
#######################################################
#                                                     #
#                        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    5 (   36),  selected    5 , name T0316TS464_4-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    5 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_4-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
  LONGEST_CONTINUOUS_SEGMENT:     5       189 - 193         2.68     2.68
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       189 - 192         1.86     3.35
  LCS_AVERAGE:      2.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       189 - 191         0.70     5.72
  LONGEST_CONTINUOUS_SEGMENT:     3       190 - 192         0.32     4.51
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.62     5.64
  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     S     189     S     189      3    4    5     0    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     190     T     190      3    4    5     3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     191     A     191      3    4    5     3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     192     K     192      3    4    5     3    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     193     K     193      3    3    5     0    3    3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.09  (   1.60    2.02    2.66 )

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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   1.60   1.60   1.60   1.60   1.60   2.13   2.13   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66
GDT RMS_LOCAL    0.32   0.32   0.32   0.32   0.32   1.86   1.86   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68
GDT RMS_ALL_CA   4.51   4.51   4.51   4.51   4.51   3.35   3.35   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.68

#      Molecule1      Molecule2       DISTANCE
LGA    S     189      S     189          1.945
LGA    T     190      T     190          3.401
LGA    A     191      A     191          1.915
LGA    K     192      K     192          2.082
LGA    K     193      K     193          3.547

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  188    4.0      5    2.68     2.128     2.129     0.180

LGA_LOCAL      RMSD =  2.681  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.681  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.681  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.393058 * X  +   0.919371 * Y  +  -0.016188 * Z  + -29.321524
  Y_new =   0.573967 * X  +  -0.231558 * Y  +   0.785457 * Z  +  16.302376
  Z_new =   0.718378 * X  +  -0.318021 * Y  +  -0.618704 * Z  +  67.104492 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.666798    0.474794  [ DEG:  -152.7963     27.2037 ]
  Theta =  -0.801469   -2.340124  [ DEG:   -45.9208   -134.0792 ]
  Phi   =   0.970338   -2.171255  [ DEG:    55.5963   -124.4037 ]
 
# 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: T0316TS464_4-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_4-D1.T0316_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  188   4.0    5   2.68   2.129     2.68
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_4-D1
PFRMAT TS
TARGET T0316
MODEL 4
PARENT N/A
ATOM    753  N   SER   189      24.486  50.078  16.255  1.00  0.00
ATOM    754  CA  SER   189      24.860  49.218  15.176  1.00  0.00
ATOM    755  CB  SER   189      25.707  48.011  15.613  1.00  0.00
ATOM    756  OG  SER   189      24.949  47.165  16.464  1.00  0.00
ATOM    757  C   SER   189      23.605  48.680  14.581  1.00  0.00
ATOM    758  O   SER   189      22.677  48.297  15.293  1.00  0.00
ATOM    759  N   THR   190      23.540  48.663  13.238  1.00  0.00
ATOM    760  CA  THR   190      22.393  48.124  12.577  1.00  0.00
ATOM    761  CB  THR   190      21.568  49.154  11.863  1.00  0.00
ATOM    762  OG1 THR   190      21.111  50.138  12.779  1.00  0.00
ATOM    763  CG2 THR   190      20.371  48.452  11.200  1.00  0.00
ATOM    764  C   THR   190      22.913  47.187  11.543  1.00  0.00
ATOM    765  O   THR   190      23.993  47.394  10.994  1.00  0.00
ATOM    766  N   ALA   191      22.164  46.106  11.263  1.00  0.00
ATOM    767  CA  ALA   191      22.628  45.198  10.262  1.00  0.00
ATOM    768  CB  ALA   191      21.824  43.889  10.192  1.00  0.00
ATOM    769  C   ALA   191      22.477  45.894   8.953  1.00  0.00
ATOM    770  O   ALA   191      21.529  46.651   8.751  1.00  0.00
ATOM    771  N   LYS   192      23.433  45.676   8.033  1.00  0.00
ATOM    772  CA  LYS   192      23.309  46.301   6.753  1.00  0.00
ATOM    773  CB  LYS   192      24.370  47.379   6.468  1.00  0.00
ATOM    774  CG  LYS   192      24.246  48.608   7.369  1.00  0.00
ATOM    775  CD  LYS   192      25.396  49.604   7.203  1.00  0.00
ATOM    776  CE  LYS   192      25.192  50.566   6.032  1.00  0.00
ATOM    777  NZ  LYS   192      25.089  49.807   4.766  1.00  0.00
ATOM    778  C   LYS   192      23.465  45.238   5.723  1.00  0.00
ATOM    779  O   LYS   192      24.221  44.284   5.903  1.00  0.00
ATOM    780  N   LYS   193      22.722  45.372   4.611  1.00  0.00
ATOM    781  CA  LYS   193      22.803  44.409   3.557  1.00  0.00
ATOM    782  CB  LYS   193      21.422  43.916   3.094  1.00  0.00
ATOM    783  CG  LYS   193      20.540  45.046   2.557  1.00  0.00
ATOM    784  CD  LYS   193      19.264  44.562   1.867  1.00  0.00
ATOM    785  CE  LYS   193      18.140  44.209   2.843  1.00  0.00
ATOM    786  NZ  LYS   193      17.609  45.439   3.473  1.00  0.00
ATOM    787  C   LYS   193      23.435  45.099   2.396  1.00  0.00
ATOM    788  O   LYS   193      23.043  46.210   2.040  1.00  0.00
TER
END
