
#######################################################
#                                                     #
#                        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    4 (   20),  selected    4 , name T0318TS239_2_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected    4 , name T0318_D1.pdb
# PARAMETERS: T0318TS239_2_2-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:     4       152 - 155         1.97     1.97
  LCS_AVERAGE:      2.60

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       152 - 155         1.97     1.97
  LCS_AVERAGE:      2.60

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       152 - 154         0.69     3.83
  LONGEST_CONTINUOUS_SEGMENT:     3       153 - 155         0.46     3.60
  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     C     152     C     152      3    4    4     0    3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     D     153     D     153      3    4    4     3    3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     K     154     K     154      3    4    4     3    3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     L     155     L     155      3    4    4     3    3    3    3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   2.38  (   1.95    2.60    2.60 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   1.95   1.95   1.95   1.95   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60   2.60
GDT RMS_LOCAL    0.46   0.46   0.46   0.46   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97
GDT RMS_ALL_CA   3.60   3.60   3.60   3.60   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97   1.97

#      Molecule1      Molecule2       DISTANCE
LGA    C     152      C     152          2.256
LGA    D     153      D     153          1.925
LGA    K     154      K     154          1.604
LGA    L     155      L     155          2.052

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  154    4.0      4    1.97     2.273     2.452     0.193

LGA_LOCAL      RMSD =  1.974  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.974  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  1.974  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.173140 * X  +   0.271556 * Y  +   0.946721 * Z  +   5.365195
  Y_new =   0.130351 * X  +  -0.946464 * Y  +   0.295321 * Z  +  39.031437
  Z_new =   0.976233 * X  +   0.174538 * Y  +   0.128473 * Z  + -16.248053 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.936266   -2.205326  [ DEG:    53.6441   -126.3559 ]
  Theta =  -1.352340   -1.789253  [ DEG:   -77.4834   -102.5166 ]
  Phi   =   2.496260   -0.645332  [ DEG:   143.0252    -36.9748 ]
 
# 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: T0318TS239_2_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS239_2_2-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4  154   4.0    4   1.97   2.452     1.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS239_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT 1rtq_A
ATOM      1  N   CYS   152      32.597  28.887  24.452  1.00  9.99
ATOM      2  CA  CYS   152      31.426  29.409  23.832  1.00  9.99
ATOM      3  C   CYS   152      30.653  28.178  23.229  1.00  9.99
ATOM      4  O   CYS   152      31.128  27.161  22.772  1.00  9.99
ATOM      5  CB  CYS   152      31.598  30.448  22.735  1.00  9.99
ATOM      6  N   ASP   153      29.345  28.292  23.239  1.00  9.99
ATOM      7  CA  ASP   153      28.480  27.172  22.825  1.00  9.99
ATOM      8  C   ASP   153      28.210  27.044  21.371  1.00  9.99
ATOM      9  O   ASP   153      28.261  28.017  20.642  1.00  9.99
ATOM     10  CB  ASP   153      27.142  27.586  23.488  1.00  9.99
ATOM     11  N   LYS   154      27.834  25.846  20.920  1.00  9.99
ATOM     12  CA  LYS   154      27.503  25.636  19.504  1.00  9.99
ATOM     13  C   LYS   154      26.285  26.465  19.124  1.00  9.99
ATOM     14  O   LYS   154      25.424  26.741  19.981  1.00  9.99
ATOM     15  CB  LYS   154      27.161  24.136  19.412  1.00  9.99
ATOM     16  N   LEU   155      26.149  26.866  17.879  1.00  9.99
ATOM     17  CA  LEU   155      24.992  27.574  17.374  1.00  9.99
ATOM     18  C   LEU   155      23.815  26.610  17.181  1.00  9.99
ATOM     19  O   LEU   155      23.906  25.652  16.415  1.00  9.99
ATOM     20  CB  LEU   155      25.334  28.309  16.050  1.00  9.99
TER
END
