
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0356AL044_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   10 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_4-D2.T0356_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       303 - 309         4.18    17.54
  LCS_AVERAGE:      2.71

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       306 - 309         0.98    19.75
  LCS_AVERAGE:      0.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       306 - 309         0.98    19.75
  LCS_AVERAGE:      0.83

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:  192
LCS_GDT     V     303     V     303      0    0    6     0    1    3    3    3    4    4    5    5    5    5    5    6    6    6    7    7    8    8    8 
LCS_GDT     T     305     T     305      0    0    6     0    0    0    1    3    4    4    4    4    4    4    5    6    6    6    7    7    8    8    8 
LCS_GDT     V     306     V     306      4    4    6     3    3    4    4    4    4    4    5    5    5    5    5    6    6    6    7    7    8    8    8 
LCS_GDT     T     307     T     307      4    4    6     3    3    4    4    4    4    4    5    5    5    5    5    6    6    6    7    7    8    8    8 
LCS_GDT     H     308     H     308      4    4    6     3    3    4    4    4    4    4    5    5    5    5    5    6    6    6    7    7    8    8    8 
LCS_GDT     I     309     I     309      4    4    6     0    3    4    4    4    4    4    5    5    5    5    5    6    6    6    6    6    6    7    7 
LCS_GDT     T     310     T     310      0    0    4     0    0    0    1    2    3    4    4    4    4    4    4    4    4    4    5    5    5    5    6 
LCS_GDT     Q     311     Q     311      0    0    4     0    0    0    0    2    3    4    4    4    4    4    4    4    4    6    7    7    8    8    8 
LCS_GDT     R     312     R     312      0    0    4     1    1    3    3    3    4    4    4    4    4    5    5    5    6    6    7    7    8    8    8 
LCS_GDT     E     313     E     313      0    0    4     0    0    3    3    3    4    4    4    4    4    5    5    5    6    6    7    7    8    8    8 
LCS_AVERAGE  LCS_A:   1.46  (   0.83    0.83    2.71 )

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      4      4      4      4      4      5      5      5      5      5      6      6      6      7      7      8      8      8 
GDT PERCENT_CA   1.56   1.56   2.08   2.08   2.08   2.08   2.08   2.60   2.60   2.60   2.60   2.60   3.12   3.12   3.12   3.65   3.65   4.17   4.17   4.17
GDT RMS_LOCAL    0.03   0.03   0.98   0.98   0.98   0.98   0.98   2.53   2.53   2.53   2.53   2.53   4.18   4.18   4.18   5.47   5.47   6.19   6.19   6.19
GDT RMS_ALL_CA  21.52  21.52  19.75  19.75  19.75  19.75  19.75  18.46  18.46  18.46  18.46  18.46  17.54  17.54  17.54   8.28   8.28   7.89   7.89   7.89

#      Molecule1      Molecule2       DISTANCE
LGA    V     303      V     303          3.517
LGA    T     305      T     305          8.348
LGA    V     306      V     306          3.540
LGA    T     307      T     307          2.769
LGA    H     308      H     308          1.958
LGA    I     309      I     309          1.055
LGA    T     310      T     310         25.877
LGA    Q     311      Q     311         26.128
LGA    R     312      R     312         29.519
LGA    E     313      E     313         27.909

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  192    4.0      5    2.53     2.474     2.002     0.190

LGA_LOCAL      RMSD =  2.533  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.635  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  7.731  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.524549 * X  +   0.059099 * Y  +  -0.849327 * Z  + 163.419556
  Y_new =  -0.100473 * X  +  -0.994914 * Y  +  -0.007176 * Z  + 164.396301
  Z_new =  -0.845431 * X  +   0.081570 * Y  +   0.527819 * Z  + 136.653275 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.153329   -2.988263  [ DEG:     8.7851   -171.2149 ]
  Theta =   1.007372    2.134221  [ DEG:    57.7181    122.2819 ]
  Phi   =  -2.952343    0.189250  [ DEG:  -169.1568     10.8432 ]
 
# 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_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_4-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  192   4.0    5   2.53   2.002     7.73
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_4-D2
REMARK Aligment from pdb entry: 1yw6_A
ATOM      1  N   VAL   303      76.549  46.558  81.790  1.00  0.00              
ATOM      2  CA  VAL   303      76.420  47.031  83.153  1.00  0.00              
ATOM      3  C   VAL   303      77.778  47.084  83.845  1.00  0.00              
ATOM      4  O   VAL   303      78.062  48.056  84.529  1.00  0.00              
ATOM      5  N   THR   305      78.633  46.079  83.650  1.00  0.00              
ATOM      6  CA  THR   305      79.942  46.125  84.298  1.00  0.00              
ATOM      7  C   THR   305      80.612  47.423  83.887  1.00  0.00              
ATOM      8  O   THR   305      81.203  48.104  84.712  1.00  0.00              
ATOM      9  N   VAL   306      82.739  58.895  90.924  1.00  0.00              
ATOM     10  CA  VAL   306      82.757  59.009  92.363  1.00  0.00              
ATOM     11  C   VAL   306      84.129  59.456  92.819  1.00  0.00              
ATOM     12  O   VAL   306      84.250  60.246  93.747  1.00  0.00              
ATOM     13  N   THR   307      85.166  58.953  92.164  1.00  0.00              
ATOM     14  CA  THR   307      86.522  59.312  92.541  1.00  0.00              
ATOM     15  C   THR   307      86.854  60.728  92.108  1.00  0.00              
ATOM     16  O   THR   307      87.565  61.430  92.815  1.00  0.00              
ATOM     17  N   HIS   308      86.348  61.157  90.956  1.00  0.00              
ATOM     18  CA  HIS   308      86.610  62.524  90.539  1.00  0.00              
ATOM     19  C   HIS   308      85.864  63.409  91.521  1.00  0.00              
ATOM     20  O   HIS   308      86.437  64.298  92.138  1.00  0.00              
ATOM     21  N   ILE   309      84.574  63.157  91.674  1.00  0.00              
ATOM     22  CA  ILE   309      83.787  63.971  92.571  1.00  0.00              
ATOM     23  C   ILE   309      84.467  64.155  93.904  1.00  0.00              
ATOM     24  O   ILE   309      84.935  65.234  94.219  1.00  0.00              
ATOM     25  N   THR   310      66.919  51.783 106.277  1.00  0.00              
ATOM     26  CA  THR   310      68.197  52.041 105.642  1.00  0.00              
ATOM     27  C   THR   310      69.209  50.940 105.914  1.00  0.00              
ATOM     28  O   THR   310      69.244  50.343 106.991  1.00  0.00              
ATOM     29  N   GLN   311      70.044  50.670 104.924  1.00  0.00              
ATOM     30  CA  GLN   311      71.061  49.641 105.037  1.00  0.00              
ATOM     31  C   GLN   311      72.405  50.332 104.829  1.00  0.00              
ATOM     32  O   GLN   311      72.607  51.011 103.816  1.00  0.00              
ATOM     33  N   ARG   312      79.591  47.835 105.474  1.00  0.00              
ATOM     34  CA  ARG   312      80.476  47.433 106.552  1.00  0.00              
ATOM     35  C   ARG   312      81.478  48.569 106.648  1.00  0.00              
ATOM     36  O   ARG   312      82.045  48.980 105.636  1.00  0.00              
ATOM     37  N   GLU   313      81.681  49.100 107.846  1.00  0.00              
ATOM     38  CA  GLU   313      82.637  50.197 108.013  1.00  0.00              
ATOM     39  C   GLU   313      83.718  49.826 109.027  1.00  0.00              
ATOM     40  O   GLU   313      83.456  49.111 109.986  1.00  0.00              
END
