.686  1.00  0.00              
ATOM    716  O   GLU   221       3.511  60.726  77.626  1.00  0.00              
ATOM    717  N   LYS   222       5.082  59.556  76.529  1.00  0.00              
ATOM    718  CA  LYS   222       6.127  59.862  77.490  1.00  0.00              
ATOM    719  C   LYS   222       6.938  61.106  77.166  1.00  0.00              
ATOM    720  O   LYS   222       8.087  61.223  77.582  1.00  0.00              
ATOM    721  N   ILE   223       6.346  62.032  76.419  1.00  0.00              
ATOM    722  CA  ILE   223       7.029  63.280  76.085  1.00  0.00              
ATOM    723  C   ILE   223       6.665  64.323  77.141  1.00  0.00              
ATOM    724  O   ILE   223       6.506  65.505  76.835  1.00  0.00              
ATOM    725  N   ARG   224       6.540  63.866  78.385  1.00  0.00              
ATOM    726  CA  ARG   224       6.181  64.722  79.510  1.00  0.00              
ATOM    727  C   ARG   224       4.803  65.339  79.289  1.00  0.00              
ATOM    728  O   ARG   224       4.720  66.585  79.201  1.00  0.00              
END
