
#######################################################
#                                                     #
#                        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   32 (   32),  selected   29 , name T0330TS464_3_2
# Molecule2: number of CA atoms  225 ( 1744),  selected   29 , name T0330.pdb
# PARAMETERS: T0330TS464_3_2.T0330.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:    12         8 - 22          4.30    20.36
  LCS_AVERAGE:      4.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        13 - 20          1.83    21.64
  LCS_AVERAGE:      2.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6         3 - 8           0.64    20.28
  LONGEST_CONTINUOUS_SEGMENT:     6        15 - 20          0.99    22.85
  LCS_AVERAGE:      2.11

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:  225
LCS_GDT     S       2     S       2      3    7   10     3    3    3    5    5    7    7    8    9   11   13   14   14   15   15   15   15   16   17   17 
LCS_GDT     R       3     R       3      6    7   10     4    6    6    6    7    9    9   10   11   12   13   14   14   15   15   15   15   16   17   17 
LCS_GDT     T       4     T       4      6    7   10     4    6    6    6    7    9    9   10   11   12   13   14   14   15   15   15   15   16   17   17 
LCS_GDT     L       5     L       5      6    7   10     4    6    6    6    7    9    9   10   11   12   13   14   14   15   15   15   15   16   17   17 
LCS_GDT     V       6     V       6      6    7   10     4    6    6    6    7    9    9   10   11   12   13   14   14   15   15   15   15   16   17   17 
LCS_GDT     L       7     L       7      6    7   10     4    6    6    6    7    9    9   10   11   12   13   14   14   15   15   15   15   16   17   17 
LCS_GDT     F       8     F       8      6    7   12     4    6    6    6    7    9    9   10   11   12   13   14   14   15   15   16   16   17   17   18 
LCS_GDT     G      12     G      12      3    4   12     3    4    4    5    6    6    6    6   11   11   11   12   14   14   15   16   16   17   17   18 
LCS_GDT     T      13     T      13      3    8   12     3    4    4    6    7    9    9   10   11   12   13   14   14   15   15   16   16   17   17   18 
LCS_GDT     L      14     L      14      3    8   12     3    4    4    5    7    7    8    9   11   12   13   14   14   15   15   16   16   17   17   18 
LCS_GDT     L      15     L      15      6    8   12     3    4    6    6    7    7    8    9   10   11   12   13   14   15   15   16   16   17   17   18 
LCS_GDT     K      16     K      16      6    8   12     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     V      17     V      17      6    8   12     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     E      18     E      18      6    8   12     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     S      19     S      19      6    8   12     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     M      20     M      20      6    8   12     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     N      21     N      21      3    5   12     3    3    4    4    4    5    5    6   10   11   11   11   13   15   15   15   16   17   17   18 
LCS_GDT     R      22     R      22      3    5   12     3    3    4    4    4    5    5    6    9   11   11   11   13   15   15   15   16   17   17   18 
LCS_GDT     E      36     E      36      4    5    8     3    3    5    5    5    5    5    6    7    7    9   10   10   11   11   12   13   14   15   15 
LCS_GDT     G      37     G      37      4    5   10     3    4    5    5    5    5    5    6    7    7    9   10   10   11   11   12   13   14   15   15 
LCS_GDT     S      38     S      38      4    5   10     3    4    5    5    5    5    5    6    7    7    9   10   10   11   11   12   13   14   15   15 
LCS_GDT     T      39     T      39      4    5   10     1    4    5    5    5    5    5    6    7    7    9   10   10   11   11   12   13   14   15   15 
LCS_GDT     F      44     F      44      4    5   10     3    4    5    5    5    6    7    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     S      45     S      45      5    5   10     3    3    5    5    5    6    7    9   10   11   12   12   14   15   15   16   16   17   17   18 
LCS_GDT     G      46     G      46      5    5   10     3    4    5    5    5    6    7    9   10   11   13   14   14   15   15   16   16   17   17   18 
LCS_GDT     K      47     K      47      5    5   10     3    4    5    5    5    6    7    9   10   12   13   14   14   15   15   16   16   17   17   18 
LCS_GDT     M      48     M      48      5    5   10     3    4    5    5    6    9    9   10   11   12   13   14   14   15   15   16   16   17   17   18 
LCS_GDT     D      49     D      49      5    5   10     3    4    5    5    6    9    9   10   11   12   13   14   14   15   15   15   16   16   17   17 
LCS_GDT     G      50     G      50      3    3   10     3    3    3    5    6    6    8   10   11   12   13   14   14   15   15   16   16   16   17   18 
LCS_AVERAGE  LCS_A:   3.22  (   2.11    2.76    4.78 )

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      4      6      6      6      7      9      9     10     11     12     13     14     14     15     15     16     16     17     17     18 
GDT PERCENT_CA   1.78   2.67   2.67   2.67   3.11   4.00   4.00   4.44   4.89   5.33   5.78   6.22   6.22   6.67   6.67   7.11   7.11   7.56   7.56   8.00
GDT RMS_LOCAL    0.31   0.64   0.64   0.64   1.47   2.19   2.19   2.48   2.86   3.51   3.76   4.19   4.12   4.66   4.53   4.97   4.97   5.52   5.52   5.90
GDT RMS_ALL_CA  20.55  20.28  20.28  20.28  23.04  19.44  19.44  19.21  19.03  18.48  18.64  18.28  18.00  17.90  17.74  17.45  17.26  17.80  17.80  17.52

#      Molecule1      Molecule2       DISTANCE
LGA    S       2      S       2          5.583
LGA    R       3      R       3          3.158
LGA    T       4      T       4          2.608
LGA    L       5      L       5          2.298
LGA    V       6      V       6          2.605
LGA    L       7      L       7          2.643
LGA    F       8      F       8          2.098
LGA    G      12      G      12          5.990
LGA    T      13      T      13          1.321
LGA    L      14      L      14          6.854
LGA    L      15      L      15         12.222
LGA    K      16      K      16         17.477
LGA    V      17      V      17         23.198
LGA    E      18      E      18         30.126
LGA    S      19      S      19         34.922
LGA    M      20      M      20         37.272
LGA    N      21      N      21         37.327
LGA    R      22      R      22         40.647
LGA    E      36      E      36         19.460
LGA    G      37      G      37         19.920
LGA    S      38      S      38         21.869
LGA    T      39      T      39         21.954
LGA    F      44      F      44         21.528
LGA    S      45      S      45         16.550
LGA    G      46      G      46          9.971
LGA    K      47      K      47          7.062
LGA    M      48      M      48          2.361
LGA    D      49      D      49          3.335
LGA    G      50      G      50          3.834

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32  225    4.0     10    2.48     4.222     3.945     0.388

LGA_LOCAL      RMSD =  2.477  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 18.905  Number of atoms =   29 
Std_ALL_ATOMS  RMSD = 14.006  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.737556 * X  +  -0.107384 * Y  +  -0.666693 * Z  +  91.934189
  Y_new =  -0.674476 * X  +   0.068810 * Y  +   0.735083 * Z  +  62.951874
  Z_new =  -0.033061 * X  +   0.991834 * Y  +  -0.123179 * Z  + -21.496611 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.694357   -1.447236  [ DEG:    97.0795    -82.9205 ]
  Theta =   0.033067    3.108526  [ DEG:     1.8946    178.1054 ]
  Phi   =  -2.400838    0.740755  [ DEG:  -137.5579     42.4421 ]
 
# 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: T0330TS464_3_2                                
REMARK     2: T0330.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0330TS464_3_2.T0330.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32  225   4.0   10   2.48   3.945    14.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS464_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0330
PARENT N/A
ATOM      1  CA  SER     2      19.980  57.201  33.182  1.00  0.00
ATOM      2  CA  ARG     3      22.987  54.877  33.398  1.00  0.00
ATOM      3  CA  THR     4      23.523  52.942  30.159  1.00  0.00
ATOM      4  CA  LEU     5      23.278  52.893  26.374  1.00  0.00
ATOM      5  CA  VAL     6      22.908  49.374  24.982  1.00  0.00
ATOM      6  CA  LEU     7      22.848  47.905  21.497  1.00  0.00
ATOM      7  CA  PHE     8      21.017  44.632  20.875  1.00  0.00
ATOM      8  CA  GLY    12      17.533  40.295  20.322  1.00  0.00
ATOM      9  CA  THR    13      20.936  39.660  21.891  1.00  0.00
ATOM     10  CA  LEU    14      22.833  42.266  23.921  1.00  0.00
ATOM     11  CA  LEU    15      26.075  43.109  22.096  1.00  0.00
ATOM     12  CA  LYS    16      27.378  46.364  23.549  1.00  0.00
ATOM     13  CA  VAL    17      27.016  48.734  26.487  1.00  0.00
ATOM     14  CA  GLU    18      28.420  52.167  27.350  1.00  0.00
ATOM     15  CA  SER    19      28.162  53.956  30.693  1.00  0.00
ATOM     16  CA  MET    20      26.425  57.293  30.213  1.00  0.00
ATOM     17  CA  ASN    21      26.146  58.611  33.777  1.00  0.00
ATOM     18  CA  ARG    22      28.172  61.732  32.944  1.00  0.00
ATOM     19  CA  GLU    36      18.352  48.392   9.390  1.00  0.00
ATOM     20  CA  GLY    37      20.318  45.673  11.110  1.00  0.00
ATOM     21  CA  SER    38      22.088  44.727  14.371  1.00  0.00
ATOM     22  CA  THR    39      23.634  47.474  16.479  1.00  0.00
ATOM     23  CA  GLY    40      26.990  45.796  17.056  1.00  0.00
ATOM     24  CA  SER    41      28.796  48.562  18.896  1.00  0.00
ATOM     25  CA  HIS    42      27.851  51.607  20.957  1.00  0.00
ATOM     26  CA  PHE    44      27.825  56.624  18.220  1.00  0.00
ATOM     27  CA  SER    45      26.613  53.311  16.812  1.00  0.00
ATOM     28  CA  GLY    46      28.201  50.780  14.467  1.00  0.00
ATOM     29  CA  LYS    47      25.841  48.440  12.645  1.00  0.00
ATOM     30  CA  MET    48      25.572  45.361  10.488  1.00  0.00
ATOM     31  CA  ASP    49      23.774  47.607   8.038  1.00  0.00
ATOM     32  CA  GLY    50      27.246  48.954   7.129  1.00  0.00
TER
END
