
#######################################################
#                                                     #
#                        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 (   38),  selected    5 , name T0318TS389_5-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected    5 , name T0318_D1.pdb
# PARAMETERS: T0318TS389_5-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
  LONGEST_CONTINUOUS_SEGMENT:     5       151 - 155         0.27     0.27
  LCS_AVERAGE:      3.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       151 - 155         0.27     0.27
  LCS_AVERAGE:      3.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       151 - 155         0.27     0.27
  LCS_AVERAGE:      3.25

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     V     151     V     151      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     C     152     C     152      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     153     D     153      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     154     K     154      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     155     L     155      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.25  (   3.25    3.25    3.25 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25   3.25
GDT RMS_LOCAL    0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27
GDT RMS_ALL_CA   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27

#      Molecule1      Molecule2       DISTANCE
LGA    V     151      V     151          0.310
LGA    C     152      C     152          0.314
LGA    D     153      D     153          0.347
LGA    K     154      K     154          0.213
LGA    L     155      L     155          0.117

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  154    4.0      5    0.27     3.247     3.247     1.338

LGA_LOCAL      RMSD =  0.274  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.274  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.274  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.895572 * X  +   0.108824 * Y  +   0.431402 * Z  +  36.734631
  Y_new =   0.179041 * X  +   0.799502 * Y  +  -0.573360 * Z  +  26.843636
  Z_new =  -0.407302 * X  +   0.590724 * Y  +   0.696527 * Z  +  16.437870 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.703389   -2.438204  [ DEG:    40.3012   -139.6988 ]
  Theta =   0.419498    2.722094  [ DEG:    24.0355    155.9645 ]
  Phi   =   0.197316   -2.944276  [ DEG:    11.3054   -168.6946 ]
 
# 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: T0318TS389_5-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS389_5-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  154   4.0    5   0.27   3.247     0.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS389_5-D1
PFRMAT TS
TARGET T0318
MODEL  5
PARENT N/A
ATOM      2  N   VAL   151      33.080  32.430  23.502  1.00  0.00
ATOM      3  CA  VAL   151      32.358  32.015  22.294  1.00  0.00
ATOM      4  CB  VAL   151      33.325  31.554  21.188  1.00  0.00
ATOM      5  CG1 VAL   151      32.551  30.999  20.001  1.00  0.00
ATOM      6  CG2 VAL   151      34.179  32.715  20.707  1.00  0.00
ATOM      7  O   VAL   151      31.853  29.851  23.248  1.00  0.00
ATOM      8  C   VAL   151      31.431  30.847  22.698  1.00  0.00
ATOM      9  N   CYS   152      30.142  30.938  22.346  1.00  0.00
ATOM     10  CA  CYS   152      29.248  29.845  22.770  1.00  0.00
ATOM     11  CB  CYS   152      27.783  30.260  22.620  1.00  0.00
ATOM     12  SG  CYS   152      26.593  28.996  23.120  1.00  0.00
ATOM     13  O   CYS   152      29.274  28.609  20.704  1.00  0.00
ATOM     14  C   CYS   152      29.468  28.592  21.937  1.00  0.00
ATOM     15  N   ASP   153      29.819  27.512  22.598  1.00  0.00
ATOM     16  CA  ASP   153      30.014  26.217  21.884  1.00  0.00
ATOM     17  CB  ASP   153      30.269  25.088  22.882  1.00  0.00
ATOM     18  CG  ASP   153      31.646  25.166  23.513  1.00  0.00
ATOM     19  OD1 ASP   153      32.481  25.952  23.017  1.00  0.00
ATOM     20  OD2 ASP   153      31.890  24.442  24.499  1.00  0.00
ATOM     21  O   ASP   153      28.924  25.370  19.927  1.00  0.00
ATOM     22  C   ASP   153      28.786  25.851  21.060  1.00  0.00
ATOM     23  N   LYS   154      27.565  26.042  21.566  1.00  0.00
ATOM     24  CA  LYS   154      26.398  25.668  20.793  1.00  0.00
ATOM     25  CB  LYS   154      25.118  26.008  21.557  1.00  0.00
ATOM     26  CG  LYS   154      24.868  25.132  22.773  1.00  0.00
ATOM     27  CD  LYS   154      23.587  25.530  23.487  1.00  0.00
ATOM     28  CE  LYS   154      23.342  24.656  24.707  1.00  0.00
ATOM     29  NZ  LYS   154      22.105  25.053  25.435  1.00  0.00
ATOM     30  O   LYS   154      25.833  25.820  18.487  1.00  0.00
ATOM     31  C   LYS   154      26.334  26.388  19.450  1.00  0.00
ATOM     32  N   LEU   155      26.831  27.642  19.370  1.00  0.00
ATOM     33  CA  LEU   155      26.754  28.369  18.114  1.00  0.00
ATOM     34  CB  LEU   155      27.049  29.855  18.338  1.00  0.00
ATOM     35  CG  LEU   155      25.997  30.643  19.119  1.00  0.00
ATOM     36  CD1 LEU   155      26.495  32.049  19.422  1.00  0.00
ATOM     37  CD2 LEU   155      24.707  30.758  18.322  1.00  0.00
ATOM     38  O   LEU   155      27.504  27.672  15.957  1.00  0.00
ATOM     39  C   LEU   155      27.789  27.794  17.131  1.00  0.00
TER
END
