
#######################################################
#                                                     #
#                        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 T0356AL333_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   10 , name T0356_D3.pdb
# PARAMETERS: T0356AL333_1-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:    10       420 - 429         3.99     3.99
  LCS_AVERAGE:      8.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       420 - 426         1.37     7.53
  LCS_AVERAGE:      5.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       420 - 425         0.88     8.60
  LCS_AVERAGE:      4.33

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     R     420     R     420      6    7   10     2    5    6    6    7    7    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     M     421     M     421      6    7   10     3    5    6    6    7    7    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     D     422     D     422      6    7   10     3    5    6    6    7    7    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     P     423     P     423      6    7   10     3    4    6    6    7    7    7    7    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     A     424     A     424      6    7   10     3    5    6    6    7    7    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     R     425     R     425      6    7   10     3    5    6    6    7    7    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     D     426     D     426      4    7   10     4    4    4    6    7    7    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     T     427     T     427      4    5   10     4    4    4    5    5    6    7    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     V     428     V     428      4    5   10     4    4    4    5    5    6    6    8    9    9    9    9    9   10   10   10   10   10   10   10 
LCS_GDT     L     429     L     429      4    5   10     4    4    4    5    5    5    5    6    7    8    9    9    9   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   6.00  (   4.33    5.33    8.33 )

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      4      5      6      6      7      7      7      8      9      9      9      9      9     10     10     10     10     10     10     10 
GDT PERCENT_CA   3.33   4.17   5.00   5.00   5.83   5.83   5.83   6.67   7.50   7.50   7.50   7.50   7.50   8.33   8.33   8.33   8.33   8.33   8.33   8.33
GDT RMS_LOCAL    0.24   0.67   0.88   0.88   1.37   1.37   1.37   2.74   3.11   3.11   3.11   3.11   3.11   3.99   3.99   3.99   3.99   3.99   3.99   3.99
GDT RMS_ALL_CA   6.65   7.65   8.60   8.60   7.53   7.53   7.53   4.42   4.54   4.54   4.54   4.54   4.54   3.99   3.99   3.99   3.99   3.99   3.99   3.99

#      Molecule1      Molecule2       DISTANCE
LGA    R     420      R     420          2.472
LGA    M     421      M     421          1.592
LGA    D     422      D     422          1.808
LGA    P     423      P     423          5.864
LGA    A     424      A     424          3.660
LGA    R     425      R     425          1.531
LGA    D     426      D     426          3.487
LGA    T     427      T     427          2.395
LGA    V     428      V     428          3.786
LGA    L     429      L     429         10.052

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  120    4.0      8    2.74     6.042     6.059     0.282

LGA_LOCAL      RMSD =  2.736  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.420  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  3.993  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.677355 * X  +  -0.618000 * Y  +  -0.399082 * Z  + 241.260605
  Y_new =   0.092150 * X  +   0.466934 * Y  +  -0.879478 * Z  +  47.311779
  Z_new =   0.729862 * X  +  -0.632494 * Y  +  -0.259331 * Z  +  67.147102 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.959905    1.181688  [ DEG:  -112.2943     67.7057 ]
  Theta =  -0.818120   -2.323473  [ DEG:   -46.8748   -133.1252 ]
  Phi   =   3.006378   -0.135214  [ DEG:   172.2528     -7.7472 ]
 
# 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: T0356AL333_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_1-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  120   4.0    8   2.74   6.059     3.99
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_1-D3
REMARK Aligment from pdb entry: 1lwh_A
ATOM    161  N   ARG   420      39.411  63.670  56.340  1.00  0.00              
ATOM    162  CA  ARG   420      38.101  63.138  55.967  1.00  0.00              
ATOM    163  C   ARG   420      38.138  61.625  55.759  1.00  0.00              
ATOM    164  O   ARG   420      38.674  61.142  54.767  1.00  0.00              
ATOM    165  N   MET   421      37.563  60.888  56.703  1.00  0.00              
ATOM    166  CA  MET   421      37.513  59.435  56.644  1.00  0.00              
ATOM    167  C   MET   421      36.266  58.940  55.918  1.00  0.00              
ATOM    168  O   MET   421      35.241  58.695  56.564  1.00  0.00              
ATOM    169  N   ASP   422      36.365  58.780  54.594  1.00  0.00              
ATOM    170  CA  ASP   422      35.257  58.301  53.750  1.00  0.00              
ATOM    171  C   ASP   422      34.660  56.962  54.207  1.00  0.00              
ATOM    172  O   ASP   422      35.265  56.242  55.006  1.00  0.00              
ATOM    173  N   PRO   423      33.461  56.608  53.701  1.00  0.00              
ATOM    174  CA  PRO   423      32.808  55.347  54.076  1.00  0.00              
ATOM    175  C   PRO   423      33.522  54.119  53.516  1.00  0.00              
ATOM    176  O   PRO   423      33.706  54.018  52.296  1.00  0.00              
ATOM    177  N   ALA   424      33.915  53.202  54.409  1.00  0.00              
ATOM    178  CA  ALA   424      34.589  51.948  54.036  1.00  0.00              
ATOM    179  C   ALA   424      35.968  52.121  53.388  1.00  0.00              
ATOM    180  O   ALA   424      36.357  51.321  52.533  1.00  0.00              
ATOM    181  N   ARG   425      36.705  53.142  53.823  1.00  0.00              
ATOM    182  CA  ARG   425      38.020  53.461  53.264  1.00  0.00              
ATOM    183  C   ARG   425      39.157  53.589  54.279  1.00  0.00              
ATOM    184  O   ARG   425      38.922  53.766  55.480  1.00  0.00              
ATOM    185  N   ASP   426      40.391  53.494  53.783  1.00  0.00              
ATOM    186  CA  ASP   426      41.582  53.609  54.630  1.00  0.00              
ATOM    187  C   ASP   426      42.368  54.815  54.148  1.00  0.00              
ATOM    188  O   ASP   426      42.429  55.082  52.943  1.00  0.00              
ATOM    189  N   THR   427      42.948  55.546  55.092  1.00  0.00              
ATOM    190  CA  THR   427      43.724  56.728  54.760  1.00  0.00              
ATOM    191  C   THR   427      45.009  56.711  55.559  1.00  0.00              
ATOM    192  O   THR   427      45.003  56.340  56.734  1.00  0.00              
ATOM    193  N   VAL   428      46.111  57.099  54.925  1.00  0.00              
ATOM    194  CA  VAL   428      47.395  57.163  55.616  1.00  0.00              
ATOM    195  C   VAL   428      47.947  58.586  55.456  1.00  0.00              
ATOM    196  O   VAL   428      47.726  59.227  54.430  1.00  0.00              
ATOM    197  N   LEU   429      48.639  59.087  56.476  1.00  0.00              
ATOM    198  CA  LEU   429      49.190  60.444  56.435  1.00  0.00              
ATOM    199  C   LEU   429      50.454  60.494  57.267  1.00  0.00              
ATOM    200  O   LEU   429      51.527  60.687  56.669  1.00  0.00              
END
