
#######################################################
#                                                     #
#                        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   11 (   11),  selected   11 , name T0318TS464_3_2-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   11 , name T0318_D2.pdb
# PARAMETERS: T0318TS464_3_2-D2.T0318_D2.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:    11       156 - 166         2.13     2.13
  LCS_AVERAGE:      3.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       156 - 165         0.72     2.51
  LCS_AVERAGE:      2.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       156 - 165         0.72     2.51
  LCS_AVERAGE:      2.80

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:  335
LCS_GDT     T     156     T     156     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     N     157     N     157     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     158     E     158     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     D     159     D     159     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A     160     A     160     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     V     161     V     161     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     F     162     F     162     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     163     L     163     10   10   11     6    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     T     164     T     164     10   10   11     8    9   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     D     165     D     165     10   10   11     3    6   10   10   10   10   10   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     166     L     166      3    3   11     0    3    3    3    3    6    7    9    9   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   2.96  (   2.80    2.80    3.28 )

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      8      9     10     10     10     10     10     10     10     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   2.39   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   3.28   3.28   3.28   3.28   3.28   3.28   3.28   3.28   3.28   3.28   3.28
GDT RMS_LOCAL    0.32   0.36   0.72   0.72   0.72   0.72   0.72   0.72   0.72   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13
GDT RMS_ALL_CA   2.87   2.81   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13   2.13

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          0.786
LGA    N     157      N     157          0.658
LGA    E     158      E     158          0.256
LGA    D     159      D     159          0.416
LGA    A     160      A     160          0.474
LGA    V     161      V     161          0.629
LGA    F     162      F     162          0.623
LGA    L     163      L     163          0.501
LGA    T     164      T     164          0.263
LGA    D     165      D     165          1.605
LGA    L     166      L     166          8.018

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  335    4.0     10    0.72     2.985     2.986     1.219

LGA_LOCAL      RMSD =  0.721  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.513  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  2.133  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.597270 * X  +   0.642830 * Y  +   0.479623 * Z  +  -6.800664
  Y_new =  -0.776466 * X  +   0.313634 * Y  +   0.546567 * Z  +  26.715145
  Z_new =   0.200923 * X  +  -0.698859 * Y  +   0.686459 * Z  + -16.082073 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.794349    2.347244  [ DEG:   -45.5128    134.4872 ]
  Theta =  -0.202300   -2.939292  [ DEG:   -11.5910   -168.4090 ]
  Phi   =  -0.915110    2.226483  [ DEG:   -52.4319    127.5681 ]
 
# 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: T0318TS464_3_2-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS464_3_2-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  335   4.0   10   0.72   2.986     2.13
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS464_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM     28  CA  THR   156      27.447  27.666  14.028  1.00  0.00
ATOM     29  CA  ASN   157      28.206  29.653  10.902  1.00  0.00
ATOM     30  CA  GLU   158      24.471  29.742  10.170  1.00  0.00
ATOM     31  CA  ASP   159      23.686  30.991  13.666  1.00  0.00
ATOM     32  CA  ALA   160      26.293  33.719  13.262  1.00  0.00
ATOM     33  CA  VAL   161      24.823  34.648   9.893  1.00  0.00
ATOM     34  CA  PHE   162      21.402  35.264  11.436  1.00  0.00
ATOM     35  CA  LEU   163      22.922  37.697  13.909  1.00  0.00
ATOM     36  CA  THR   164      25.138  39.671  11.495  1.00  0.00
ATOM     37  CA  ASP   165      23.053  39.857   8.334  1.00  0.00
ATOM     38  CA  LEU   166      24.078  42.664   5.965  1.00  0.00
TER
END
