
#######################################################
#                                                     #
#                        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 T0372AL257_5-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   20 , name T0372_D1.pdb
# PARAMETERS: T0372AL257_5-D1.T0372_D1.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        13 - 291         4.86    14.22
  LCS_AVERAGE:      9.21

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        13 - 23          1.81    27.75
  LCS_AVERAGE:      8.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        14 - 23          0.73    23.64
  LCS_AVERAGE:      5.67

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:  126
LCS_GDT     D      13     D      13      3   11   13     0    3    3    4    5    9   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     T      14     T      14     10   11   13     6    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     I      15     I      15     10   11   13     6    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     T      16     T      16     10   11   13     6    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     A      17     A      17     10   11   13     6    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     F      18     F      18     10   11   13     6    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     T      19     T      19     10   11   13     6    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   15   16   17 
LCS_GDT     M      20     M      20     10   11   13     5    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     K      21     K      21     10   11   13     5    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   16   16   17 
LCS_GDT     S      22     S      22     10   11   13     5    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   15   16   17 
LCS_GDT     D      23     D      23     10   11   13     5    9   10   10   10   10   10   11   11   11   11   11   11   12   13   14   14   15   16   17 
LCS_GDT     K     290     K     290      4    9   13     0    4    6    8    8    9    9    9    9    9    9    9   11   12   13   14   14   16   16   17 
LCS_GDT     Y     291     Y     291      4    9   13     3    4    6    8    8    9    9    9    9    9    9    9   10   11   13   14   14   16   16   17 
LCS_GDT     M     292     M     292      5    9    9     4    4    6    8    8    9    9    9    9    9    9    9   11   12   13   14   14   16   16   17 
LCS_GDT     A     293     A     293      5    9    9     4    4    6    8    8    9    9    9    9    9    9    9    9    9   11   13   14   16   16   17 
LCS_GDT     C     294     C     294      5    9    9     4    4    6    8    8    9    9    9    9    9    9    9    9    9   10   12   14   16   16   17 
LCS_GDT     L     295     L     295      5    9    9     4    4    6    8    8    9    9    9    9    9    9    9    9    9    9   10   11   16   16   17 
LCS_GDT     K     296     K     296      5    9    9     3    4    6    8    8    9    9    9    9    9    9    9    9    9    9   11   13   16   16   17 
LCS_GDT     D     297     D     297      4    9    9     3    4    6    8    8    9    9    9    9    9    9    9    9    9    9   10   10   16   16   17 
LCS_GDT     H     298     H     298      3    9    9     3    3    3    3    5    9    9    9    9    9    9    9    9    9    9   10   10   10   11   11 
LCS_AVERAGE  LCS_A:   7.63  (   5.67    8.02    9.21 )

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      6      9     10     10     10     10     10     11     11     11     11     11     11     12     13     14     14     16     16     17 
GDT PERCENT_CA   4.76   7.14   7.94   7.94   7.94   7.94   7.94   8.73   8.73   8.73   8.73   8.73   8.73   9.52  10.32  11.11  11.11  12.70  12.70  13.49
GDT RMS_LOCAL    0.36   0.64   0.73   0.73   0.73   0.73   0.73   1.81   1.81   1.81   1.81   1.81   1.81   4.49   4.86   5.25   5.25   7.34   6.46   7.04
GDT RMS_ALL_CA  22.56  23.99  23.64  23.64  23.64  23.64  23.64  27.75  27.75  27.75  27.75  27.75  27.75  14.73  14.22  12.77  12.77   8.64  10.10   9.13

#      Molecule1      Molecule2       DISTANCE
LGA    D      13      D      13          3.732
LGA    T      14      T      14          1.680
LGA    I      15      I      15          0.489
LGA    T      16      T      16          1.724
LGA    A      17      A      17          2.211
LGA    F      18      F      18          1.076
LGA    T      19      T      19          0.615
LGA    M      20      M      20          0.424
LGA    K      21      K      21          1.410
LGA    S      22      S      22          1.938
LGA    D      23      D      23          3.826
LGA    K     290      K     290         39.360
LGA    Y     291      Y     291         42.536
LGA    M     292      M     292         41.733
LGA    A     293      A     293         41.176
LGA    C     294      C     294         45.121
LGA    L     295      L     295         44.548
LGA    K     296      K     296         49.729
LGA    D     297      D     297         50.743
LGA    H     298      H     298         48.974

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  126    4.0     11    1.81     8.730     8.346     0.577

LGA_LOCAL      RMSD =  1.808  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 30.257  Number of atoms =   20 
Std_ALL_ATOMS  RMSD =  8.362  (standard rmsd on all 20 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.951890 * X  +   0.296279 * Y  +  -0.078253 * Z  +  61.471222
  Y_new =  -0.305637 * X  +  -0.899469 * Y  +   0.312316 * Z  + 104.571373
  Z_new =   0.022147 * X  +   0.321208 * Y  +   0.946750 * Z  + -115.865013 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.327088   -2.814505  [ DEG:    18.7408   -161.2592 ]
  Theta =  -0.022148   -3.119444  [ DEG:    -1.2690   -178.7310 ]
  Phi   =  -2.830906    0.310686  [ DEG:  -162.1990     17.8010 ]
 
# 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: T0372AL257_5-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL257_5-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  126   4.0   11   1.81   8.346     8.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL257_5-D1
REMARK Aligment from pdb entry: 1lrz_A
ATOM      1  N   ASP    13      48.112  63.361  11.074  1.00  0.00              
ATOM      2  CA  ASP    13      46.970  62.545  11.459  1.00  0.00              
ATOM      3  C   ASP    13      47.031  61.173  10.828  1.00  0.00              
ATOM      4  O   ASP    13      47.620  61.000   9.760  1.00  0.00              
ATOM      5  N   THR    14      46.450  60.196  11.518  1.00  0.00              
ATOM      6  CA  THR    14      46.385  58.829  11.030  1.00  0.00              
ATOM      7  C   THR    14      44.934  58.607  10.641  1.00  0.00              
ATOM      8  O   THR    14      44.060  59.435  10.936  1.00  0.00              
ATOM      9  N   ILE    15      44.678  57.473  10.002  1.00  0.00              
ATOM     10  CA  ILE    15      43.331  57.122   9.587  1.00  0.00              
ATOM     11  C   ILE    15      42.392  57.063  10.796  1.00  0.00              
ATOM     12  O   ILE    15      41.225  57.462  10.705  1.00  0.00              
ATOM     13  N   THR    16      42.896  56.567  11.931  1.00  0.00              
ATOM     14  CA  THR    16      42.072  56.476  13.142  1.00  0.00              
ATOM     15  C   THR    16      41.680  57.862  13.627  1.00  0.00              
ATOM     16  O   THR    16      40.570  58.048  14.112  1.00  0.00              
ATOM     17  N   ALA    17      42.599  58.821  13.514  1.00  0.00              
ATOM     18  CA  ALA    17      42.312  60.204  13.907  1.00  0.00              
ATOM     19  C   ALA    17      41.200  60.752  13.007  1.00  0.00              
ATOM     20  O   ALA    17      40.280  61.443  13.460  1.00  0.00              
ATOM     21  N   PHE    18      41.301  60.453  11.716  1.00  0.00              
ATOM     22  CA  PHE    18      40.321  60.965  10.767  1.00  0.00              
ATOM     23  C   PHE    18      38.932  60.417  11.061  1.00  0.00              
ATOM     24  O   PHE    18      37.952  61.169  11.084  1.00  0.00              
ATOM     25  N   THR    19      38.844  59.115  11.293  1.00  0.00              
ATOM     26  CA  THR    19      37.560  58.499  11.605  1.00  0.00              
ATOM     27  C   THR    19      37.028  59.049  12.925  1.00  0.00              
ATOM     28  O   THR    19      35.831  59.305  13.059  1.00  0.00              
ATOM     29  N   MET    20      37.912  59.244  13.899  1.00  0.00              
ATOM     30  CA  MET    20      37.468  59.751  15.196  1.00  0.00              
ATOM     31  C   MET    20      36.890  61.155  15.109  1.00  0.00              
ATOM     32  O   MET    20      36.004  61.497  15.879  1.00  0.00              
ATOM     33  N   LYS    21      37.380  61.961  14.165  1.00  0.00              
ATOM     34  CA  LYS    21      36.897  63.330  14.024  1.00  0.00              
ATOM     35  C   LYS    21      35.661  63.469  13.134  1.00  0.00              
ATOM     36  O   LYS    21      35.138  64.566  12.988  1.00  0.00              
ATOM     37  N   SER    22      35.212  62.369  12.527  1.00  0.00              
ATOM     38  CA  SER    22      34.011  62.393  11.685  1.00  0.00              
ATOM     39  C   SER    22      32.809  62.517  12.615  1.00  0.00              
ATOM     40  O   SER    22      32.909  62.180  13.792  1.00  0.00              
ATOM     41  N   ASP    23      31.674  62.990  12.100  1.00  0.00              
ATOM     42  CA  ASP    23      30.493  63.056  12.947  1.00  0.00              
ATOM     43  C   ASP    23      29.872  61.645  12.975  1.00  0.00              
ATOM     44  O   ASP    23      30.294  60.749  12.222  1.00  0.00              
ATOM    561  N   LYS   290      38.941  81.692  -1.242  1.00  0.00              
ATOM    562  CA  LYS   290      40.086  82.272  -1.926  1.00  0.00              
ATOM    563  C   LYS   290      39.839  83.725  -2.346  1.00  0.00              
ATOM    564  O   LYS   290      38.702  84.192  -2.355  1.00  0.00              
ATOM    565  N   TYR   291      40.906  84.439  -2.690  1.00  0.00              
ATOM    566  CA  TYR   291      40.782  85.843  -3.068  1.00  0.00              
ATOM    567  C   TYR   291      39.888  86.104  -4.272  1.00  0.00              
ATOM    568  O   TYR   291      39.231  87.141  -4.336  1.00  0.00              
ATOM    569  N   MET   292      39.850  85.172  -5.219  1.00  0.00              
ATOM    570  CA  MET   292      39.001  85.373  -6.384  1.00  0.00              
ATOM    571  C   MET   292      39.732  85.736  -7.667  1.00  0.00              
ATOM    572  O   MET   292      40.915  85.412  -7.850  1.00  0.00              
ATOM    573  N   ALA   293      39.022  86.438  -8.547  1.00  0.00              
ATOM    574  CA  ALA   293      39.529  86.822  -9.863  1.00  0.00              
ATOM    575  C   ALA   293      39.892  88.284 -10.057  1.00  0.00              
ATOM    576  O   ALA   293      39.216  89.177  -9.554  1.00  0.00              
ATOM    577  N   CYS   294      40.962  88.517 -10.812  1.00  0.00              
ATOM    578  CA  CYS   294      41.413  89.869 -11.109  1.00  0.00              
ATOM    579  C   CYS   294      41.673  89.983 -12.609  1.00  0.00              
ATOM    580  O   CYS   294      42.266  89.090 -13.235  1.00  0.00              
ATOM    581  N   LEU   295      41.238  91.097 -13.181  1.00  0.00              
ATOM    582  CA  LEU   295      41.392  91.329 -14.604  1.00  0.00              
ATOM    583  C   LEU   295      42.127  92.633 -14.862  1.00  0.00              
ATOM    584  O   LEU   295      41.795  93.667 -14.289  1.00  0.00              
ATOM    585  N   LYS   296      43.156  92.574 -15.698  1.00  0.00              
ATOM    586  CA  LYS   296      43.890  93.774 -16.041  1.00  0.00              
ATOM    587  C   LYS   296      43.726  94.018 -17.531  1.00  0.00              
ATOM    588  O   LYS   296      44.283  93.293 -18.362  1.00  0.00              
ATOM    589  N   ASP   297      42.928  95.027 -17.893  1.00  0.00              
ATOM    590  CA  ASP   297      42.707  95.350 -19.308  1.00  0.00              
ATOM    591  C   ASP   297      44.004  95.938 -19.855  1.00  0.00              
ATOM    592  O   ASP   297      44.579  96.822 -19.221  1.00  0.00              
ATOM    593  N   HIS   298      44.470  95.455 -21.006  1.00  0.00              
ATOM    594  CA  HIS   298      45.699  95.988 -21.601  1.00  0.00              
ATOM    595  C   HIS   298      45.380  97.132 -22.574  1.00  0.00              
ATOM    596  O   HIS   298      46.087  98.142 -22.608  1.00  0.00              
END
