
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected    5 , name T0318_D1.pdb
# PARAMETERS: T0318TS389_4-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         0.31     0.31
  LCS_AVERAGE:      3.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       151 - 155         0.31     0.31
  LCS_AVERAGE:      3.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       151 - 155         0.31     0.31
  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    0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31
GDT RMS_ALL_CA   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31   0.31

#      Molecule1      Molecule2       DISTANCE
LGA    V     151      V     151          0.385
LGA    C     152      C     152          0.359
LGA    D     153      D     153          0.384
LGA    K     154      K     154          0.204
LGA    L     155      L     155          0.099

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  154    4.0      5    0.31     3.247     3.247     1.224

LGA_LOCAL      RMSD =  0.309  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.309  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.309  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.893249 * X  +   0.136020 * Y  +   0.428492 * Z  +  36.468456
  Y_new =   0.160475 * X  +   0.793867 * Y  +  -0.586535 * Z  +  27.181986
  Z_new =  -0.419946 * X  +   0.592683 * Y  +   0.687293 * Z  +  16.713209 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.711617   -2.429976  [ DEG:    40.7727   -139.2273 ]
  Theta =   0.433386    2.708207  [ DEG:    24.8312    155.1688 ]
  Phi   =   0.177756   -2.963836  [ DEG:    10.1847   -169.8153 ]
 
# 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_4-D1                               
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS389_4-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   0.31   3.247     0.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS389_4-D1
PFRMAT TS
TARGET T0318
MODEL  4
PARENT N/A
ATOM      2  N   VAL   151      33.079  32.367  23.497  1.00  0.00
ATOM      3  CA  VAL   151      32.363  31.940  22.290  1.00  0.00
ATOM      4  CB  VAL   151      33.334  31.449  21.201  1.00  0.00
ATOM      5  CG1 VAL   151      32.564  30.920  20.001  1.00  0.00
ATOM      6  CG2 VAL   151      34.230  32.586  20.735  1.00  0.00
ATOM      7  O   VAL   151      31.840  29.786  23.191  1.00  0.00
ATOM      8  C   VAL   151      31.419  30.800  22.650  1.00  0.00
ATOM      9  N   CYS   152      30.117  30.957  22.349  1.00  0.00
ATOM     10  CA  CYS   152      29.200  29.876  22.751  1.00  0.00
ATOM     11  CB  CYS   152      27.744  30.312  22.569  1.00  0.00
ATOM     12  SG  CYS   152      26.525  29.064  23.040  1.00  0.00
ATOM     13  O   CYS   152      29.267  28.627  20.694  1.00  0.00
ATOM     14  C   CYS   152      29.426  28.618  21.909  1.00  0.00
ATOM     15  N   ASP   153      29.799  27.524  22.574  1.00  0.00
ATOM     16  CA  ASP   153      30.024  26.268  21.886  1.00  0.00
ATOM     17  CB  ASP   153      30.264  25.143  22.895  1.00  0.00
ATOM     18  CG  ASP   153      31.620  25.239  23.566  1.00  0.00
ATOM     19  OD1 ASP   153      32.459  26.035  23.096  1.00  0.00
ATOM     20  OD2 ASP   153      31.843  24.518  24.561  1.00  0.00
ATOM     21  O   ASP   153      28.996  25.416  19.908  1.00  0.00
ATOM     22  C   ASP   153      28.840  25.886  21.033  1.00  0.00
ATOM     23  N   LYS   154      27.613  26.076  21.529  1.00  0.00
ATOM     24  CA  LYS   154      26.433  25.648  20.785  1.00  0.00
ATOM     25  CB  LYS   154      25.160  25.971  21.566  1.00  0.00
ATOM     26  CG  LYS   154      24.959  25.116  22.808  1.00  0.00
ATOM     27  CD  LYS   154      23.676  25.489  23.533  1.00  0.00
ATOM     28  CE  LYS   154      23.488  24.652  24.789  1.00  0.00
ATOM     29  NZ  LYS   154      22.252  25.027  25.528  1.00  0.00
ATOM     30  O   LYS   154      25.924  25.816  18.437  1.00  0.00
ATOM     31  C   LYS   154      26.385  26.368  19.446  1.00  0.00
ATOM     32  N   LEU   155      26.812  27.635  19.410  1.00  0.00
ATOM     33  CA  LEU   155      26.752  28.383  18.144  1.00  0.00
ATOM     34  CB  LEU   155      27.082  29.858  18.377  1.00  0.00
ATOM     35  CG  LEU   155      26.050  30.668  19.166  1.00  0.00
ATOM     36  CD1 LEU   155      26.581  32.058  19.477  1.00  0.00
ATOM     37  CD2 LEU   155      24.762  30.818  18.370  1.00  0.00
ATOM     38  O   LEU   155      27.487  27.766  15.947  1.00  0.00
ATOM     39  C   LEU   155      27.751  27.825  17.130  1.00  0.00
TER
END
