
#######################################################
#                                                     #
#                        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 T0356AL044_3-D3
# Molecule2: number of CA atoms  120 (  972),  selected    5 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_3-D3.T0356_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
  LONGEST_CONTINUOUS_SEGMENT:     5       349 - 355         3.53     3.53
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       349 - 351         1.37     6.68
  LONGEST_CONTINUOUS_SEGMENT:     3       350 - 353         1.42     4.61
  LONGEST_CONTINUOUS_SEGMENT:     3       351 - 355         1.79     5.54
  LCS_AVERAGE:      2.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LCS_AVERAGE:      0.00

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:  120
LCS_GDT     P     349     P     349      0    3    5     0    0    2    3    3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     E     350     E     350      0    3    5     0    1    2    3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     I     351     I     351      0    3    5     0    0    2    3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     353     D     353      0    3    5     0    1    2    3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     Y     355     Y     355      0    3    5     0    0    0    0    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.22  (   0.00    2.50    4.17 )

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      1      2      3      3      4      4      4      4      4      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   0.00   0.83   1.67   2.50   2.50   3.33   3.33   3.33   3.33   3.33   4.17   4.17   4.17   4.17   4.17   4.17   4.17   4.17   4.17   4.17
GDT RMS_LOCAL  1000.00  31.63  22.39   1.37   1.37   2.04   2.04   2.04   2.04   2.04   3.53   3.53   3.53   3.53   3.53   3.53   3.53   3.53   3.53   3.53
GDT RMS_ALL_CA 1000.00   3.53   6.68   6.68   6.68   4.43   4.43   4.43   4.43   4.43   3.53   3.53   3.53   3.53   3.53   3.53   3.53   3.53   3.53   3.53

#      Molecule1      Molecule2       DISTANCE
LGA    P     349      P     349          9.030
LGA    E     350      E     350          1.430
LGA    I     351      I     351          2.588
LGA    D     353      D     353          1.037
LGA    Y     355      Y     355          2.599

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  120    4.0      4    2.04     2.708     2.855     0.187

LGA_LOCAL      RMSD =  2.035  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.430  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  3.530  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.137486 * X  +   0.988514 * Y  +   0.062743 * Z  +   6.785665
  Y_new =   0.963313 * X  +  -0.118703 * Y  +  -0.240704 * Z  +  66.248100
  Z_new =  -0.230491 * X  +   0.093535 * Y  +  -0.968569 * Z  +  70.378319 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.045321   -0.096272  [ DEG:   174.4840     -5.5160 ]
  Theta =   0.232583    2.909010  [ DEG:    13.3260    166.6740 ]
  Phi   =   1.429031   -1.712561  [ DEG:    81.8775    -98.1225 ]
 
# 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: T0356AL044_3-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_3-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  120   4.0    4   2.04   2.855     3.53
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_3-D3
REMARK Aligment from pdb entry: 2bco_A
ATOM    125  N   PRO   349      49.715  69.443  56.697  1.00  0.00              
ATOM    126  CA  PRO   349      51.013  68.835  56.944  1.00  0.00              
ATOM    127  C   PRO   349      51.848  68.791  55.664  1.00  0.00              
ATOM    128  O   PRO   349      53.022  69.174  55.660  1.00  0.00              
ATOM    129  N   GLU   350      51.390  70.517  52.751  1.00  0.00              
ATOM    130  CA  GLU   350      51.634  71.793  52.098  1.00  0.00              
ATOM    131  C   GLU   350      52.149  72.928  52.950  1.00  0.00              
ATOM    132  O   GLU   350      52.538  73.963  52.415  1.00  0.00              
ATOM    133  N   ILE   351      53.805  72.077  56.286  1.00  0.00              
ATOM    134  CA  ILE   351      54.609  71.478  57.348  1.00  0.00              
ATOM    135  C   ILE   351      54.026  71.717  58.734  1.00  0.00              
ATOM    136  O   ILE   351      54.770  71.898  59.695  1.00  0.00              
ATOM    137  N   ASP   353      52.703  71.722  58.841  1.00  0.00              
ATOM    138  CA  ASP   353      52.073  71.957  60.134  1.00  0.00              
ATOM    139  C   ASP   353      52.076  70.690  60.985  1.00  0.00              
ATOM    140  O   ASP   353      52.015  69.585  60.462  1.00  0.00              
ATOM    141  N   TYR   355      52.171  70.863  62.298  1.00  0.00              
ATOM    142  CA  TYR   355      52.138  69.736  63.232  1.00  0.00              
ATOM    143  C   TYR   355      50.637  69.462  63.239  1.00  0.00              
ATOM    144  O   TYR   355      49.864  70.094  63.961  1.00  0.00              
END
