
#######################################################
#                                                     #
#                        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   23 (   92),  selected   23 , name T0386AL257_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   23 , name T0386_D2.pdb
# PARAMETERS: T0386AL257_1-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:    16       239 - 254         4.92    10.17
  LCS_AVERAGE:     17.23

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       239 - 244         1.27    14.70
  LONGEST_CONTINUOUS_SEGMENT:     6       249 - 254         1.86    14.43
  LCS_AVERAGE:      6.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       240 - 244         0.90    14.56
  LCS_AVERAGE:      4.67

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    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3   13   13   14   14 
LCS_GDT     P     220     P     220      3    3    3     3    3    3    3    3    3    3    3    3    8    9    9   10   11   11   11   13   13   14   14 
LCS_GDT     E     221     E     221      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3   13   13   13   14 
LCS_GDT     N     235     N     235      4    5   14     3    4    4    5    5    5    8    8    9   10   13   13   15   16   17   18   19   20   20   20 
LCS_GDT     T     236     T     236      4    5   14     3    4    4    5    5    6    8    8    9    9   13   13   15   16   17   18   19   20   20   20 
LCS_GDT     G     237     G     237      4    5   14     3    4    4    5    5    5    6    8    9    9   13   13   13   15   16   18   19   20   20   20 
LCS_GDT     R     238     R     238      4    5   14     3    4    4    5    5    6    8    8    9   10   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     N     239     N     239      3    6   16     3    3    4    6    6    6    8    8    9   10   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     V     240     V     240      5    6   16     4    4    5    6    6    6    8    8    9   12   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     N     241     N     241      5    6   16     4    4    5    6    6    6    8    8    9   10   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     D     242     D     242      5    6   16     4    4    5    6    6    6    8    8    9   10   13   13   15   15   16   18   19   20   20   20 
LCS_GDT     R     243     R     243      5    6   16     4    4    5    6    6    6    8    8    9   10   13   13   15   16   17   18   19   20   20   20 
LCS_GDT     P     244     P     244      5    6   16     1    3    5    6    6    6    7    8    9   12   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     V     245     V     245      3    3   16     0    3    3    3    4    4    7    8   10   12   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     M     246     M     246      3    3   16     0    3    3    4    5    5    7    9   10   12   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     V     247     V     247      3    3   16     1    3    3    3    5    5    7    9   10   12   13   14   15   16   17   18   19   20   20   20 
LCS_GDT     A     248     A     248      3    3   16     1    3    3    3    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_GDT     K     249     K     249      4    6   16     3    4    4    4    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_GDT     E     250     E     250      4    6   16     3    4    4    4    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_GDT     G     251     G     251      4    6   16     3    4    4    4    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_GDT     E     252     E     252      4    6   16     3    4    4    4    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_GDT     T     253     T     253      3    6   16     3    3    4    4    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_GDT     Y     254     Y     254      3    6   16     3    3    4    4    5    6    7    9   10   12   12   14   15   16   17   18   19   20   20   20 
LCS_AVERAGE  LCS_A:   9.32  (   4.67    6.07   17.23 )

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      4      5      6      6      6      8      9     10     12     13     14     15     16     17     18     19     20     20     20 
GDT PERCENT_CA   4.94   4.94   6.17   7.41   7.41   7.41   9.88  11.11  12.35  14.81  16.05  17.28  18.52  19.75  20.99  22.22  23.46  24.69  24.69  24.69
GDT RMS_LOCAL    0.10   0.10   0.90   1.27   1.27   1.27   2.87   3.04   3.29   3.84   4.35   4.32   4.50   4.73   5.12   5.33   5.56   5.88   5.88   5.88
GDT RMS_ALL_CA  14.66  14.66  14.56  14.70  14.70  14.70  14.32   9.61   9.47   9.34  12.20   9.49   9.46   9.72   9.43   9.49   9.52   9.72   9.72   9.72

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219         15.066
LGA    P     220      P     220         14.872
LGA    E     221      E     221         16.048
LGA    N     235      N     235         15.739
LGA    T     236      T     236         13.356
LGA    G     237      G     237         14.612
LGA    R     238      R     238          9.228
LGA    N     239      N     239          9.610
LGA    V     240      V     240          8.727
LGA    N     241      N     241          7.539
LGA    D     242      D     242         11.268
LGA    R     243      R     243         10.973
LGA    P     244      P     244          7.028
LGA    V     245      V     245          4.726
LGA    M     246      M     246          3.963
LGA    V     247      V     247          3.002
LGA    A     248      A     248          3.597
LGA    K     249      K     249          3.944
LGA    E     250      E     250          3.055
LGA    G     251      G     251          3.160
LGA    E     252      E     252          1.731
LGA    T     253      T     253          3.134
LGA    Y     254      Y     254          0.701

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   81    4.0      9    3.04    11.420    10.034     0.287

LGA_LOCAL      RMSD =  3.040  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.466  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  8.619  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.417427 * X  +   0.758618 * Y  +  -0.500253 * Z  + -20.852043
  Y_new =  -0.507567 * X  +  -0.261981 * Y  +  -0.820817 * Z  +  64.193512
  Z_new =  -0.753744 * X  +   0.596544 * Y  +   0.275692 * Z  +  27.991699 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.137886   -2.003707  [ DEG:    65.1961   -114.8039 ]
  Theta =   0.853741    2.287852  [ DEG:    48.9157    131.0843 ]
  Phi   =  -0.882541    2.259052  [ DEG:   -50.5658    129.4342 ]
 
# 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: T0386AL257_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL257_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   81   4.0    9   3.04  10.034     8.62
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL257_1-D2
REMARK Aligment from pdb entry: 2f6s_A
ATOM    621  N   ASN   219       5.061  69.210  70.085  1.00  0.00              
ATOM    622  CA  ASN   219       5.007  69.525  68.650  1.00  0.00              
ATOM    623  C   ASN   219       6.381  69.459  67.980  1.00  0.00              
ATOM    624  O   ASN   219       6.487  69.462  66.759  1.00  0.00              
ATOM    625  N   PRO   220       7.421  69.377  68.795  1.00  0.00              
ATOM    626  CA  PRO   220       8.785  69.376  68.317  1.00  0.00              
ATOM    627  C   PRO   220       9.226  67.990  67.843  1.00  0.00              
ATOM    628  O   PRO   220      10.164  67.392  68.384  1.00  0.00              
ATOM    629  N   GLU   221       8.565  67.500  66.805  1.00  0.00              
ATOM    630  CA  GLU   221       8.646  66.082  66.447  1.00  0.00              
ATOM    631  C   GLU   221       9.947  65.682  65.764  1.00  0.00              
ATOM    632  O   GLU   221      10.174  64.496  65.495  1.00  0.00              
ATOM    633  N   ASN   235      10.788  66.669  65.472  1.00  0.00              
ATOM    634  CA  ASN   235      11.940  66.449  64.613  1.00  0.00              
ATOM    635  C   ASN   235      13.277  66.751  65.273  1.00  0.00              
ATOM    636  O   ASN   235      14.320  66.404  64.720  1.00  0.00              
ATOM    637  N   THR   236      13.251  67.401  66.437  1.00  0.00              
ATOM    638  CA  THR   236      14.474  67.673  67.175  1.00  0.00              
ATOM    639  C   THR   236      15.194  66.368  67.584  1.00  0.00              
ATOM    640  O   THR   236      14.657  65.584  68.394  1.00  0.00              
ATOM    641  N   GLY   237      16.408  66.115  67.030  1.00  0.00              
ATOM    642  CA  GLY   237      16.964  64.792  67.369  1.00  0.00              
ATOM    643  C   GLY   237      17.462  64.704  68.829  1.00  0.00              
ATOM    644  O   GLY   237      17.495  63.595  69.379  1.00  0.00              
ATOM    645  N   ARG   238      17.794  65.838  69.463  1.00  0.00              
ATOM    646  CA  ARG   238      18.114  65.822  70.905  1.00  0.00              
ATOM    647  C   ARG   238      16.908  65.314  71.721  1.00  0.00              
ATOM    648  O   ARG   238      17.033  64.386  72.537  1.00  0.00              
ATOM    649  N   ASN   239      15.744  65.915  71.472  1.00  0.00              
ATOM    650  CA  ASN   239      14.482  65.513  72.088  1.00  0.00              
ATOM    651  C   ASN   239      14.191  64.024  71.851  1.00  0.00              
ATOM    652  O   ASN   239      13.778  63.312  72.762  1.00  0.00              
ATOM    653  N   VAL   240      14.434  63.571  70.627  1.00  0.00              
ATOM    654  CA  VAL   240      14.160  62.203  70.240  1.00  0.00              
ATOM    655  C   VAL   240      15.097  61.223  70.946  1.00  0.00              
ATOM    656  O   VAL   240      14.660  60.176  71.422  1.00  0.00              
ATOM    657  N   ASN   241      16.373  61.579  71.038  1.00  0.00              
ATOM    658  CA  ASN   241      17.360  60.746  71.720  1.00  0.00              
ATOM    659  C   ASN   241      17.070  60.659  73.225  1.00  0.00              
ATOM    660  O   ASN   241      17.104  59.569  73.794  1.00  0.00              
ATOM    661  N   ASP   242      16.769  61.795  73.854  1.00  0.00              
ATOM    662  CA  ASP   242      16.318  61.802  75.246  1.00  0.00              
ATOM    663  C   ASP   242      15.119  60.884  75.456  1.00  0.00              
ATOM    664  O   ASP   242      15.058  60.144  76.442  1.00  0.00              
ATOM    665  N   ARG   243      14.184  60.923  74.512  1.00  0.00              
ATOM    666  CA  ARG   243      13.025  60.068  74.528  1.00  0.00              
ATOM    667  C   ARG   243      13.377  58.594  74.476  1.00  0.00              
ATOM    668  O   ARG   243      12.874  57.793  75.284  1.00  0.00              
ATOM    669  N   PRO   244      14.242  58.221  73.538  1.00  0.00              
ATOM    670  CA  PRO   244      14.574  56.815  73.356  1.00  0.00              
ATOM    671  C   PRO   244      15.424  56.298  74.504  1.00  0.00              
ATOM    672  O   PRO   244      15.279  55.156  74.900  1.00  0.00              
ATOM    673  N   VAL   245      16.295  57.144  75.053  1.00  0.00              
ATOM    674  CA  VAL   245      17.079  56.784  76.222  1.00  0.00              
ATOM    675  C   VAL   245      16.134  56.430  77.378  1.00  0.00              
ATOM    676  O   VAL   245      16.374  55.481  78.110  1.00  0.00              
ATOM    677  N   MET   246      15.051  57.181  77.533  1.00  0.00              
ATOM    678  CA  MET   246      14.111  56.924  78.608  1.00  0.00              
ATOM    679  C   MET   246      13.351  55.629  78.341  1.00  0.00              
ATOM    680  O   MET   246      13.127  54.831  79.261  1.00  0.00              
ATOM    681  N   VAL   247      12.977  55.414  77.077  1.00  0.00              
ATOM    682  CA  VAL   247      12.312  54.191  76.683  1.00  0.00              
ATOM    683  C   VAL   247      13.148  52.975  77.113  1.00  0.00              
ATOM    684  O   VAL   247      12.615  52.016  77.672  1.00  0.00              
ATOM    685  N   ALA   248      14.456  53.024  76.854  1.00  0.00              
ATOM    686  CA  ALA   248      15.367  51.942  77.247  1.00  0.00              
ATOM    687  C   ALA   248      15.544  51.863  78.759  1.00  0.00              
ATOM    688  O   ALA   248      15.736  50.778  79.321  1.00  0.00              
ATOM    689  N   LYS   249      15.452  53.019  79.410  1.00  0.00              
ATOM    690  CA  LYS   249      15.490  53.069  80.849  1.00  0.00              
ATOM    691  C   LYS   249      14.306  52.342  81.483  1.00  0.00              
ATOM    692  O   LYS   249      14.445  51.783  82.575  1.00  0.00              
ATOM    693  N   GLU   250      13.151  52.352  80.796  1.00  0.00              
ATOM    694  CA  GLU   250      11.938  51.708  81.287  1.00  0.00              
ATOM    695  C   GLU   250      12.168  50.201  81.421  1.00  0.00              
ATOM    696  O   GLU   250      11.527  49.545  82.229  1.00  0.00              
ATOM    697  N   GLY   251      13.069  49.673  80.588  1.00  0.00              
ATOM    698  CA  GLY   251      13.401  48.265  80.558  1.00  0.00              
ATOM    699  C   GLY   251      14.565  47.922  81.497  1.00  0.00              
ATOM    700  O   GLY   251      15.030  46.780  81.507  1.00  0.00              
ATOM    701  N   GLU   252      15.043  48.904  82.273  1.00  0.00              
ATOM    702  CA  GLU   252      16.121  48.685  83.242  1.00  0.00              
ATOM    703  C   GLU   252      17.541  49.034  82.803  1.00  0.00              
ATOM    704  O   GLU   252      18.509  48.670  83.476  1.00  0.00              
ATOM    705  N   THR   253      17.684  49.733  81.678  1.00  0.00              
ATOM    706  CA  THR   253      19.003  50.192  81.237  1.00  0.00              
ATOM    707  C   THR   253      19.340  51.537  81.882  1.00  0.00              
ATOM    708  O   THR   253      18.648  52.530  81.647  1.00  0.00              
ATOM    709  N   TYR   254      20.404  51.564  82.691  1.00  0.00              
ATOM    710  CA  TYR   254      20.733  52.732  83.517  1.00  0.00              
ATOM    711  C   TYR   254      22.026  53.409  83.104  1.00  0.00              
ATOM    712  O   TYR   254      22.080  54.096  82.078  1.00  0.00              
END
