
#######################################################
#                                                     #
#                        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   20 (   80),  selected   20 , name T0316AL316_5-D2
# Molecule2: number of CA atoms   60 (  457),  selected   20 , name T0316_D2.pdb
# PARAMETERS: T0316AL316_5-D2.T0316_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:    13       224 - 236         4.99     9.08
  LONGEST_CONTINUOUS_SEGMENT:    13       226 - 238         4.93     8.65
  LONGEST_CONTINUOUS_SEGMENT:    13       227 - 239         4.87     8.98
  LCS_AVERAGE:     20.83

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       234 - 239         1.88    15.13
  LCS_AVERAGE:      7.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       235 - 239         0.59    17.75
  LCS_AVERAGE:      6.17

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:   60
LCS_GDT     G     220     G     220      3    3   10     0    3    3    3    3    3    4    4    7    8    9    9    9    9   11   11   11   12   12   12 
LCS_GDT     R     221     R     221      3    3   10     0    3    3    3    3    3    6    6    7    8    9    9    9    9   11   11   11   12   12   12 
LCS_GDT     M     222     M     222      3    3   10     1    3    3    3    3    4    6    6    7    8    9    9    9    9   11   11   11   12   13   15 
LCS_GDT     M     223     M     223      3    4   12     0    3    3    3    4    5    6    6    7    8    9    9   11   14   16   17   17   17   17   17 
LCS_GDT     T     224     T     224      4    4   13     4    4    4    4    5    5    6    6    8    9   10   14   15   16   16   17   17   17   17   17 
LCS_GDT     V     225     V     225      4    4   13     4    4    4    4    4    5    6    6    8    9   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     D     226     D     226      4    4   13     4    4    4    4    4    5    6    6    8    9   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     G     227     G     227      4    4   13     4    4    4    4    4    5    6    6    8    9   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     R     228     R     228      3    3   13     3    3    4    4    4    4    6    6    7   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     D     229     D     229      3    4   13     3    3    4    4    5    5    7    8    9   10   11   13   15   16   16   17   17   17   17   17 
LCS_GDT     M     230     M     230      3    4   13     3    3    4    4    5    5    6    6    7   10   10   14   15   16   16   17   17   17   17   17 
LCS_GDT     G     231     G     231      3    4   13     3    3    3    3    5    5    7    7    9   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     E     232     E     232      3    4   13     0    3    3    3    5    7    7    8    9   10   11   13   14   16   16   17   17   17   17   17 
LCS_GDT     H     233     H     233      3    4   13     3    4    4    4    4    7    7    8    9   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     A     234     A     234      3    6   13     3    4    4    5    5    7    7    8    9   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     G     235     G     235      5    6   13     3    5    5    5    5    6    6    7    8   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     L     236     L     236      5    6   13     3    5    5    5    5    7    7    8    9   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     M     237     M     237      5    6   13     3    5    5    5    5    7    7    8    9   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     Y     238     Y     238      5    6   13     3    5    5    5    5    7    7    8    9   10   11   14   15   16   16   17   17   17   17   17 
LCS_GDT     Y     239     Y     239      5    6   13     3    5    5    5    5    7    7    8    9   10   10   14   15   16   16   17   17   17   17   17 
LCS_AVERAGE  LCS_A:  11.44  (   6.17    7.33   20.83 )

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      5      5      5      7      7      8      9     10     11     14     15     16     16     17     17     17     17     17 
GDT PERCENT_CA   6.67   8.33   8.33   8.33   8.33  11.67  11.67  13.33  15.00  16.67  18.33  23.33  25.00  26.67  26.67  28.33  28.33  28.33  28.33  28.33
GDT RMS_LOCAL    0.17   0.59   0.59   0.59   0.59   2.17   2.17   3.10   3.22   3.52   4.74   4.97   5.12   5.38   5.38   5.60   5.60   5.60   5.60   5.60
GDT RMS_ALL_CA  18.43  17.75  17.75  17.75  17.75  13.06  13.06  10.78  10.48  10.44   8.65   8.64   8.64   8.57   8.57   8.44   8.44   8.44   8.44   8.44

#      Molecule1      Molecule2       DISTANCE
LGA    G     220      G     220         18.966
LGA    R     221      R     221         15.315
LGA    M     222      M     222         13.766
LGA    M     223      M     223         13.622
LGA    T     224      T     224         15.049
LGA    V     225      V     225         14.445
LGA    D     226      D     226         13.698
LGA    G     227      G     227         13.402
LGA    R     228      R     228          9.488
LGA    D     229      D     229          3.896
LGA    M     230      M     230          7.510
LGA    G     231      G     231          4.301
LGA    E     232      E     232          3.734
LGA    H     233      H     233          3.186
LGA    A     234      A     234          2.547
LGA    G     235      G     235          4.984
LGA    L     236      L     236          3.925
LGA    M     237      M     237          3.572
LGA    Y     238      Y     238          2.608
LGA    Y     239      Y     239          3.015

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   60    4.0      8    3.10    14.583    12.623     0.250

LGA_LOCAL      RMSD =  3.101  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.127  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  7.904  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.660810 * X  +   0.306538 * Y  +  -0.685102 * Z  +  38.930660
  Y_new =   0.402142 * X  +  -0.626115 * Y  +  -0.668029 * Z  +  47.730690
  Z_new =  -0.633728 * X  +  -0.716948 * Y  +   0.290471 * Z  +  36.725544 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.185859    1.955734  [ DEG:   -67.9447    112.0553 ]
  Theta =   0.686363    2.455229  [ DEG:    39.3257    140.6743 ]
  Phi   =   2.594903   -0.546689  [ DEG:   148.6770    -31.3230 ]
 
# 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: T0316AL316_5-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL316_5-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20   60   4.0    8   3.10  12.623     7.90
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL316_5-D2
REMARK Aligment from pdb entry: 1ni5_A
ATOM    789  N   GLY   220      46.009  22.940 -41.284  1.00  0.00              
ATOM    790  CA  GLY   220      46.324  22.643 -39.893  1.00  0.00              
ATOM    791  C   GLY   220      45.070  22.654 -39.011  1.00  0.00              
ATOM    792  O   GLY   220      45.135  22.950 -37.816  1.00  0.00              
ATOM    793  N   ARG   221      43.930  22.317 -39.596  1.00  0.00              
ATOM    794  CA  ARG   221      42.696  22.309 -38.834  1.00  0.00              
ATOM    795  C   ARG   221      42.799  21.449 -37.586  1.00  0.00              
ATOM    796  O   ARG   221      42.423  21.876 -36.495  1.00  0.00              
ATOM    797  N   MET   222      43.299  20.231 -37.749  1.00  0.00              
ATOM    798  CA  MET   222      43.415  19.324 -36.617  1.00  0.00              
ATOM    799  C   MET   222      44.299  19.880 -35.502  1.00  0.00              
ATOM    800  O   MET   222      44.121  19.539 -34.334  1.00  0.00              
ATOM    801  N   MET   223      45.246  20.737 -35.862  1.00  0.00              
ATOM    802  CA  MET   223      46.146  21.318 -34.882  1.00  0.00              
ATOM    803  C   MET   223      45.407  22.400 -34.096  1.00  0.00              
ATOM    804  O   MET   223      45.575  22.535 -32.884  1.00  0.00              
ATOM    805  N   THR   224      44.575  23.159 -34.794  1.00  0.00              
ATOM    806  CA  THR   224      43.802  24.222 -34.167  1.00  0.00              
ATOM    807  C   THR   224      42.816  23.649 -33.152  1.00  0.00              
ATOM    808  O   THR   224      42.551  24.256 -32.111  1.00  0.00              
ATOM    809  N   VAL   225      42.282  22.473 -33.467  1.00  0.00              
ATOM    810  CA  VAL   225      41.304  21.806 -32.624  1.00  0.00              
ATOM    811  C   VAL   225      41.878  21.321 -31.303  1.00  0.00              
ATOM    812  O   VAL   225      41.209  21.383 -30.273  1.00  0.00              
ATOM    813  N   ASP   226      43.116  20.841 -31.332  1.00  0.00              
ATOM    814  CA  ASP   226      43.775  20.377 -30.112  1.00  0.00              
ATOM    815  C   ASP   226      44.000  21.611 -29.257  1.00  0.00              
ATOM    816  O   ASP   226      43.927  21.560 -28.029  1.00  0.00              
ATOM    817  N   GLY   227      44.271  22.721 -29.931  1.00  0.00              
ATOM    818  CA  GLY   227      44.492  23.988 -29.263  1.00  0.00              
ATOM    819  C   GLY   227      43.219  24.352 -28.513  1.00  0.00              
ATOM    820  O   GLY   227      43.270  24.706 -27.334  1.00  0.00              
ATOM    821  N   ARG   228      42.074  24.261 -29.185  1.00  0.00              
ATOM    822  CA  ARG   228      40.815  24.573 -28.522  1.00  0.00              
ATOM    823  C   ARG   228      40.569  23.590 -27.382  1.00  0.00              
ATOM    824  O   ARG   228      40.194  23.986 -26.277  1.00  0.00              
ATOM    825  N   ASP   229      40.770  22.304 -27.644  1.00  0.00              
ATOM    826  CA  ASP   229      40.557  21.317 -26.603  1.00  0.00              
ATOM    827  C   ASP   229      41.372  21.734 -25.393  1.00  0.00              
ATOM    828  O   ASP   229      40.857  21.807 -24.280  1.00  0.00              
ATOM    829  N   MET   230      42.644  22.037 -25.625  1.00  0.00              
ATOM    830  CA  MET   230      43.540  22.420 -24.549  1.00  0.00              
ATOM    831  C   MET   230      43.044  23.620 -23.780  1.00  0.00              
ATOM    832  O   MET   230      43.169  23.671 -22.556  1.00  0.00              
ATOM    833  N   GLY   231      42.484  24.594 -24.486  1.00  0.00              
ATOM    834  CA  GLY   231      41.991  25.796 -23.822  1.00  0.00              
ATOM    835  C   GLY   231      40.754  25.509 -22.972  1.00  0.00              
ATOM    836  O   GLY   231      40.572  26.106 -21.909  1.00  0.00              
ATOM    837  N   GLU   232      39.908  24.597 -23.438  1.00  0.00              
ATOM    838  CA  GLU   232      38.727  24.243 -22.685  1.00  0.00              
ATOM    839  C   GLU   232      39.194  23.607 -21.399  1.00  0.00              
ATOM    840  O   GLU   232      38.655  23.880 -20.325  1.00  0.00              
ATOM    841  N   HIS   233      40.203  22.755 -21.510  1.00  0.00              
ATOM    842  CA  HIS   233      40.750  22.086 -20.344  1.00  0.00              
ATOM    843  C   HIS   233      41.316  23.116 -19.361  1.00  0.00              
ATOM    844  O   HIS   233      41.025  23.057 -18.169  1.00  0.00              
ATOM    845  N   ALA   234      42.105  24.067 -19.849  1.00  0.00              
ATOM    846  CA  ALA   234      42.663  25.071 -18.960  1.00  0.00              
ATOM    847  C   ALA   234      41.578  25.778 -18.168  1.00  0.00              
ATOM    848  O   ALA   234      41.747  26.069 -16.988  1.00  0.00              
ATOM    849  N   GLY   235      40.458  26.056 -18.814  1.00  0.00              
ATOM    850  CA  GLY   235      39.366  26.745 -18.140  1.00  0.00              
ATOM    851  C   GLY   235      38.701  25.865 -17.088  1.00  0.00              
ATOM    852  O   GLY   235      38.350  26.339 -16.008  1.00  0.00              
ATOM    853  N   LEU   236      38.517  24.584 -17.397  1.00  0.00              
ATOM    854  CA  LEU   236      37.886  23.684 -16.435  1.00  0.00              
ATOM    855  C   LEU   236      38.775  23.565 -15.209  1.00  0.00              
ATOM    856  O   LEU   236      38.285  23.434 -14.092  1.00  0.00              
ATOM    857  N   MET   237      40.083  23.624 -15.409  1.00  0.00              
ATOM    858  CA  MET   237      40.988  23.520 -14.281  1.00  0.00              
ATOM    859  C   MET   237      40.965  24.841 -13.533  1.00  0.00              
ATOM    860  O   MET   237      41.187  24.871 -12.326  1.00  0.00              
ATOM    861  N   TYR   238      40.696  25.932 -14.250  1.00  0.00              
ATOM    862  CA  TYR   238      40.623  27.241 -13.609  1.00  0.00              
ATOM    863  C   TYR   238      39.445  27.158 -12.649  1.00  0.00              
ATOM    864  O   TYR   238      39.547  27.569 -11.493  1.00  0.00              
ATOM    865  N   TYR   239      38.328  26.616 -13.124  1.00  0.00              
ATOM    866  CA  TYR   239      37.163  26.467 -12.271  1.00  0.00              
ATOM    867  C   TYR   239      37.495  25.536 -11.126  1.00  0.00              
ATOM    868  O   TYR   239      37.066  25.772 -10.000  1.00  0.00              
END
