
#######################################################
#                                                     #
#                        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   15 (   75),  selected   15 , name T0320TS239_2_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   15 , name T0320_D1.pdb
# PARAMETERS: T0320TS239_2_1-D1.T0320_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:    15         1 - 16          4.45     4.45
  LCS_AVERAGE:      7.01

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10         1 - 11          1.26     8.63
  LCS_AVERAGE:      3.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8         2 - 10          0.99     8.80
  LONGEST_CONTINUOUS_SEGMENT:     8         4 - 11          0.16     7.94
  LCS_AVERAGE:      2.83

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:  214
LCS_GDT     M       1     M       1      0   10   15     0    0    2    9   10   10   10   10   11   11   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     Q       2     Q       2      8   10   15     0    2    4    8   10   10   10   10   10   11   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     S       4     S       4      8   10   15     8    8    8    9   10   10   10   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     K       5     K       5      8   10   15     8    8    8    9   10   10   10   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     A       6     A       6      8   10   15     8    8    8    9   10   10   10   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     A       7     A       7      8   10   15     8    8    8    9   10   10   10   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     E       8     E       8      8   10   15     8    8    8    9   10   10   10   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     M       9     M       9      8   10   15     8    8    8    9   10   10   10   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     C      10     C      10      8   10   15     8    8    8    9   10   10   10   10   10   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     Y      11     Y      11      8   10   15     8    8    8    9   10   10   10   10   10   11   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     E      12     E      12      3    3   15     3    3    3    5    7    8    9   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     I      13     I      13      4    4   15     3    3    4    6    6    8    9   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     T      14     T      14      4    4   15     3    3    4    6    7    8    9   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     N      15     N      15      4    4   15     3    3    4    6    7    8    9   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_GDT     S      16     S      16      4    4   15     0    3    4    6    7    8    9   10   11   12   12   13   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   4.52  (   2.83    3.71    7.01 )

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      8      8      8      9     10     10     10     10     11     12     12     13     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   3.74   3.74   3.74   4.21   4.67   4.67   4.67   4.67   5.14   5.61   5.61   6.07   7.01   7.01   7.01   7.01   7.01   7.01   7.01   7.01
GDT RMS_LOCAL    0.16   0.16   0.16   0.93   1.26   1.26   1.26   1.26   2.99   3.35   3.35   3.75   4.45   4.45   4.45   4.45   4.45   4.45   4.45   4.45
GDT RMS_ALL_CA   7.94   7.94   7.94   8.37   8.63   8.63   8.63   8.63   4.81   4.96   4.96   5.01   4.45   4.45   4.45   4.45   4.45   4.45   4.45   4.45

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          2.077
LGA    Q       2      Q       2          2.460
LGA    S       4      S       4          1.424
LGA    K       5      K       5          0.973
LGA    A       6      A       6          0.860
LGA    A       7      A       7          0.659
LGA    E       8      E       8          0.371
LGA    M       9      M       9          0.334
LGA    C      10      C      10          0.258
LGA    Y      11      Y      11          0.963
LGA    E      12      E      12          8.573
LGA    I      13      I      13         13.128
LGA    T      14      T      14         15.218
LGA    N      15      N      15         16.427
LGA    S      16      S      16         18.835

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  214    4.0     10    1.26     4.907     4.692     0.738

LGA_LOCAL      RMSD =  1.255  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.632  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  4.448  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.497310 * X  +  -0.649353 * Y  +   0.575346 * Z  +  19.180782
  Y_new =   0.848046 * X  +   0.223939 * Y  +  -0.480280 * Z  +  13.934649
  Z_new =   0.183029 * X  +   0.726768 * Y  +   0.662049 * Z  + -58.675915 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.831965   -2.309628  [ DEG:    47.6681   -132.3319 ]
  Theta =  -0.184066   -2.957526  [ DEG:   -10.5462   -169.4538 ]
  Phi   =   1.040423   -2.101170  [ DEG:    59.6118   -120.3882 ]
 
# 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: T0320TS239_2_1-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_2_1-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  214   4.0   10   1.26   4.692     4.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_2_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1       6.954  43.544  24.044  1.00  9.99
ATOM      2  CA  MET     1       6.793  42.339  23.200  1.00  9.99
ATOM      3  C   MET     1       7.227  41.127  24.030  1.00  9.99
ATOM      4  O   MET     1       6.596  40.071  23.800  1.00  9.99
ATOM      5  CB  MET     1       7.578  42.431  21.912  1.00  9.99
ATOM      6  N   GLN     2       8.116  41.282  24.979  1.00  9.99
ATOM      7  CA  GLN     2       8.478  40.161  25.844  1.00  9.99
ATOM      8  C   GLN     2       7.279  39.620  26.576  1.00  9.99
ATOM      9  O   GLN     2       7.014  38.388  26.665  1.00  9.99
ATOM     10  CB  GLN     2       9.661  40.543  26.744  1.00  9.99
ATOM     11  N   SER     4       6.524  40.500  27.215  1.00  9.99
ATOM     12  CA  SER     4       5.326  40.142  27.945  1.00  9.99
ATOM     13  C   SER     4       4.290  39.532  27.048  1.00  9.99
ATOM     14  O   SER     4       3.607  38.541  27.387  1.00  9.99
ATOM     15  CB  SER     4       4.709  41.387  28.623  1.00  9.99
ATOM     16  N   LYS     5       4.126  40.003  25.834  1.00  9.99
ATOM     17  CA  LYS     5       3.198  39.508  24.869  1.00  9.99
ATOM     18  C   LYS     5       3.603  38.062  24.522  1.00  9.99
ATOM     19  O   LYS     5       2.769  37.153  24.464  1.00  9.99
ATOM     20  CB  LYS     5       3.096  40.332  23.621  1.00  9.99
ATOM     21  N   ALA     6       4.861  37.817  24.169  1.00  9.99
ATOM     22  CA  ALA     6       5.308  36.485  23.767  1.00  9.99
ATOM     23  C   ALA     6       5.185  35.520  24.933  1.00  9.99
ATOM     24  O   ALA     6       4.682  34.391  24.732  1.00  9.99
ATOM     25  CB  ALA     6       6.767  36.551  23.315  1.00  9.99
ATOM     26  N   ALA     7       5.463  35.955  26.154  1.00  9.99
ATOM     27  CA  ALA     7       5.259  35.120  27.329  1.00  9.99
ATOM     28  C   ALA     7       3.845  34.694  27.414  1.00  9.99
ATOM     29  O   ALA     7       3.495  33.530  27.729  1.00  9.99
ATOM     30  CB  ALA     7       5.571  35.918  28.584  1.00  9.99
ATOM     31  N   GLU     8       2.865  35.600  27.238  1.00  9.99
ATOM     32  CA  GLU     8       1.449  35.278  27.330  1.00  9.99
ATOM     33  C   GLU     8       1.046  34.339  26.242  1.00  9.99
ATOM     34  O   GLU     8       0.308  33.328  26.390  1.00  9.99
ATOM     35  CB  GLU     8       0.568  36.556  27.323  1.00  9.99
ATOM     36  N   MET     9       1.498  34.586  25.011  1.00  9.99
ATOM     37  CA  MET     9       1.127  33.802  23.856  1.00  9.99
ATOM     38  C   MET     9       1.651  32.361  23.997  1.00  9.99
ATOM     39  O   MET     9       0.976  31.455  23.479  1.00  9.99
ATOM     40  CB  MET     9       1.596  34.459  22.547  1.00  9.99
ATOM     41  N   CYS    10       2.811  32.198  24.559  1.00  9.99
ATOM     42  CA  CYS    10       3.420  30.854  24.683  1.00  9.99
ATOM     43  C   CYS    10       3.048  30.208  26.000  1.00  9.99
ATOM     44  O   CYS    10       3.564  29.098  26.294  1.00  9.99
ATOM     45  CB  CYS    10       4.923  30.968  24.468  1.00  9.99
ATOM     46  N   TYR    11       2.250  30.879  26.835  1.00  9.99
ATOM     47  CA  TYR    11       1.741  30.282  28.096  1.00  9.99
ATOM     48  C   TYR    11       2.808  30.134  29.104  1.00  9.99
ATOM     49  O   TYR    11       2.789  29.152  29.953  1.00  9.99
ATOM     50  CB  TYR    11       0.862  29.068  27.793  1.00  9.99
ATOM     51  N   GLU    12       3.866  30.900  29.275  1.00  9.99
ATOM     52  CA  GLU    12       4.967  30.750  30.127  1.00  9.99
ATOM     53  C   GLU    12       4.882  31.399  31.536  1.00  9.99
ATOM     54  O   GLU    12       4.534  32.603  31.618  1.00  9.99
ATOM     55  CB  GLU    12       6.284  31.301  29.553  1.00  9.99
ATOM     56  N   ILE    13       5.241  30.744  32.617  1.00  9.99
ATOM     57  CA  ILE    13       5.384  31.334  33.965  1.00  9.99
ATOM     58  C   ILE    13       6.777  31.670  34.337  1.00  9.99
ATOM     59  O   ILE    13       7.706  30.971  34.059  1.00  9.99
ATOM     60  CB  ILE    13       5.043  30.259  35.044  1.00  9.99
ATOM     61  N   THR    14       6.993  32.771  35.100  1.00  9.99
ATOM     62  CA  THR    14       8.278  33.207  35.562  1.00  9.99
ATOM     63  C   THR    14       8.756  32.218  36.638  1.00  9.99
ATOM     64  O   THR    14       9.886  31.956  36.789  1.00  9.99
ATOM     65  CB  THR    14       8.113  34.562  36.297  1.00  9.99
ATOM     66  N   ASN    15       7.615  31.755  37.247  1.00  9.99
ATOM     67  CA  ASN    15       7.439  30.931  38.395  1.00  9.99
ATOM     68  C   ASN    15       6.359  29.773  38.328  1.00  9.99
ATOM     69  O   ASN    15       5.177  30.035  38.154  1.00  9.99
ATOM     70  CB  ASN    15       6.992  31.814  39.609  1.00  9.99
ATOM     71  N   SER    16       6.991  28.635  38.579  1.00  9.99
ATOM     72  CA  SER    16       6.235  27.367  38.667  1.00  9.99
ATOM     73  C   SER    16       6.669  26.592  39.960  1.00  9.99
ATOM     74  O   SER    16       7.670  26.597  40.658  1.00  9.99
ATOM     75  CB  SER    16       6.441  26.461  37.428  1.00  9.99
TER
END
