
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0318AL257_4-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   13 , name T0318_D2.pdb
# PARAMETERS: T0318AL257_4-D2.T0318_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       156 - 170         3.08     3.08
  LCS_AVERAGE:      3.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       161 - 170         1.42     4.81
  LCS_AVERAGE:      2.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       164 - 170         0.29     3.69
  LCS_AVERAGE:      1.77

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:  335
LCS_GDT     T     156     T     156      3    6   13     3    6    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     N     157     N     157      5    6   13     0    4    8    8    9    9   10   11   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     158     E     158      5    6   13     4    4    5    5    6    8    9   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     159     D     159      5    6   13     4    4    5    5    6    8    8   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     A     160     A     160      5    6   13     4    4    5    5    6    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     161     V     161      5    8   13     4    4    5    5    7    8    8   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     T     164     T     164      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     165     D     165      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     166     L     166      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     S     167     S     167      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     E     168     E     168      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     S     169     S     169      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     170     V     170      7    8   13     7    7    8    8    9    9   10   12   13   13   13   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   2.60  (   1.77    2.16    3.88 )

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      7      7      8      8      9      9     10     12     13     13     13     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   2.09   2.09   2.39   2.39   2.69   2.69   2.99   3.58   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88   3.88
GDT RMS_LOCAL    0.29   0.29   0.93   0.93   1.39   1.39   1.72   2.97   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08
GDT RMS_ALL_CA   3.69   3.69   3.39   3.39   3.40   3.40   3.42   3.14   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          3.112
LGA    N     157      N     157          4.902
LGA    E     158      E     158          3.039
LGA    D     159      D     159          3.659
LGA    A     160      A     160          3.534
LGA    V     161      V     161          3.777
LGA    T     164      T     164          2.904
LGA    D     165      D     165          3.188
LGA    L     166      L     166          2.835
LGA    S     167      S     167          3.088
LGA    E     168      E     168          2.935
LGA    S     169      S     169          2.584
LGA    V     170      V     170          2.456

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13  335    4.0     12    2.97     2.985     2.874     0.391

LGA_LOCAL      RMSD =  2.969  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.289  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  3.083  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.305146 * X  +  -0.583221 * Y  +  -0.752821 * Z  +  21.931295
  Y_new =  -0.891693 * X  +   0.452511 * Y  +   0.010869 * Z  +  45.065258
  Z_new =   0.334320 * X  +   0.674601 * Y  +  -0.658136 * Z  + -34.396267 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.343840   -0.797752  [ DEG:   134.2922    -45.7078 ]
  Theta =  -0.340884   -2.800709  [ DEG:   -19.5312   -160.4688 ]
  Phi   =  -1.900515    1.241078  [ DEG:  -108.8915     71.1085 ]
 
# 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: T0318AL257_4-D2                               
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318AL257_4-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13  335   4.0   12   2.97   2.874     3.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL257_4-D2
REMARK Aligment from pdb entry: 1gyt_A
ATOM    585  N   THR   156      26.565  25.230  13.771  1.00  0.00              
ATOM    586  CA  THR   156      25.987  25.284  12.436  1.00  0.00              
ATOM    587  C   THR   156      25.326  26.622  12.196  1.00  0.00              
ATOM    588  O   THR   156      25.676  27.316  11.235  1.00  0.00              
ATOM    589  N   ASN   157      24.387  26.994  13.070  1.00  0.00              
ATOM    590  CA  ASN   157      23.698  28.268  12.925  1.00  0.00              
ATOM    591  C   ASN   157      24.435  29.457  13.535  1.00  0.00              
ATOM    592  O   ASN   157      23.821  30.450  13.915  1.00  0.00              
ATOM    593  N   GLU   158      26.656  31.015  11.739  1.00  0.00              
ATOM    594  CA  GLU   158      26.775  31.881  10.566  1.00  0.00              
ATOM    595  C   GLU   158      25.463  32.625  10.267  1.00  0.00              
ATOM    596  O   GLU   158      25.464  33.837  10.005  1.00  0.00              
ATOM    597  N   ASP   159      24.355  31.893  10.303  1.00  0.00              
ATOM    598  CA  ASP   159      23.071  32.497  10.021  1.00  0.00              
ATOM    599  C   ASP   159      22.748  33.510  11.112  1.00  0.00              
ATOM    600  O   ASP   159      22.028  34.476  10.889  1.00  0.00              
ATOM    601  N   ALA   160      23.311  33.287  12.289  1.00  0.00              
ATOM    602  CA  ALA   160      23.061  34.185  13.391  1.00  0.00              
ATOM    603  C   ALA   160      23.838  35.479  13.282  1.00  0.00              
ATOM    604  O   ALA   160      23.349  36.541  13.685  1.00  0.00              
ATOM    605  N   VAL   161      25.049  35.410  12.742  1.00  0.00              
ATOM    606  CA  VAL   161      25.847  36.611  12.638  1.00  0.00              
ATOM    607  C   VAL   161      25.233  37.522  11.594  1.00  0.00              
ATOM    608  O   VAL   161      25.311  38.748  11.700  1.00  0.00              
ATOM    609  N   THR   164      24.612  36.900  10.596  1.00  0.00              
ATOM    610  CA  THR   164      23.939  37.611   9.526  1.00  0.00              
ATOM    611  C   THR   164      22.687  38.272  10.087  1.00  0.00              
ATOM    612  O   THR   164      22.334  39.379   9.698  1.00  0.00              
ATOM    613  N   ASP   165      22.015  37.570  10.996  1.00  0.00              
ATOM    614  CA  ASP   165      20.804  38.084  11.614  1.00  0.00              
ATOM    615  C   ASP   165      21.117  39.343  12.447  1.00  0.00              
ATOM    616  O   ASP   165      20.383  40.329  12.401  1.00  0.00              
ATOM    617  N   LEU   166      22.213  39.314  13.190  1.00  0.00              
ATOM    618  CA  LEU   166      22.589  40.467  13.980  1.00  0.00              
ATOM    619  C   LEU   166      22.931  41.595  13.021  1.00  0.00              
ATOM    620  O   LEU   166      22.548  42.743  13.248  1.00  0.00              
ATOM    621  N   SER   167      23.652  41.274  11.948  1.00  0.00              
ATOM    622  CA  SER   167      24.034  42.301  10.984  1.00  0.00              
ATOM    623  C   SER   167      22.785  43.011  10.404  1.00  0.00              
ATOM    624  O   SER   167      22.689  44.241  10.421  1.00  0.00              
ATOM    625  N   GLU   168      21.833  42.225   9.906  1.00  0.00              
ATOM    626  CA  GLU   168      20.615  42.773   9.340  1.00  0.00              
ATOM    627  C   GLU   168      19.800  43.486  10.390  1.00  0.00              
ATOM    628  O   GLU   168      19.389  44.620  10.199  1.00  0.00              
ATOM    629  N   SER   169      19.563  42.802  11.496  1.00  0.00              
ATOM    630  CA  SER   169      18.782  43.361  12.582  1.00  0.00              
ATOM    631  C   SER   169      19.287  44.719  13.036  1.00  0.00              
ATOM    632  O   SER   169      18.489  45.603  13.306  1.00  0.00              
ATOM    633  N   VAL   170      20.601  44.906  13.114  1.00  0.00              
ATOM    634  CA  VAL   170      21.101  46.186  13.550  1.00  0.00              
ATOM    635  C   VAL   170      20.911  47.269  12.492  1.00  0.00              
ATOM    636  O   VAL   170      20.634  48.414  12.828  1.00  0.00              
END
