
#######################################################
#                                                     #
#                        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   18 (   72),  selected   18 , name T0295AL333_3-D2
# Molecule2: number of CA atoms   95 (  803),  selected   18 , name T0295_D2.pdb
# PARAMETERS: T0295AL333_3-D2.T0295_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:     9       212 - 220         4.62    10.29
  LONGEST_CONTINUOUS_SEGMENT:     9       213 - 221         4.79    10.67
  LONGEST_CONTINUOUS_SEGMENT:     9       214 - 222         4.86    10.51
  LCS_AVERAGE:      9.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       206 - 209         1.86    17.55
  LONGEST_CONTINUOUS_SEGMENT:     4       213 - 216         1.93    15.82
  LCS_AVERAGE:      3.63

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       205 - 207         0.05    31.88
  LONGEST_CONTINUOUS_SEGMENT:     3       206 - 208         0.45    31.25
  LONGEST_CONTINUOUS_SEGMENT:     3       207 - 209         0.82    24.88
  LONGEST_CONTINUOUS_SEGMENT:     3       212 - 214         0.70    13.40
  LONGEST_CONTINUOUS_SEGMENT:     3       213 - 215         0.57    20.73
  LONGEST_CONTINUOUS_SEGMENT:     3       214 - 216         0.41    18.56
  LONGEST_CONTINUOUS_SEGMENT:     3       215 - 217         0.56    17.34
  LONGEST_CONTINUOUS_SEGMENT:     3       216 - 218         0.70    14.73
  LONGEST_CONTINUOUS_SEGMENT:     3       217 - 219         0.72    21.22
  LONGEST_CONTINUOUS_SEGMENT:     3       218 - 220         0.43    15.18
  LONGEST_CONTINUOUS_SEGMENT:     3       219 - 221         0.41    19.79
  LONGEST_CONTINUOUS_SEGMENT:     3       220 - 222         0.94    20.52
  LONGEST_CONTINUOUS_SEGMENT:     3       221 - 223         0.87    23.40
  LONGEST_CONTINUOUS_SEGMENT:     3       222 - 224         0.84    34.27
  LCS_AVERAGE:      3.16

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:   95
LCS_GDT     F     205     F     205      3    3    8     3    3    3    3    4    4    5    5    6    7    7    7    8    9   10   11   11   11   13   14 
LCS_GDT     K     206     K     206      3    4    8     3    3    3    3    4    4    5    5    6    7    7    7    8    9   10   11   11   11   13   14 
LCS_GDT     R     207     R     207      3    4    8     3    3    3    3    4    4    5    5    6    7    7    7    8    9   10   11   11   11   13   14 
LCS_GDT     N     208     N     208      3    4    8     2    3    3    3    4    4    5    5    6    7    7    7    8    9   10   11   11   11   13   14 
LCS_GDT     A     209     A     209      3    4    8     0    3    3    3    4    4    5    5    6    7    7    7    8    9   10   11   11   11   13   14 
LCS_GDT     N     212     N     212      3    3    9     0    3    3    3    3    3    4    6    6    7    8    8    8    9   10   11   11   12   13   14 
LCS_GDT     M     213     M     213      3    4    9     0    3    3    3    4    4    5    6    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     L     214     L     214      3    4    9     3    3    3    3    4    4    5    6    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     E     215     E     215      3    4    9     3    3    3    3    4    4    4    6    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     H     216     H     216      3    4    9     3    3    3    3    4    4    5    6    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     N     217     N     217      3    3    9     0    3    3    3    4    4    5    6    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     Y     218     Y     218      3    3    9     3    3    3    3    3    4    5    6    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     K     219     K     219      3    3    9     3    3    3    3    3    4    4    5    7    7    8    8    9    9   10   11   11   12   13   14 
LCS_GDT     N     220     N     220      3    3    9     3    3    3    3    3    4    4    5    6    7    7    8    9    9   10   11   11   12   12   14 
LCS_GDT     W     221     W     221      3    3    9     3    3    3    3    3    4    4    5    6    7    7    8    9    9   10   11   11   12   12   13 
LCS_GDT     C     222     C     222      3    3    9     0    3    3    3    3    4    4    5    6    7    7    7    8    8   10   11   11   12   12   13 
LCS_GDT     T     223     T     223      3    3    8     0    3    3    3    3    4    4    5    5    7    7    7    8    8   10   11   11   12   12   13 
LCS_GDT     L     224     L     224      3    3    8     0    3    3    3    3    4    4    4    4    7    7    7    8    8    9    9   10   12   12   13 
LCS_AVERAGE  LCS_A:   5.28  (   3.16    3.63    9.06 )

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      3      3      4      4      5      6      7      7      8      8      9      9     10     11     11     12     13     14 
GDT PERCENT_CA   3.16   3.16   3.16   3.16   4.21   4.21   5.26   6.32   7.37   7.37   8.42   8.42   9.47   9.47  10.53  11.58  11.58  12.63  13.68  14.74
GDT RMS_LOCAL    0.05   0.05   0.05   0.05   1.33   1.33   2.15   3.45   3.86   3.85   4.18   4.18   4.79   4.62   5.24   5.68   5.59   5.97   6.91   7.25
GDT RMS_ALL_CA  31.88  31.88  31.88  31.88  26.36  26.36  20.94  11.08  11.00  10.97  10.48  10.48  10.67  10.29  10.16  10.55  10.13  10.60  10.51  10.14

#      Molecule1      Molecule2       DISTANCE
LGA    F     205      F     205         14.509
LGA    K     206      K     206         16.874
LGA    R     207      R     207         15.133
LGA    N     208      N     208         14.727
LGA    A     209      A     209         11.550
LGA    N     212      N     212          7.125
LGA    M     213      M     213          3.890
LGA    L     214      L     214          3.581
LGA    E     215      E     215          3.884
LGA    H     216      H     216          2.845
LGA    N     217      N     217          2.609
LGA    Y     218      Y     218          3.684
LGA    K     219      K     219          8.020
LGA    N     220      N     220          9.435
LGA    W     221      W     221          9.245
LGA    C     222      C     222         12.263
LGA    T     223      T     223         16.930
LGA    L     224      L     224         18.394

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   95    4.0      6    3.45     6.053     5.385     0.169

LGA_LOCAL      RMSD =  3.452  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.083  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  9.003  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.464534 * X  +  -0.418721 * Y  +   0.780308 * Z  + -18.688141
  Y_new =  -0.590284 * X  +  -0.510437 * Y  +  -0.625315 * Z  +  58.504642
  Z_new =   0.660131 * X  +  -0.751084 * Y  +  -0.010049 * Z  +  15.754284 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.584174    1.557418  [ DEG:   -90.7665     89.2335 ]
  Theta =  -0.720993   -2.420600  [ DEG:   -41.3098   -138.6902 ]
  Phi   =  -2.237540    0.904053  [ DEG:  -128.2016     51.7984 ]
 
# 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: T0295AL333_3-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295AL333_3-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   95   4.0    6   3.45   5.385     9.00
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL333_3-D2
REMARK Aligment from pdb entry: 1l3i_A
ATOM    577  N   PHE   205       6.043  22.401 -12.973  1.00  0.00              
ATOM    578  CA  PHE   205       5.576  23.561 -13.753  1.00  0.00              
ATOM    579  C   PHE   205       5.365  23.209 -15.225  1.00  0.00              
ATOM    580  O   PHE   205       6.292  22.737 -15.885  1.00  0.00              
ATOM    581  N   LYS   206       4.168  23.487 -15.748  1.00  0.00              
ATOM    582  CA  LYS   206       3.821  23.203 -17.152  1.00  0.00              
ATOM    583  C   LYS   206       4.186  21.782 -17.557  1.00  0.00              
ATOM    584  O   LYS   206       4.886  21.548 -18.549  1.00  0.00              
ATOM    585  N   ARG   207       3.718  20.852 -16.734  1.00  0.00              
ATOM    586  CA  ARG   207       3.948  19.430 -16.922  1.00  0.00              
ATOM    587  C   ARG   207       5.419  18.999 -16.792  1.00  0.00              
ATOM    588  O   ARG   207       5.725  17.808 -16.845  1.00  0.00              
ATOM    589  N   ASN   208       6.310  19.964 -16.573  1.00  0.00              
ATOM    590  CA  ASN   208       7.718  19.663 -16.406  1.00  0.00              
ATOM    591  C   ASN   208       8.201  19.990 -15.002  1.00  0.00              
ATOM    592  O   ASN   208       7.381  20.229 -14.116  1.00  0.00              
ATOM    593  N   ALA   209       9.523  20.014 -14.794  1.00  0.00              
ATOM    594  CA  ALA   209      10.136  20.305 -13.485  1.00  0.00              
ATOM    595  C   ALA   209      11.087  21.496 -13.578  1.00  0.00              
ATOM    596  O   ALA   209      12.145  21.381 -14.188  1.00  0.00              
ATOM    597  N   ASN   212      14.038  25.637  -8.752  1.00  0.00              
ATOM    598  CA  ASN   212      13.859  26.844  -7.951  1.00  0.00              
ATOM    599  C   ASN   212      15.028  26.984  -6.980  1.00  0.00              
ATOM    600  O   ASN   212      15.237  26.116  -6.136  1.00  0.00              
ATOM    601  N   MET   213      15.791  28.065  -7.103  1.00  0.00              
ATOM    602  CA  MET   213      16.942  28.276  -6.235  1.00  0.00              
ATOM    603  C   MET   213      16.614  28.956  -4.907  1.00  0.00              
ATOM    604  O   MET   213      15.614  29.649  -4.767  1.00  0.00              
ATOM    605  N   LEU   214      17.466  28.722  -3.926  1.00  0.00              
ATOM    606  CA  LEU   214      17.321  29.338  -2.617  1.00  0.00              
ATOM    607  C   LEU   214      18.493  30.282  -2.553  1.00  0.00              
ATOM    608  O   LEU   214      19.508  30.051  -3.224  1.00  0.00              
ATOM    609  N   GLU   215      18.358  31.360  -1.792  1.00  0.00              
ATOM    610  CA  GLU   215      19.447  32.315  -1.662  1.00  0.00              
ATOM    611  C   GLU   215      20.667  31.594  -1.092  1.00  0.00              
ATOM    612  O   GLU   215      20.531  30.693  -0.268  1.00  0.00              
ATOM    613  N   HIS   216      21.864  31.931  -1.587  1.00  0.00              
ATOM    614  CA  HIS   216      23.045  31.263  -1.056  1.00  0.00              
ATOM    615  C   HIS   216      23.258  31.533   0.425  1.00  0.00              
ATOM    616  O   HIS   216      22.908  32.589   0.930  1.00  0.00              
ATOM    617  N   ASN   217      23.782  30.540   1.121  1.00  0.00              
ATOM    618  CA  ASN   217      24.070  30.660   2.529  1.00  0.00              
ATOM    619  C   ASN   217      25.470  30.094   2.745  1.00  0.00              
ATOM    620  O   ASN   217      25.828  29.055   2.166  1.00  0.00              
ATOM    621  N   TYR   218      26.286  30.801   3.515  1.00  0.00              
ATOM    622  CA  TYR   218      27.631  30.325   3.809  1.00  0.00              
ATOM    623  C   TYR   218      27.713  29.876   5.277  1.00  0.00              
ATOM    624  O   TYR   218      27.020  30.411   6.155  1.00  0.00              
ATOM    625  N   LYS   219      28.509  28.844   5.523  1.00  0.00              
ATOM    626  CA  LYS   219      28.708  28.344   6.871  1.00  0.00              
ATOM    627  C   LYS   219      30.186  28.522   7.184  1.00  0.00              
ATOM    628  O   LYS   219      31.043  27.977   6.474  1.00  0.00              
ATOM    629  N   ASN   220      30.480  29.399   8.146  1.00  0.00              
ATOM    630  CA  ASN   220      31.847  29.657   8.579  1.00  0.00              
ATOM    631  C   ASN   220      32.010  28.835   9.865  1.00  0.00              
ATOM    632  O   ASN   220      31.296  29.059  10.848  1.00  0.00              
ATOM    633  N   TRP   221      32.923  27.869   9.862  1.00  0.00              
ATOM    634  CA  TRP   221      33.098  27.014  11.027  1.00  0.00              
ATOM    635  C   TRP   221      34.550  26.833  11.458  1.00  0.00              
ATOM    636  O   TRP   221      35.474  26.922  10.641  1.00  0.00              
ATOM    637  N   CYS   222      34.726  26.555  12.752  1.00  0.00              
ATOM    638  CA  CYS   222      36.042  26.390  13.376  1.00  0.00              
ATOM    639  C   CYS   222      36.670  24.992  13.368  1.00  0.00              
ATOM    640  O   CYS   222      36.019  23.994  13.016  1.00  0.00              
ATOM    641  N   THR   223      37.936  24.954  13.811  1.00  0.00              
ATOM    642  CA  THR   223      38.753  23.740  13.875  1.00  0.00              
ATOM    643  C   THR   223      38.317  22.526  14.688  1.00  0.00              
ATOM    644  O   THR   223      37.194  22.465  15.207  1.00  0.00              
ATOM    645  N   LEU   224      39.266  21.595  14.866  1.00  0.00              
ATOM    646  CA  LEU   224      39.052  20.317  15.569  1.00  0.00              
ATOM    647  C   LEU   224      38.322  20.433  16.928  1.00  0.00              
ATOM    648  O   LEU   224      38.695  21.307  17.751  1.00  0.00              
END
