
#######################################################
#                                                     #
#                        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 (   20),  selected    5 , name T0316AL257_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected    5 , name T0316_D3.pdb
# PARAMETERS: T0316AL257_5-D3.T0316_D3.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       355 - 359         2.25     2.25
  LCS_AVERAGE:      5.56

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       355 - 358         1.18     3.14
  LCS_AVERAGE:      4.22

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       355 - 357         0.45     3.72
  LCS_AVERAGE:      2.00

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:   90
LCS_GDT     L     355     L     355      3    4    5     3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     356     G     356      3    4    5     3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     357     G     357      3    4    5     3    3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     G     358     G     358      0    4    5     0    0    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     359     L     359      0    3    5     0    0    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.93  (   2.00    4.22    5.56 )

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      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   3.33   3.33   4.44   4.44   4.44   4.44   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56
GDT RMS_LOCAL    0.45   0.45   1.18   1.18   1.18   1.18   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25
GDT RMS_ALL_CA   3.72   3.72   3.14   3.14   3.14   3.14   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25   2.25

#      Molecule1      Molecule2       DISTANCE
LGA    L     355      L     355          1.684
LGA    G     356      G     356          2.319
LGA    G     357      G     357          2.146
LGA    G     358      G     358          1.520
LGA    L     359      L     359          3.203

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   90    4.0      5    2.25     4.722     4.745     0.212

LGA_LOCAL      RMSD =  2.254  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.254  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.254  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.468931 * X  +  -0.636988 * Y  +  -0.611841 * Z  +  22.585430
  Y_new =  -0.881910 * X  +  -0.299760 * Y  +  -0.363838 * Z  +   3.494105
  Z_new =   0.048355 * X  +   0.710204 * Y  +  -0.702333 * Z  +  13.572959 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.350623   -0.790970  [ DEG:   134.6808    -45.3192 ]
  Theta =  -0.048373   -3.093219  [ DEG:    -2.7716   -177.2284 ]
  Phi   =  -1.082095    2.059498  [ DEG:   -61.9995    118.0005 ]
 
# 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: T0316AL257_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL257_5-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   90   4.0    5   2.25   4.745     2.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL257_5-D3
REMARK Aligment from pdb entry: 1ru8_A
ATOM    877  N   LEU   355      21.603  12.617  10.139  1.00  0.00              
ATOM    878  CA  LEU   355      22.385  13.042   8.990  1.00  0.00              
ATOM    879  C   LEU   355      23.814  12.537   8.969  1.00  0.00              
ATOM    880  O   LEU   355      24.394  12.210   9.994  1.00  0.00              
ATOM    881  N   GLY   356      24.372  12.472   7.773  1.00  0.00              
ATOM    882  CA  GLY   356      25.742  12.051   7.613  1.00  0.00              
ATOM    883  C   GLY   356      26.425  13.154   6.805  1.00  0.00              
ATOM    884  O   GLY   356      26.213  13.260   5.596  1.00  0.00              
ATOM    885  N   GLY   357      27.214  13.999   7.474  1.00  0.00              
ATOM    886  CA  GLY   357      27.910  15.093   6.783  1.00  0.00              
ATOM    887  C   GLY   357      29.224  14.611   6.151  1.00  0.00              
ATOM    888  O   GLY   357      30.014  15.401   5.622  1.00  0.00              
ATOM    889  N   GLY   358      29.438  13.300   6.203  1.00  0.00              
ATOM    890  CA  GLY   358      30.625  12.683   5.631  1.00  0.00              
ATOM    891  C   GLY   358      30.642  12.902   4.113  1.00  0.00              
ATOM    892  O   GLY   358      31.708  12.988   3.494  1.00  0.00              
ATOM    893  N   LEU   359      29.447  12.996   3.526  1.00  0.00              
ATOM    894  CA  LEU   359      29.279  13.197   2.083  1.00  0.00              
ATOM    895  C   LEU   359      28.293  14.312   1.744  1.00  0.00              
ATOM    896  O   LEU   359      27.868  15.022   2.680  1.00  0.00              
END
