
#######################################################
#                                                     #
#                        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    7 (   35),  selected    7 , name T0347TS261_1_2-D1
# Molecule2: number of CA atoms   89 (  730),  selected    7 , name T0347_D1.pdb
# PARAMETERS: T0347TS261_1_2-D1.T0347_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:     7        30 - 36          1.93     1.93
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        30 - 36          1.93     1.93
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        31 - 36          0.21     2.58
  LCS_AVERAGE:      6.26

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:   89
LCS_GDT     E      30     E      30      3    7    7     3    3    3    3    3    4    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L      31     L      31      6    7    7     6    6    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K      32     K      32      6    7    7     6    6    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     R      33     R      33      6    7    7     6    6    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K      34     K      34      6    7    7     6    6    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     E      35     E      35      6    7    7     6    6    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     W      36     W      36      6    7    7     6    6    6    6    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   7.33  (   6.26    7.87    7.87 )

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      6      6      6      6      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   6.74   6.74   6.74   6.74   6.74   6.74   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87
GDT RMS_LOCAL    0.21   0.21   0.21   0.21   0.21   0.21   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93
GDT RMS_ALL_CA   2.58   2.58   2.58   2.58   2.58   2.58   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93   1.93

#      Molecule1      Molecule2       DISTANCE
LGA    E      30      E      30          3.775
LGA    L      31      L      31          2.096
LGA    K      32      K      32          1.428
LGA    R      33      R      33          1.552
LGA    K      34      K      34          1.023
LGA    E      35      E      35          0.772
LGA    W      36      W      36          1.189

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      7    1.93     7.303     7.471     0.344

LGA_LOCAL      RMSD =  1.933  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.933  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.933  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.523275 * X  +  -0.083158 * Y  +  -0.848097 * Z  +  -0.883477
  Y_new =  -0.637239 * X  +   0.622582 * Y  +  -0.454222 * Z  +  83.874672
  Z_new =   0.565783 * X  +   0.778123 * Y  +   0.272790 * Z  + -22.470642 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.233610   -1.907983  [ DEG:    70.6806   -109.3194 ]
  Theta =  -0.601382   -2.540211  [ DEG:   -34.4566   -145.5434 ]
  Phi   =  -0.883286    2.258307  [ DEG:   -50.6086    129.3914 ]
 
# 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: T0347TS261_1_2-D1                             
REMARK     2: T0347_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS261_1_2-D1.T0347_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   89   4.0    7   1.93   7.471     1.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS261_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0347
PARENT 1vz0_A
ATOM    387  N   GLU    30      11.446  55.454 -10.963  1.00  5.59
ATOM    388  CA  GLU    30      11.394  54.038 -11.305  1.00  5.59
ATOM    389  C   GLU    30      10.537  53.886 -12.555  1.00  5.59
ATOM    390  O   GLU    30       9.329  54.116 -12.517  1.00  5.59
ATOM    391  CB  GLU    30      10.766  53.227 -10.167  1.00  5.59
ATOM    392  N   LEU    31      11.167  53.511 -13.660  1.00  4.81
ATOM    393  CA  LEU    31      10.459  53.314 -14.916  1.00  4.81
ATOM    394  C   LEU    31      10.845  51.944 -15.451  1.00  4.81
ATOM    395  O   LEU    31      11.430  51.839 -16.530  1.00  4.81
ATOM    396  CB  LEU    31      10.862  54.395 -15.924  1.00  4.81
ATOM    397  N   LYS    32      10.513  50.873 -14.706  1.00  6.95
ATOM    398  CA  LYS    32      10.841  49.504 -15.112  1.00  6.95
ATOM    399  C   LYS    32      10.500  49.134 -16.560  1.00  6.95
ATOM    400  O   LYS    32      11.270  48.435 -17.226  1.00  6.95
ATOM    401  CB  LYS    32      10.104  48.649 -14.071  1.00  6.95
ATOM    402  N   ARG    33       9.362  49.606 -17.054  1.00  3.25
ATOM    403  CA  ARG    33       8.973  49.306 -18.426  1.00  3.25
ATOM    404  C   ARG    33      10.029  49.822 -19.417  1.00  3.25
ATOM    405  O   ARG    33      10.488  49.083 -20.292  1.00  3.25
ATOM    406  CB  ARG    33       7.614  49.932 -18.733  1.00  3.25
ATOM    407  N   LYS    34      10.415  51.087 -19.278  1.00  5.67
ATOM    408  CA  LYS    34      11.424  51.677 -20.156  1.00  5.67
ATOM    409  C   LYS    34      12.771  50.980 -19.981  1.00  5.67
ATOM    410  O   LYS    34      13.517  50.784 -20.942  1.00  5.67
ATOM    411  CB  LYS    34      11.591  53.167 -19.855  1.00  5.67
ATOM    412  N   GLU    35      13.082  50.608 -18.749  1.00  8.01
ATOM    413  CA  GLU    35      14.334  49.927 -18.467  1.00  8.01
ATOM    414  C   GLU    35      14.360  48.576 -19.171  1.00  8.01
ATOM    415  O   GLU    35      15.363  48.202 -19.768  1.00  8.01
ATOM    416  CB  GLU    35      14.503  49.758 -16.955  1.00  8.01
ATOM    417  N   TRP    36      13.253  47.845 -19.106  1.00  5.34
ATOM    418  CA  TRP    36      13.163  46.546 -19.771  1.00  5.34
ATOM    419  C   TRP    36      13.293  46.692 -21.296  1.00  5.34
ATOM    420  O   TRP    36      13.974  45.902 -21.943  1.00  5.34
ATOM    421  CB  TRP    36      11.836  45.866 -19.426  1.00  5.34
TER
END
