
#######################################################
#                                                     #
#                        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 T0386AL380_4-D2
# Molecule2: number of CA atoms   81 (  636),  selected   18 , name T0386_D2.pdb
# PARAMETERS: T0386AL380_4-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:    18       219 - 236         2.23     2.23
  LCS_AVERAGE:     22.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       219 - 235         1.64     2.36
  LCS_AVERAGE:     20.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       219 - 233         0.90     2.31
  LCS_AVERAGE:     16.05

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     15   17   18     8   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     P     220     P     220     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     E     221     E     221     15   17   18     8   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     222     K     222     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     I     223     I     223     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     R     224     R     224     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     225     L     225     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     L     226     L     226     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     227     K     227     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     E     228     E     228     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     F     229     F     229     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     M     230     M     230     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     H     231     H     231     15   17   18    10   13   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     T     232     T     232     15   17   18     4    8   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     M     233     M     233     15   17   18     4    5   14   15   15   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     K     234     K     234      3   17   18     1    3    4    5    9   13   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     N     235     N     235      3   17   18     0    3    4    4    9   16   17   17   17   17   17   18   18   18   18   18   18   18   18   18 
LCS_GDT     T     236     T     236      3    5   18     0    3    4    4    4   14   15   16   16   17   17   18   18   18   18   18   18   18   18   18 
LCS_AVERAGE  LCS_A:  19.48  (  16.05   20.16   22.22 )

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     10     13     14     15     15     16     17     17     17     17     17     18     18     18     18     18     18     18     18     18 
GDT PERCENT_CA  12.35  16.05  17.28  18.52  18.52  19.75  20.99  20.99  20.99  20.99  20.99  22.22  22.22  22.22  22.22  22.22  22.22  22.22  22.22  22.22
GDT RMS_LOCAL    0.31   0.47   0.71   0.90   0.90   1.28   1.64   1.64   1.64   1.64   1.64   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23
GDT RMS_ALL_CA   2.33   2.37   2.34   2.31   2.31   2.25   2.36   2.36   2.36   2.36   2.36   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23   2.23

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          1.418
LGA    P     220      P     220          1.439
LGA    E     221      E     221          1.469
LGA    K     222      K     222          0.724
LGA    I     223      I     223          0.408
LGA    R     224      R     224          0.349
LGA    L     225      L     225          0.670
LGA    L     226      L     226          1.155
LGA    K     227      K     227          0.717
LGA    E     228      E     228          0.455
LGA    F     229      F     229          1.354
LGA    M     230      M     230          1.396
LGA    H     231      H     231          1.003
LGA    T     232      T     232          1.799
LGA    M     233      M     233          1.715
LGA    K     234      K     234          3.944
LGA    N     235      N     235          3.215
LGA    T     236      T     236          7.447

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   81    4.0     17    1.64    19.444    19.899     0.976

LGA_LOCAL      RMSD =  1.642  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.379  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  2.230  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.625020 * X  +   0.104483 * Y  +  -0.773585 * Z  +  15.772438
  Y_new =  -0.414561 * X  +   0.884129 * Y  +  -0.215533 * Z  +  54.951141
  Z_new =   0.661429 * X  +   0.455410 * Y  +   0.595913 * Z  +  20.920713 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.652541   -2.489051  [ DEG:    37.3879   -142.6121 ]
  Theta =  -0.722723   -2.418870  [ DEG:   -41.4090   -138.5910 ]
  Phi   =  -0.585652    2.555941  [ DEG:   -33.5554    146.4446 ]
 
# 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: T0386AL380_4-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL380_4-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   81   4.0   17   1.64  19.899     2.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL380_4-D2
REMARK Aligment from pdb entry: 1eh9A
ATOM    517  N   ASN   219       4.460  55.304  74.605  1.00  0.00              
ATOM    518  CA  ASN   219       3.533  55.342  75.680  1.00  0.00              
ATOM    519  C   ASN   219       3.380  56.767  76.172  1.00  0.00              
ATOM    520  O   ASN   219       4.288  57.603  76.079  1.00  0.00              
ATOM    521  N   PRO   220       2.219  57.023  76.708  1.00  0.00              
ATOM    522  CA  PRO   220       1.852  58.321  77.204  1.00  0.00              
ATOM    523  C   PRO   220       2.855  58.904  78.159  1.00  0.00              
ATOM    524  O   PRO   220       3.116  60.095  78.107  1.00  0.00              
ATOM    525  N   GLU   221       3.412  58.102  79.063  1.00  0.00              
ATOM    526  CA  GLU   221       4.370  58.723  79.970  1.00  0.00              
ATOM    527  C   GLU   221       5.478  59.332  79.145  1.00  0.00              
ATOM    528  O   GLU   221       5.820  60.507  79.307  1.00  0.00              
ATOM    529  N   LYS   222       5.981  58.493  78.226  1.00  0.00              
ATOM    530  CA  LYS   222       7.012  58.834  77.271  1.00  0.00              
ATOM    531  C   LYS   222       6.642  60.158  76.602  1.00  0.00              
ATOM    532  O   LYS   222       7.159  61.257  76.934  1.00  0.00              
ATOM    533  N   ILE   223       5.677  60.084  75.693  1.00  0.00              
ATOM    534  CA  ILE   223       5.210  61.298  75.039  1.00  0.00              
ATOM    535  C   ILE   223       5.174  62.534  75.984  1.00  0.00              
ATOM    536  O   ILE   223       5.248  63.686  75.602  1.00  0.00              
ATOM    537  N   ARG   224       5.043  62.334  77.268  1.00  0.00              
ATOM    538  CA  ARG   224       5.006  63.489  78.130  1.00  0.00              
ATOM    539  C   ARG   224       6.422  63.932  78.406  1.00  0.00              
ATOM    540  O   ARG   224       6.736  65.134  78.534  1.00  0.00              
ATOM    541  N   LEU   225       7.264  62.918  78.520  1.00  0.00              
ATOM    542  CA  LEU   225       8.644  63.146  78.788  1.00  0.00              
ATOM    543  C   LEU   225       9.226  63.943  77.657  1.00  0.00              
ATOM    544  O   LEU   225       9.770  65.021  77.863  1.00  0.00              
ATOM    545  N   LEU   226       9.090  63.388  76.444  1.00  0.00              
ATOM    546  CA  LEU   226       9.596  64.050  75.240  1.00  0.00              
ATOM    547  C   LEU   226       9.314  65.522  75.302  1.00  0.00              
ATOM    548  O   LEU   226      10.208  66.386  75.398  1.00  0.00              
ATOM    549  N   LYS   227       8.034  65.794  75.234  1.00  0.00              
ATOM    550  CA  LYS   227       7.644  67.153  75.292  1.00  0.00              
ATOM    551  C   LYS   227       8.527  67.918  76.259  1.00  0.00              
ATOM    552  O   LYS   227       9.072  68.959  75.911  1.00  0.00              
ATOM    553  N   GLU   228       8.719  67.386  77.458  1.00  0.00              
ATOM    554  CA  GLU   228       9.574  68.072  78.421  1.00  0.00              
ATOM    555  C   GLU   228      10.904  68.499  77.801  1.00  0.00              
ATOM    556  O   GLU   228      11.204  69.712  77.667  1.00  0.00              
ATOM    557  N   PHE   229      11.682  67.445  77.455  1.00  0.00              
ATOM    558  CA  PHE   229      13.001  67.486  76.825  1.00  0.00              
ATOM    559  C   PHE   229      13.186  68.646  75.876  1.00  0.00              
ATOM    560  O   PHE   229      14.046  69.526  76.039  1.00  0.00              
ATOM    561  N   MET   230      12.339  68.640  74.877  1.00  0.00              
ATOM    562  CA  MET   230      12.403  69.644  73.875  1.00  0.00              
ATOM    563  C   MET   230      12.001  71.003  74.268  1.00  0.00              
ATOM    564  O   MET   230      12.287  71.889  73.516  1.00  0.00              
ATOM    565  N   HIS   231      11.300  71.191  75.379  1.00  0.00              
ATOM    566  CA  HIS   231      10.891  72.540  75.663  1.00  0.00              
ATOM    567  C   HIS   231      11.668  73.036  76.778  1.00  0.00              
ATOM    568  O   HIS   231      11.622  74.216  77.099  1.00  0.00              
ATOM    569  N   THR   232      12.386  72.110  77.356  1.00  0.00              
ATOM    570  CA  THR   232      13.185  72.477  78.488  1.00  0.00              
ATOM    571  C   THR   232      14.643  72.621  78.129  1.00  0.00              
ATOM    572  O   THR   232      15.532  72.796  78.988  1.00  0.00              
ATOM    573  N   MET   233      14.836  72.569  76.798  1.00  0.00              
ATOM    574  CA  MET   233      16.118  72.735  76.136  1.00  0.00              
ATOM    575  C   MET   233      16.433  74.224  76.014  1.00  0.00              
ATOM    576  O   MET   233      15.515  75.063  76.059  1.00  0.00              
ATOM    577  N   LYS   234      17.737  74.549  75.853  1.00  0.00              
ATOM    578  CA  LYS   234      18.233  75.941  75.695  1.00  0.00              
ATOM    579  C   LYS   234      17.945  76.431  74.297  1.00  0.00              
ATOM    580  O   LYS   234      17.980  77.618  74.015  1.00  0.00              
ATOM    581  N   ASN   235      17.629  75.437  73.466  1.00  0.00              
ATOM    582  CA  ASN   235      17.259  75.542  72.094  1.00  0.00              
ATOM    583  C   ASN   235      16.024  76.353  71.862  1.00  0.00              
ATOM    584  O   ASN   235      15.673  77.232  72.649  1.00  0.00              
ATOM    585  N   THR   236      15.439  76.150  70.711  1.00  0.00              
ATOM    586  CA  THR   236      14.319  76.950  70.336  1.00  0.00              
ATOM    587  C   THR   236      13.247  76.069  69.876  1.00  0.00              
ATOM    588  O   THR   236      13.093  75.775  68.704  1.00  0.00              
END
