
#######################################################
#                                                     #
#                        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 (   75),  selected    9 , name T0356TS013_1_2-D1
# Molecule2: number of CA atoms  124 (  963),  selected    9 , name T0356_D1.pdb
# PARAMETERS: T0356TS013_1_2-D1.T0356_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:     9       314 - 322         1.36     1.36
  LCS_AVERAGE:      7.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       314 - 322         1.36     1.36
  LCS_AVERAGE:      7.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       314 - 320         0.95     1.94
  LONGEST_CONTINUOUS_SEGMENT:     7       316 - 322         0.85     1.95
  LCS_AVERAGE:      5.65

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:  124
LCS_GDT     D     314     D     314      7    9    9     4    5    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     315     A     315      7    9    9     4    5    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     I     316     I     316      7    9    9     5    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     317     Y     317      7    9    9     5    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     318     H     318      7    9    9     5    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     S     319     S     319      7    9    9     5    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     T     320     T     320      7    9    9     5    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     321     Y     321      7    9    9     3    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     T     322     T     322      7    9    9     3    6    7    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   6.72  (   5.65    7.26    7.26 )

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      5      6      7      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   4.03   4.84   5.65   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26   7.26
GDT RMS_LOCAL    0.38   0.65   0.85   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36
GDT RMS_ALL_CA   2.03   2.01   1.95   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36   1.36

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          1.950
LGA    A     315      A     315          1.024
LGA    I     316      I     316          0.925
LGA    Y     317      Y     317          1.852
LGA    H     318      H     318          0.931
LGA    S     319      S     319          0.756
LGA    T     320      T     320          1.265
LGA    Y     321      Y     321          1.087
LGA    T     322      T     322          1.808

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  124    4.0      9    1.36     6.653     6.947     0.617

LGA_LOCAL      RMSD =  1.359  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.359  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  1.359  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.988522 * X  +   0.146322 * Y  +   0.037613 * Z  +  66.065086
  Y_new =   0.119521 * X  +   0.909692 * Y  +  -0.397712 * Z  +  68.942734
  Z_new =  -0.092410 * X  +  -0.388651 * Y  +  -0.916739 * Z  +  82.754555 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.740612    0.400981  [ DEG:  -157.0255     22.9745 ]
  Theta =   0.092542    3.049051  [ DEG:     5.3023    174.6977 ]
  Phi   =   3.021268   -0.120325  [ DEG:   173.1059     -6.8941 ]
 
# 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: T0356TS013_1_2-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS013_1_2-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  124   4.0    9   1.36   6.947     1.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS013_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0356
PARENT N/A
ATOM   2449  N   ASP   314      76.263  73.228  98.942  1.00  8.97
ATOM   2450  CA  ASP   314      75.763  74.363  98.161  1.00  8.97
ATOM   2451  C   ASP   314      75.769  74.099  96.652  1.00  8.97
ATOM   2452  O   ASP   314      75.422  74.970  95.844  1.00  8.97
ATOM   2453  CB  ASP   314      76.555  75.642  98.524  1.00  8.97
ATOM   2454  CG  ASP   314      76.026  76.526  99.647  1.00  8.97
ATOM   2455  OD1 ASP   314      74.821  76.739  99.779  1.00  8.97
ATOM   2456  OD2 ASP   314      76.858  77.041 100.391  1.00  8.97
ATOM   2457  N   ALA   315      76.126  72.877  96.217  1.00  9.42
ATOM   2458  CA  ALA   315      75.940  72.601  94.791  1.00  9.42
ATOM   2459  C   ALA   315      74.457  72.563  94.425  1.00  9.42
ATOM   2460  O   ALA   315      73.629  72.189  95.235  1.00  9.42
ATOM   2461  CB  ALA   315      76.663  71.305  94.428  1.00  9.42
ATOM   2462  N   ILE   316      74.163  72.968  93.198  1.00  0.10
ATOM   2463  CA  ILE   316      72.799  72.985  92.653  1.00  0.10
ATOM   2464  C   ILE   316      72.826  72.045  91.448  1.00  0.10
ATOM   2465  O   ILE   316      73.572  72.328  90.485  1.00  0.10
ATOM   2466  CB  ILE   316      72.396  74.389  92.236  1.00  0.10
ATOM   2467  CG1 ILE   316      72.496  75.373  93.410  1.00  0.10
ATOM   2468  CG2 ILE   316      70.955  74.424  91.719  1.00  0.10
ATOM   2469  CD1 ILE   316      72.270  76.843  93.028  1.00  0.10
ATOM   2470  N   TYR   317      72.056  70.974  91.521  1.00  4.60
ATOM   2471  CA  TYR   317      72.094  69.949  90.480  1.00  4.60
ATOM   2472  C   TYR   317      70.730  69.785  89.849  1.00  4.60
ATOM   2473  O   TYR   317      69.714  69.831  90.558  1.00  4.60
ATOM   2474  CB  TYR   317      72.597  68.624  91.064  1.00  4.60
ATOM   2475  CG  TYR   317      74.023  68.735  91.598  1.00  4.60
ATOM   2476  CD1 TYR   317      75.089  68.880  90.709  1.00  4.60
ATOM   2477  CD2 TYR   317      74.245  68.673  92.967  1.00  4.60
ATOM   2478  CE1 TYR   317      76.378  68.962  91.205  1.00  4.60
ATOM   2479  CE2 TYR   317      75.527  68.751  93.460  1.00  4.60
ATOM   2480  CZ  TYR   317      76.583  68.892  92.578  1.00  4.60
ATOM   2481  OH  TYR   317      77.870  68.920  93.094  1.00  4.60
ATOM   2482  N   HIS   318      70.681  69.603  88.546  1.00  6.17
ATOM   2483  CA  HIS   318      69.408  69.350  87.852  1.00  6.17
ATOM   2484  C   HIS   318      69.145  67.868  87.716  1.00  6.17
ATOM   2485  O   HIS   318      70.030  67.137  87.195  1.00  6.17
ATOM   2486  CB  HIS   318      69.418  70.009  86.457  1.00  6.17
ATOM   2487  CG  HIS   318      69.521  71.488  86.402  1.00  6.17
ATOM   2488  ND1 HIS   318      68.550  72.318  86.892  1.00  6.17
ATOM   2489  CD2 HIS   318      70.420  72.292  85.797  1.00  6.17
ATOM   2490  CE1 HIS   318      68.896  73.579  86.569  1.00  6.17
ATOM   2491  NE2 HIS   318      70.042  73.607  85.893  1.00  6.17
ATOM   2492  N   SER   319      67.970  67.410  88.129  1.00  8.31
ATOM   2493  CA  SER   319      67.603  66.009  87.883  1.00  8.31
ATOM   2494  C   SER   319      66.202  65.999  87.292  1.00  8.31
ATOM   2495  O   SER   319      65.424  66.935  87.415  1.00  8.31
ATOM   2496  CB  SER   319      67.665  65.140  89.153  1.00  8.31
ATOM   2497  OG  SER   319      66.614  65.309  90.097  1.00  8.31
ATOM   2498  N   THR   320      65.896  64.870  86.608  1.00  9.25
ATOM   2499  CA  THR   320      64.634  64.764  85.880  1.00  9.25
ATOM   2500  C   THR   320      63.875  63.527  86.344  1.00  9.25
ATOM   2501  O   THR   320      64.493  62.443  86.415  1.00  9.25
ATOM   2502  CB  THR   320      64.868  64.636  84.372  1.00  9.25
ATOM   2503  OG1 THR   320      65.563  63.431  84.094  1.00  9.25
ATOM   2504  CG2 THR   320      65.677  65.821  83.801  1.00  9.25
ATOM   2505  N   TYR   321      62.601  63.660  86.664  1.00  6.58
ATOM   2506  CA  TYR   321      61.878  62.469  87.152  1.00  6.58
ATOM   2507  C   TYR   321      60.497  62.476  86.528  1.00  6.58
ATOM   2508  O   TYR   321      59.855  63.525  86.516  1.00  6.58
ATOM   2509  CB  TYR   321      61.734  62.481  88.684  1.00  6.58
ATOM   2510  CG  TYR   321      63.089  62.447  89.383  1.00  6.58
ATOM   2511  CD1 TYR   321      63.859  61.285  89.351  1.00  6.58
ATOM   2512  CD2 TYR   321      63.530  63.572  90.066  1.00  6.58
ATOM   2513  CE1 TYR   321      65.076  61.262  90.010  1.00  6.58
ATOM   2514  CE2 TYR   321      64.739  63.548  90.724  1.00  6.58
ATOM   2515  CZ  TYR   321      65.501  62.395  90.693  1.00  6.58
ATOM   2516  OH  TYR   321      66.691  62.377  91.404  1.00  6.58
ATOM   2517  N   THR   322      60.188  61.386  85.796  1.00  8.66
ATOM   2518  CA  THR   322      58.909  61.297  85.147  1.00  8.66
ATOM   2519  C   THR   322      57.836  60.744  86.077  1.00  8.66
ATOM   2520  O   THR   322      56.675  61.113  85.958  1.00  8.66
ATOM   2521  CB  THR   322      59.016  60.426  83.881  1.00  8.66
ATOM   2522  OG1 THR   322      59.977  61.056  83.013  1.00  8.66
ATOM   2523  CG2 THR   322      57.668  60.240  83.177  1.00  8.66
TER
END
