
#######################################################
#                                                     #
#                        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    9 (   76),  selected    9 , name T0316TS658_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected    9 , name T0316_D3.pdb
# PARAMETERS: T0316TS658_1-D3.T0316_D3.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:     9       284 - 292         1.43     1.43
  LCS_AVERAGE:     10.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       284 - 292         1.43     1.43
  LCS_AVERAGE:     10.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       284 - 290         0.97     1.66
  LONGEST_CONTINUOUS_SEGMENT:     7       285 - 291         1.00     1.73
  LCS_AVERAGE:      7.28

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:   90
LCS_GDT     M     284     M     284      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S     285     S     285      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     T     286     T     286      7    9    9     3    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S     287     S     287      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     288     L     288      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     E     289     E     289      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     290     A     290      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S     291     S     291      7    9    9     4    6    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Q     292     Q     292      3    9    9     0    3    3    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   9.09  (   7.28   10.00   10.00 )

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      8      8      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   4.44   6.67   8.89   8.89  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
GDT RMS_LOCAL    0.38   0.63   1.00   1.00   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43
GDT RMS_ALL_CA   2.73   1.57   1.62   1.62   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284          0.782
LGA    S     285      S     285          0.922
LGA    T     286      T     286          2.198
LGA    S     287      S     287          0.631
LGA    L     288      L     288          1.251
LGA    E     289      E     289          0.355
LGA    A     290      A     290          0.899
LGA    S     291      S     291          1.367
LGA    Q     292      Q     292          2.718

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9   90    4.0      9    1.43     8.889     9.576     0.588

LGA_LOCAL      RMSD =  1.432  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.432  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  1.432  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.126861 * X  +   0.701455 * Y  +  -0.701332 * Z  +  33.228294
  Y_new =  -0.855432 * X  +   0.280558 * Y  +   0.435344 * Z  +  29.711405
  Z_new =   0.502138 * X  +   0.655170 * Y  +   0.564455 * Z  + -82.993546 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.859640   -2.281952  [ DEG:    49.2538   -130.7462 ]
  Theta =  -0.526070   -2.615523  [ DEG:   -30.1416   -149.8584 ]
  Phi   =  -1.718024    1.423568  [ DEG:   -98.4355     81.5645 ]
 
# 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: T0316TS658_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS658_1-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9   90   4.0    9   1.43   9.576     1.43
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS658_1-D3
PFRMAT TS
TARGET T0316
MODEL  1
PARENT 1aab 1aac 1aaf 1aaj 1aalA
ATOM   2548  H   MET   284      25.514  10.941 -15.193  1.00  1.00              
ATOM   2549  N   MET   284      24.705  11.434 -15.224  1.00 28.50              
ATOM   2550  CA  MET   284      23.628  11.089 -14.269  1.00 20.18              
ATOM   2551  CB  MET   284      22.317  10.949 -15.048  1.00  3.04              
ATOM   2552  C   MET   284      23.787   9.829 -13.400  1.00 17.05              
ATOM   2553  O   MET   284      22.761   9.233 -13.066  1.00  1.00              
ATOM   2554  CG  MET   284      22.266   9.727 -15.954  1.00  2.85              
ATOM   2555  SD  MET   284      20.716   9.615 -16.873  1.00 20.33              
ATOM   2556  CE  MET   284      20.960  10.897 -18.093  1.00 27.05              
ATOM   2557  H   SER   285      25.731   9.967 -13.065  1.00  1.00              
ATOM   2558  N   SER   285      24.964   9.455 -12.909  1.00  8.79              
ATOM   2559  CA  SER   285      25.022   8.375 -11.905  1.00  1.00              
ATOM   2560  CB  SER   285      26.470   8.103 -11.494  1.00  1.00              
ATOM   2561  C   SER   285      24.225   8.738 -10.651  1.00  1.00              
ATOM   2562  O   SER   285      24.269   9.883 -10.195  1.00  1.00              
ATOM   2563  OG  SER   285      26.518   7.131 -10.463  1.00  1.00              
ATOM   2564  H   THR   286      23.418   6.946 -10.521  1.00  1.00              
ATOM   2565  N   THR   286      23.529   7.761 -10.073  1.00  1.00              
ATOM   2566  CA  THR   286      22.750   7.997  -8.858  1.00  1.00              
ATOM   2567  CB  THR   286      21.287   7.538  -9.026  1.00  1.00              
ATOM   2568  C   THR   286      23.375   7.244  -7.683  1.00  1.00              
ATOM   2569  O   THR   286      22.852   7.302  -6.568  1.00  1.00              
ATOM   2570  CG2 THR   286      20.575   8.359 -10.093  1.00  1.00              
ATOM   2571  OG1 THR   286      21.282   6.159  -9.411  1.00  1.00              
ATOM   2572  H   SER   287      24.920   6.599  -8.731  1.00  1.00              
ATOM   2573  N   SER   287      24.589   6.721  -7.866  1.00  1.00              
ATOM   2574  CA  SER   287      25.354   6.172  -6.746  1.00  1.14              
ATOM   2575  CB  SER   287      24.884   4.751  -6.433  1.00  1.00              
ATOM   2576  C   SER   287      26.857   6.140  -6.993  1.00  3.46              
ATOM   2577  O   SER   287      27.325   6.684  -7.995  1.00  1.00              
ATOM   2578  OG  SER   287      25.147   3.897  -7.534  1.00  1.00              
ATOM   2579  H   LEU   288      27.122   5.594  -5.135  1.00  1.00              
ATOM   2580  N   LEU   288      27.529   6.049  -5.857  1.00  8.44              
ATOM   2581  CA  LEU   288      28.876   6.562  -5.662  1.00  9.21              
ATOM   2582  CB  LEU   288      28.851   8.094  -5.666  1.00  3.53              
ATOM   2583  C   LEU   288      29.315   6.046  -4.300  1.00  6.26              
ATOM   2584  O   LEU   288      28.446   5.876  -3.441  1.00  1.00              
ATOM   2585  CG  LEU   288      27.751   8.735  -4.813  1.00  3.52              
ATOM   2586  CD1 LEU   288      28.297   9.158  -3.456  1.00 21.53              
ATOM   2587  CD2 LEU   288      27.129   9.914  -5.549  1.00 24.78              
ATOM   2588  H   GLU   289      31.156   6.677  -4.557  1.00  1.00              
ATOM   2589  N   GLU   289      30.570   6.254  -3.947  1.00  3.69              
ATOM   2590  CA  GLU   289      30.837   6.362  -2.521  1.00  1.31              
ATOM   2591  CB  GLU   289      31.968   5.413  -2.109  1.00  1.00              
ATOM   2592  C   GLU   289      31.192   7.797  -2.131  1.00  1.19              
ATOM   2593  O   GLU   289      31.898   8.487  -2.871  1.00  1.00              
ATOM   2594  CG  GLU   289      31.631   3.938  -2.281  1.00  1.00              
ATOM   2595  CD  GLU   289      32.781   3.013  -1.923  1.00  1.00              
ATOM   2596  OE1 GLU   289      33.871   3.519  -1.574  1.00  1.00              
ATOM   2597  OE2 GLU   289      32.562   1.783  -1.874  1.00  1.00              
ATOM   2598  H   ALA   290      30.248   7.653  -0.413  1.00  1.00              
ATOM   2599  N   ALA   290      30.808   8.204  -0.919  1.00  1.54              
ATOM   2600  CA  ALA   290      31.242   9.482  -0.349  1.00  1.19              
ATOM   2601  CB  ALA   290      30.108  10.125   0.442  1.00  1.00              
ATOM   2602  C   ALA   290      32.450   9.251   0.543  1.00  4.57              
ATOM   2603  O   ALA   290      32.525   8.218   1.214  1.00  1.00              
ATOM   2604  H   SER   291      33.052  11.116   0.437  1.00  1.00              
ATOM   2605  N   SER   291      33.306  10.254   0.693  1.00  8.93              
ATOM   2606  CA  SER   291      34.316  10.108   1.723  1.00  8.97              
ATOM   2607  CB  SER   291      35.517  11.007   1.420  1.00  1.03              
ATOM   2608  C   SER   291      33.700  10.492   3.061  1.00  7.58              
ATOM   2609  O   SER   291      34.380  11.133   3.865  1.00  1.00              
ATOM   2610  OG  SER   291      36.188  10.562   0.254  1.00  1.02              
ATOM   2611  H   GLN   292      32.173   9.301   2.849  1.00  1.00              
ATOM   2612  N   GLN   292      32.797   9.609   3.472  1.00  4.29              
ATOM   2613  CA  GLN   292      32.587   9.280   4.873  1.00  1.00              
ATOM   2614  CB  GLN   292      31.382  10.044   5.430  1.00  1.00              
ATOM   2615  C   GLN   292      32.375   7.780   5.054  1.00  1.00              
ATOM   2616  O   GLN   292      33.014   7.192   5.951  1.00  1.00              
ATOM   2617  OXT GLN   292      31.580   7.197   4.289  1.00  1.00              
ATOM   2618  CG  GLN   292      31.572  11.553   5.476  1.00  1.00              
ATOM   2619  CD  GLN   292      32.713  11.969   6.386  1.00  1.00              
ATOM   2620  NE2 GLN   292      33.521  12.918   5.927  1.00  1.00              
ATOM   2621 HE21 GLN   292      33.338  13.290   5.080  1.00  1.00              
ATOM   2622 HE22 GLN   292      34.192  13.267   6.489  1.00  1.00              
ATOM   2623  OE1 GLN   292      32.754  11.581   7.559  1.00  1.00              
TER
END
