
#######################################################
#                                                     #
#                        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    5 (   20),  selected    5 , name T0299AL243_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected    5 , name T0299_D2.pdb
# PARAMETERS: T0299AL243_4-D2.T0299_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:     5        79 - 83          1.23     1.23
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        79 - 83          1.23     1.23
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        79 - 82          0.49     1.83
  LCS_AVERAGE:      4.27

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:   89
LCS_GDT     L      79     L      79      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     E      80     E      80      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D      81     D      81      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F      82     F      82      4    5    5     3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     E      83     E      83      3    5    5     0    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.17  (   4.27    5.62    5.62 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   3.37   4.49   4.49   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62
GDT RMS_LOCAL    0.06   0.49   0.49   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23
GDT RMS_ALL_CA   1.48   1.83   1.83   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23   1.23

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79          0.784
LGA    E      80      E      80          1.765
LGA    D      81      D      81          0.315
LGA    F      82      F      82          0.782
LGA    E      83      E      83          1.763

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   89    4.0      5    1.23     5.337     5.445     0.376

LGA_LOCAL      RMSD =  1.229  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.229  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.229  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.487060 * X  +  -0.815941 * Y  +  -0.311467 * Z  +  20.750843
  Y_new =  -0.715527 * X  +  -0.168306 * Y  +  -0.678008 * Z  + 119.517632
  Z_new =   0.500793 * X  +   0.553094 * Y  +  -0.665803 * Z  +   3.987880 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.448400   -0.693192  [ DEG:   140.2830    -39.7170 ]
  Theta =  -0.524515   -2.617078  [ DEG:   -30.0525   -149.9475 ]
  Phi   =  -0.973140    2.168453  [ DEG:   -55.7568    124.2432 ]
 
# 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: T0299AL243_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_4-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   89   4.0    5   1.23   5.445     1.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_4-D2
REMARK Aligment from pdb entry: 1cbkA
ATOM    281  N   LEU    79     -10.206  57.371  -6.644  1.00  0.00              
ATOM    282  CA  LEU    79     -10.984  56.983  -5.459  1.00  0.00              
ATOM    283  C   LEU    79     -10.999  58.075  -4.394  1.00  0.00              
ATOM    284  O   LEU    79     -10.634  59.208  -4.677  1.00  0.00              
ATOM    285  N   GLU    80     -11.371  57.729  -3.165  1.00  0.00              
ATOM    286  CA  GLU    80     -11.452  58.703  -2.065  1.00  0.00              
ATOM    287  C   GLU    80     -10.163  59.434  -1.712  1.00  0.00              
ATOM    288  O   GLU    80     -10.203  60.603  -1.328  1.00  0.00              
ATOM    289  N   ASP    81      -9.038  58.723  -1.818  1.00  0.00              
ATOM    290  CA  ASP    81      -7.725  59.270  -1.493  1.00  0.00              
ATOM    291  C   ASP    81      -6.805  59.539  -2.684  1.00  0.00              
ATOM    292  O   ASP    81      -5.865  60.326  -2.566  1.00  0.00              
ATOM    293  N   PHE    82      -7.065  58.907  -3.828  1.00  0.00              
ATOM    294  CA  PHE    82      -6.200  59.091  -4.998  1.00  0.00              
ATOM    295  C   PHE    82      -6.888  59.567  -6.270  1.00  0.00              
ATOM    296  O   PHE    82      -8.013  59.200  -6.541  1.00  0.00              
ATOM    297  N   GLU    83      -6.132  60.308  -7.073  1.00  0.00              
ATOM    298  CA  GLU    83      -6.568  60.856  -8.353  1.00  0.00              
ATOM    299  C   GLU    83      -5.339  60.657  -9.238  1.00  0.00              
ATOM    300  O   GLU    83      -4.475  61.536  -9.319  1.00  0.00              
END
