
#######################################################
#                                                     #
#                        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 (   25),  selected    3 , name T0318TS338_3-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected    3 , name T0318_D1.pdb
# PARAMETERS: T0318TS338_3-D1.T0318_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       153 - 155         0.14     0.14
  LCS_AVERAGE:      1.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       153 - 155         0.14     0.14
  LCS_AVERAGE:      1.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       153 - 155         0.14     0.14
  LCS_AVERAGE:      1.95

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:  154
LCS_GDT     D     153     D     153      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     154     K     154      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     L     155     L     155      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:   1.95  (   1.95    1.95    1.95 )

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   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95   1.95
GDT RMS_LOCAL    0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14
GDT RMS_ALL_CA   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14   0.14

#      Molecule1      Molecule2       DISTANCE
LGA    D     153      D     153          0.168
LGA    K     154      K     154          0.076
LGA    L     155      L     155          0.168

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  154    4.0      3    0.14     1.948     1.948     1.230

LGA_LOCAL      RMSD =  0.144  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.144  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.144  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.054541 * X  +  -0.616413 * Y  +   0.785532 * Z  +  65.706543
  Y_new =   0.450462 * X  +   0.686908 * Y  +   0.570299 * Z  + -54.017822
  Z_new =  -0.891128 * X  +   0.384957 * Y  +   0.240206 * Z  +  10.302325 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.012930   -2.128663  [ DEG:    58.0366   -121.9634 ]
  Theta =   1.099825    2.041767  [ DEG:    63.0153    116.9847 ]
  Phi   =   1.691288   -1.450304  [ DEG:    96.9037    -83.0963 ]
 
# 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: T0318TS338_3-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS338_3-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  154   4.0    3   0.14   1.948     0.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS338_3-D1
PFRMAT TS
TARGET T0318
MODEL  3
PARENT 2ewb_A
ATOM      1  N   ASP   153      30.282  27.383  21.440  1.00  0.01
ATOM      2  CA  ASP   153      29.761  26.105  21.965  1.00  0.01
ATOM      3  CB  ASP   153      29.209  26.318  23.387  1.00  0.01
ATOM      4  CG  ASP   153      29.024  24.965  24.063  1.00  0.01
ATOM      5  OD1 ASP   153      29.057  23.933  23.342  1.00  0.01
ATOM      6  OD2 ASP   153      28.851  24.947  25.312  1.00  0.01
ATOM      7  C   ASP   153      28.661  25.637  21.071  1.00  0.01
ATOM      8  O   ASP   153      28.903  25.037  20.025  1.00  0.01
ATOM      9  N   LYS   154      27.405  25.900  21.464  1.00  0.01
ATOM     10  CA  LYS   154      26.306  25.491  20.641  1.00  0.01
ATOM     11  CB  LYS   154      24.933  25.765  21.283  1.00  0.01
ATOM     12  CG  LYS   154      23.760  25.101  20.552  1.00  0.01
ATOM     13  CD  LYS   154      23.731  23.572  20.667  1.00  0.01
ATOM     14  CE  LYS   154      24.367  22.837  19.481  1.00  0.01
ATOM     15  NZ  LYS   154      24.317  21.372  19.700  1.00  0.01
ATOM     16  C   LYS   154      26.381  26.254  19.354  1.00  0.01
ATOM     17  O   LYS   154      26.139  25.700  18.285  1.00  0.01
ATOM     18  N   LEU   155      26.728  27.555  19.431  1.00  0.02
ATOM     19  CA  LEU   155      26.796  28.397  18.268  1.00  0.02
ATOM     20  CB  LEU   155      27.001  29.895  18.566  1.00  0.02
ATOM     21  CG  LEU   155      25.767  30.570  19.196  1.00  0.02
ATOM     22  CD1 LEU   155      25.555  30.113  20.646  1.00  0.02
ATOM     23  CD2 LEU   155      25.807  32.097  19.029  1.00  0.02
ATOM     24  C   LEU   155      27.899  27.963  17.348  1.00  0.02
ATOM     25  O   LEU   155      27.761  28.064  16.131  1.00  0.02
TER
END
