
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    3 , name T0316_D1.pdb
# PARAMETERS: T0316TS020_2_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         0.12     0.12
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.12     0.12
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.12     0.12
  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    0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12
GDT RMS_ALL_CA   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12   0.12

#      Molecule1      Molecule2       DISTANCE
LGA    A     191      A     191          0.135
LGA    K     192      K     192          0.107
LGA    K     193      K     193          0.127

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  188    4.0      3    0.12     1.596     1.596     1.342

LGA_LOCAL      RMSD =  0.124  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.123  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.124  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.316503 * X  +   0.741545 * Y  +   0.591555 * Z  + -12.110573
  Y_new =  -0.892812 * X  +  -0.022178 * Y  +  -0.449884 * Z  +  22.873795
  Z_new =  -0.320489 * X  +  -0.670537 * Y  +   0.669079 * Z  +  30.735073 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.786486    2.355106  [ DEG:   -45.0623    134.9377 ]
  Theta =   0.326246    2.815347  [ DEG:    18.6925    161.3075 ]
  Phi   =  -1.911475    1.230117  [ DEG:  -109.5195     70.4805 ]
 
# 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_2_2-D1                             
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS020_2_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   0.12   1.596     0.12
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS020_2_2-D1
REMARK PARENT number 2
PFRMAT    TS
TARGET    T0316
PARENT    N/A
ATOM   2954  N   ALA   191      19.505  45.783  11.266  1.00  1.00
ATOM   2955  CA  ALA   191      20.767  45.981  10.562  1.00  1.00
ATOM   2956  C   ALA   191      20.537  46.214   9.075  1.00  1.00
ATOM   2957  O   ALA   191      19.444  45.981   8.561  1.00  1.00
ATOM   2958  CB  ALA   191      21.687  44.789  10.780  1.00  1.00
ATOM   2959  H   ALA   191      18.843  45.108  10.908  1.00  1.00
ATOM   2960  HA  ALA   191      21.252  46.873  10.960  1.00  1.00
ATOM   2961 1HB  ALA   191      22.625  44.953  10.249  1.00  1.00
ATOM   2962 2HB  ALA   191      21.889  44.675  11.845  1.00  1.00
ATOM   2963 3HB  ALA   191      21.209  43.887  10.402  1.00  1.00
ATOM   2964  N   LYS   192      21.507  46.687   8.357  1.00  1.00
ATOM   2965  CA  LYS   192      21.401  46.880   6.916  1.00  1.00
ATOM   2966  C   LYS   192      22.520  46.153   6.179  1.00  1.00
ATOM   2967  O   LYS   192      22.343  45.712   5.043  1.00  1.00
ATOM   2968  CB  LYS   192      21.428  48.370   6.570  1.00  1.00
ATOM   2969  CG  LYS   192      20.301  49.181   7.197  1.00  1.00
ATOM   2970  CD  LYS   192      18.942  48.736   6.676  1.00  1.00
ATOM   2971  CE  LYS   192      17.830  49.643   7.181  1.00  1.00
ATOM   2972  NZ  LYS   192      16.492  49.203   6.699  1.00  1.00
ATOM   2973  H   LYS   192      22.372  46.934   8.815  1.00  1.00
ATOM   2974 1HZ  LYS   192      15.784  49.830   7.056  1.00  1.00
ATOM   2975 2HZ  LYS   192      16.476  49.216   5.690  1.00  1.00
ATOM   2976 3HZ  LYS   192      16.308  48.266   7.028  1.00  1.00
ATOM   2977  HA  LYS   192      20.464  46.456   6.554  1.00  1.00
ATOM   2978 1HB  LYS   192      22.387  48.760   6.911  1.00  1.00
ATOM   2979 2HB  LYS   192      21.370  48.449   5.485  1.00  1.00
ATOM   2980 1HG  LYS   192      20.336  49.045   8.279  1.00  1.00
ATOM   2981 2HG  LYS   192      20.456  50.232   6.958  1.00  1.00
ATOM   2982 1HD  LYS   192      18.964  48.759   5.586  1.00  1.00
ATOM   2983 2HD  LYS   192      18.758  47.716   7.012  1.00  1.00
ATOM   2984 1HE  LYS   192      17.847  49.630   8.270  1.00  1.00
ATOM   2985 2HE  LYS   192      18.028  50.655   6.827  1.00  1.00
ATOM   2986  N   LYS   193      23.670  46.032   6.832  1.00  1.00
ATOM   2987  CA  LYS   193      24.797  45.297   6.270  1.00  1.00
ATOM   2988  C   LYS   193      25.437  44.388   7.311  1.00  1.00
ATOM   2989  O   LYS   193      25.862  44.847   8.372  1.00  1.00
ATOM   2990  CB  LYS   193      25.838  46.264   5.704  1.00  1.00
ATOM   2991  CG  LYS   193      25.352  47.088   4.519  1.00  1.00
ATOM   2992  CD  LYS   193      26.433  48.037   4.025  1.00  1.00
ATOM   2993  CE  LYS   193      25.940  48.882   2.859  1.00  1.00
ATOM   2994  NZ  LYS   193      26.978  49.834   2.382  1.00  1.00
ATOM   2995  H   LYS   193      23.766  46.459   7.743  1.00  1.00
ATOM   2996 1HZ  LYS   193      26.612  50.373   1.610  1.00  1.00
ATOM   2997 2HZ  LYS   193      27.237  50.456   3.135  1.00  1.00
ATOM   2998 3HZ  LYS   193      27.793  49.320   2.077  1.00  1.00
ATOM   2999  HA  LYS   193      24.450  44.649   5.465  1.00  1.00
ATOM   3000 1HB  LYS   193      26.128  46.932   6.516  1.00  1.00
ATOM   3001 2HB  LYS   193      26.698  45.667   5.401  1.00  1.00
ATOM   3002 1HG  LYS   193      25.071  46.407   3.715  1.00  1.00
ATOM   3003 2HG  LYS   193      24.480  47.661   4.830  1.00  1.00
ATOM   3004 1HD  LYS   193      26.726  48.691   4.849  1.00  1.00
ATOM   3005 2HD  LYS   193      27.293  47.449   3.707  1.00  1.00
ATOM   3006 1HE  LYS   193      25.662  48.211   2.046  1.00  1.00
ATOM   3007 2HE  LYS   193      25.062  49.437   3.187  1.00  1.00
TER
END
