
#######################################################
#                                                     #
#                        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    3 (   54),  selected    3 , name T0316TS020_3_2-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    3 , name T0316_D1.pdb
# PARAMETERS: T0316TS020_3_2-D1.T0316_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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.20     0.20
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.20     0.20
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.20     0.20
  LCS_AVERAGE:      1.60

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:  188
LCS_GDT     A     191     A     191      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     K     192     K     192      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     K     193     K     193      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   1.60  (   1.60    1.60    1.60 )

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      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60   1.60
GDT RMS_LOCAL    0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20
GDT RMS_ALL_CA   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20   0.20

#      Molecule1      Molecule2       DISTANCE
LGA    A     191      A     191          0.227
LGA    K     192      K     192          0.137
LGA    K     193      K     193          0.235

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  188    4.0      3    0.20     1.596     1.596     0.986

LGA_LOCAL      RMSD =  0.204  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.204  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.204  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.778287 * X  +  -0.031102 * Y  +   0.627138 * Z  +   2.625919
  Y_new =  -0.423273 * X  +   0.763720 * Y  +  -0.487413 * Z  +   5.152292
  Z_new =  -0.463798 * X  +  -0.644798 * Y  +  -0.607558 * Z  +  19.357012 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.326468    0.815125  [ DEG:  -133.2968     46.7032 ]
  Theta =   0.482278    2.659315  [ DEG:    27.6325    152.3675 ]
  Phi   =  -2.643481    0.498111  [ DEG:  -151.4603     28.5397 ]
 
# 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: T0316TS020_3_2-D1                             
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS020_3_2-D1.T0316_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  188   4.0    3   0.20   1.596     0.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS020_3_2-D1
REMARK PARENT number 2
PFRMAT    TS
TARGET    T0316
PARENT    N/A
ATOM   2954  N   ALA   191      20.273  44.825  11.011  1.00  1.00
ATOM   2955  CA  ALA   191      21.069  45.879  10.391  1.00  1.00
ATOM   2956  C   ALA   191      20.973  45.820   8.873  1.00  1.00
ATOM   2957  O   ALA   191      20.641  44.781   8.301  1.00  1.00
ATOM   2958  CB  ALA   191      22.520  45.779  10.839  1.00  1.00
ATOM   2959  H   ALA   191      20.703  44.224  11.700  1.00  1.00
ATOM   2960  HA  ALA   191      20.674  46.845  10.705  1.00  1.00
ATOM   2961 1HB  ALA   191      23.100  46.572  10.367  1.00  1.00
ATOM   2962 2HB  ALA   191      22.576  45.884  11.922  1.00  1.00
ATOM   2963 3HB  ALA   191      22.925  44.811  10.547  1.00  1.00
ATOM   2964  N   LYS   192      21.266  46.941   8.222  1.00  1.00
ATOM   2965  CA  LYS   192      21.259  47.006   6.766  1.00  1.00
ATOM   2966  C   LYS   192      22.459  46.278   6.176  1.00  1.00
ATOM   2967  O   LYS   192      22.526  46.048   4.968  1.00  1.00
ATOM   2968  CB  LYS   192      21.242  48.462   6.295  1.00  1.00
ATOM   2969  CG  LYS   192      19.991  49.237   6.686  1.00  1.00
ATOM   2970  CD  LYS   192      18.774  48.745   5.917  1.00  1.00
ATOM   2971  CE  LYS   192      18.852  49.134   4.448  1.00  1.00
ATOM   2972  NZ  LYS   192      17.686  48.625   3.676  1.00  1.00
ATOM   2973  H   LYS   192      21.500  47.769   8.751  1.00  1.00
ATOM   2974 1HZ  LYS   192      17.776  48.903   2.709  1.00  1.00
ATOM   2975 2HZ  LYS   192      17.656  47.617   3.734  1.00  1.00
ATOM   2976 3HZ  LYS   192      16.835  49.010   4.059  1.00  1.00
ATOM   2977  HA  LYS   192      20.370  46.506   6.379  1.00  1.00
ATOM   2978 1HB  LYS   192      22.118  48.947   6.727  1.00  1.00
ATOM   2979 2HB  LYS   192      21.335  48.448   5.209  1.00  1.00
ATOM   2980 1HG  LYS   192      19.823  49.105   7.756  1.00  1.00
ATOM   2981 2HG  LYS   192      20.155  50.291   6.471  1.00  1.00
ATOM   2982 1HD  LYS   192      18.723  47.658   6.004  1.00  1.00
ATOM   2983 2HD  LYS   192      17.880  49.185   6.362  1.00  1.00
ATOM   2984 1HE  LYS   192      18.883  50.220   4.384  1.00  1.00
ATOM   2985 2HE  LYS   192      19.771  48.718   4.034  1.00  1.00
ATOM   2986  N   LYS   193      23.407  45.917   7.034  1.00  1.00
ATOM   2987  CA  LYS   193      24.637  45.273   6.591  1.00  1.00
ATOM   2988  C   LYS   193      25.849  45.841   7.318  1.00  1.00
ATOM   2989  O   LYS   193      26.790  46.326   6.691  1.00  1.00
ATOM   2990  CB  LYS   193      24.810  45.430   5.079  1.00  1.00
ATOM   2991  CG  LYS   193      26.041  44.736   4.512  1.00  1.00
ATOM   2992  CD  LYS   193      26.062  44.805   2.992  1.00  1.00
ATOM   2993  CE  LYS   193      26.364  46.215   2.505  1.00  1.00
ATOM   2994  NZ  LYS   193      26.440  46.286   1.021  1.00  1.00
ATOM   2995  H   LYS   193      23.270  46.093   8.019  1.00  1.00
ATOM   2996 1HZ  LYS   193      26.643  47.235   0.740  1.00  1.00
ATOM   2997 2HZ  LYS   193      27.174  45.674   0.691  1.00  1.00
ATOM   2998 3HZ  LYS   193      25.558  45.998   0.624  1.00  1.00
ATOM   2999  HA  LYS   193      24.602  44.209   6.829  1.00  1.00
ATOM   3000 1HB  LYS   193      23.914  45.020   4.611  1.00  1.00
ATOM   3001 2HB  LYS   193      24.869  46.499   4.874  1.00  1.00
ATOM   3002 1HG  LYS   193      26.929  45.226   4.911  1.00  1.00
ATOM   3003 2HG  LYS   193      26.027  43.694   4.829  1.00  1.00
ATOM   3004 1HD  LYS   193      26.829  44.121   2.624  1.00  1.00
ATOM   3005 2HD  LYS   193      25.088  44.493   2.616  1.00  1.00
ATOM   3006 1HE  LYS   193      25.574  46.875   2.860  1.00  1.00
ATOM   3007 2HE  LYS   193      27.317  46.527   2.933  1.00  1.00
TER
END
