
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    3 , name T0316_D1.pdb
# PARAMETERS: T0316TS020_4_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         0.63     0.63
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.63     0.63
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.63     0.63
  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     0    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     0    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     0    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      0      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   0.00   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  1000.00   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63
GDT RMS_ALL_CA 1000.00   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63   0.63

#      Molecule1      Molecule2       DISTANCE
LGA    A     191      A     191          0.649
LGA    K     192      K     192          0.588
LGA    K     193      K     193          0.640

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  188    4.0      3    0.63     1.596     1.596     0.413

LGA_LOCAL      RMSD =  0.626  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.626  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.626  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.774599 * X  +   0.499473 * Y  +   0.387973 * Z  + -17.393612
  Y_new =   0.151430 * X  +   0.742067 * Y  +  -0.652997 * Z  +  21.031734
  Z_new =  -0.614057 * X  +  -0.447060 * Y  +  -0.650439 * Z  +   8.327726 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.539427    0.602166  [ DEG:  -145.4984     34.5016 ]
  Theta =   0.661191    2.480402  [ DEG:    37.8834    142.1166 ]
  Phi   =   2.948533   -0.193059  [ DEG:   168.9385    -11.0615 ]
 
# 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_4_2-D1                             
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS020_4_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   0.63   1.596     0.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS020_4_2-D1
REMARK PARENT number 2
PFRMAT    TS
TARGET    T0316
PARENT    N/A
ATOM   2954  N   ALA   191      19.092  45.445  11.077  1.00  1.00
ATOM   2955  CA  ALA   191      20.317  46.160  10.738  1.00  1.00
ATOM   2956  C   ALA   191      20.786  45.811   9.331  1.00  1.00
ATOM   2957  O   ALA   191      20.739  44.652   8.921  1.00  1.00
ATOM   2958  CB  ALA   191      21.407  45.857  11.754  1.00  1.00
ATOM   2959  H   ALA   191      19.156  44.560  11.558  1.00  1.00
ATOM   2960  HA  ALA   191      20.112  47.232  10.755  1.00  1.00
ATOM   2961 1HB  ALA   191      22.315  46.398  11.486  1.00  1.00
ATOM   2962 2HB  ALA   191      21.078  46.169  12.745  1.00  1.00
ATOM   2963 3HB  ALA   191      21.612  44.787  11.760  1.00  1.00
ATOM   2964  N   LYS   192      21.239  46.821   8.595  1.00  1.00
ATOM   2965  CA  LYS   192      21.680  46.630   7.219  1.00  1.00
ATOM   2966  C   LYS   192      23.144  46.217   7.162  1.00  1.00
ATOM   2967  O   LYS   192      23.843  46.231   8.175  1.00  1.00
ATOM   2968  CB  LYS   192      21.461  47.906   6.404  1.00  1.00
ATOM   2969  CG  LYS   192      20.010  48.365   6.333  1.00  1.00
ATOM   2970  CD  LYS   192      19.153  47.371   5.562  1.00  1.00
ATOM   2971  CE  LYS   192      17.745  47.907   5.343  1.00  1.00
ATOM   2972  NZ  LYS   192      16.903  46.957   4.567  1.00  1.00
ATOM   2973  H   LYS   192      21.280  47.745   9.002  1.00  1.00
ATOM   2974 1HZ  LYS   192      15.980  47.349   4.444  1.00  1.00
ATOM   2975 2HZ  LYS   192      17.324  46.795   3.663  1.00  1.00
ATOM   2976 3HZ  LYS   192      16.834  46.082   5.068  1.00  1.00
ATOM   2977  HA  LYS   192      21.110  45.822   6.759  1.00  1.00
ATOM   2978 1HB  LYS   192      22.065  48.686   6.865  1.00  1.00
ATOM   2979 2HB  LYS   192      21.828  47.709   5.397  1.00  1.00
ATOM   2980 1HG  LYS   192      19.627  48.465   7.349  1.00  1.00
ATOM   2981 2HG  LYS   192      19.978  49.334   5.836  1.00  1.00
ATOM   2982 1HD  LYS   192      19.624  47.181   4.597  1.00  1.00
ATOM   2983 2HD  LYS   192      19.103  46.442   6.130  1.00  1.00
ATOM   2984 1HE  LYS   192      17.291  48.082   6.317  1.00  1.00
ATOM   2985 2HE  LYS   192      17.819  48.850   4.803  1.00  1.00
ATOM   2986  N   LYS   193      23.604  45.849   5.970  1.00  1.00
ATOM   2987  CA  LYS   193      24.969  45.368   5.791  1.00  1.00
ATOM   2988  C   LYS   193      25.984  46.433   6.182  1.00  1.00
ATOM   2989  O   LYS   193      26.271  47.346   5.407  1.00  1.00
ATOM   2990  CB  LYS   193      25.196  44.931   4.342  1.00  1.00
ATOM   2991  CG  LYS   193      26.573  44.340   4.074  1.00  1.00
ATOM   2992  CD  LYS   193      26.670  43.784   2.660  1.00  1.00
ATOM   2993  CE  LYS   193      28.069  43.261   2.364  1.00  1.00
ATOM   2994  NZ  LYS   193      28.166  42.672   1.001  1.00  1.00
ATOM   2995  H   LYS   193      22.992  45.904   5.168  1.00  1.00
ATOM   2996 1HZ  LYS   193      29.107  42.339   0.846  1.00  1.00
ATOM   2997 2HZ  LYS   193      27.517  41.903   0.920  1.00  1.00
ATOM   2998 3HZ  LYS   193      27.940  43.378   0.314  1.00  1.00
ATOM   2999  HA  LYS   193      25.148  44.513   6.444  1.00  1.00
ATOM   3000 1HB  LYS   193      24.432  44.190   4.108  1.00  1.00
ATOM   3001 2HB  LYS   193      25.052  45.811   3.716  1.00  1.00
ATOM   3002 1HG  LYS   193      27.319  45.123   4.209  1.00  1.00
ATOM   3003 2HG  LYS   193      26.753  43.540   4.791  1.00  1.00
ATOM   3004 1HD  LYS   193      25.949  42.973   2.555  1.00  1.00
ATOM   3005 2HD  LYS   193      26.425  44.579   1.957  1.00  1.00
ATOM   3006 1HE  LYS   193      28.769  44.091   2.452  1.00  1.00
ATOM   3007 2HE  LYS   193      28.312  42.501   3.106  1.00  1.00
TER
END
