
#######################################################
#                                                     #
#                        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 (   23),  selected    3 , name T0316TS273_1_2-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    3 , name T0316_D1.pdb
# PARAMETERS: T0316TS273_1_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         0.04     0.04
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.04     0.04
  LCS_AVERAGE:      1.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.04     0.04
  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    0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04
GDT RMS_ALL_CA   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04   0.04

#      Molecule1      Molecule2       DISTANCE
LGA    A     191      A     191          0.048
LGA    K     192      K     192          0.032
LGA    K     193      K     193          0.023

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  188    4.0      3    0.04     1.596     1.596     2.201

LGA_LOCAL      RMSD =  0.036  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.036  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.036  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.788584 * X  +  -0.351271 * Y  +  -0.504722 * Z  + 114.479767
  Y_new =  -0.132967 * X  +  -0.703959 * Y  +   0.697683 * Z  +  33.911777
  Z_new =  -0.600379 * X  +   0.617293 * Y  +   0.508423 * Z  + -18.681179 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.881810   -2.259783  [ DEG:    50.5240   -129.4760 ]
  Theta =   0.643975    2.497617  [ DEG:    36.8971    143.1030 ]
  Phi   =  -2.974549    0.167044  [ DEG:  -170.4291      9.5709 ]
 
# 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: T0316TS273_1_2-D1                             
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS273_1_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   0.04   1.596     0.04
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS273_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0316
PARENT 1tyv
ATOM      1  C   ALA   191      21.194  45.744   9.057  1.00  9.00
ATOM      2  O   ALA   191      21.441  44.616   8.628  1.00  9.00
ATOM      3  N   ALA   191      22.008  46.523  11.261  1.00  9.00
ATOM      4  CA  ALA   191      20.864  45.936  10.544  1.00  9.00
ATOM      5  CB  ALA   191      19.578  46.765  10.746  1.00  9.00
ATOM      6  C   LYS   192      22.439  46.084   6.199  1.00  9.00
ATOM      7  O   LYS   192      22.225  45.434   5.178  1.00  9.00
ATOM      8  N   LYS   192      21.222  46.850   8.293  1.00  9.00
ATOM      9  CA  LYS   192      21.328  46.948   6.830  1.00  9.00
ATOM     10  CB  LYS   192      21.438  48.443   6.439  1.00  9.00
ATOM     11  CG  LYS   192      21.302  48.732   4.928  1.00  9.00
ATOM     12  CD  LYS   192      21.271  50.230   4.570  1.00  9.00
ATOM     13  CE  LYS   192      19.940  50.933   4.914  1.00  9.00
ATOM     14  NZ  LYS   192      19.942  52.354   4.528  1.00  9.00
ATOM     15  C   LYS   193      24.516  43.759   6.486  1.00  9.00
ATOM     16  O   LYS   193      24.874  43.003   5.581  1.00  9.00
ATOM     17  N   LYS   193      23.630  46.075   6.812  1.00  9.00
ATOM     18  CA  LYS   193      24.773  45.274   6.374  1.00  9.00
ATOM     19  CB  LYS   193      26.069  45.738   7.077  1.00  9.00
ATOM     20  CG  LYS   193      26.108  45.548   8.610  1.00  9.00
ATOM     21  CD  LYS   193      27.414  46.043   9.256  1.00  9.00
ATOM     22  CE  LYS   193      27.541  47.579   9.300  1.00  9.00
ATOM     23  NZ  LYS   193      28.760  48.015   9.996  1.00  9.00
TER
END
