
#######################################################
#                                                     #
#                        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   36 (   36),  selected   36 , name T0335TS599_2-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS599_2-D1.T0335_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:    36         5 - 40          2.39     2.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32         5 - 36          1.98     2.70
  LONGEST_CONTINUOUS_SEGMENT:    32         9 - 40          1.98     2.69
  LCS_AVERAGE:     88.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24        17 - 40          0.95     4.36
  LCS_AVERAGE:     63.04

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:   36
LCS_GDT     A       5     A       5     20   32   36     8   15   18   22   27   29   31   32   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K       6     K       6     20   32   36     9   15   21   24   27   30   31   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I       7     I       7     20   32   36     9   15   21   24   27   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A       8     A       8     20   32   36     9   15   21   24   27   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R       9     R       9     20   32   36     9   15   21   24   27   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      10     I      10     20   32   36     9   15   21   24   27   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     N      11     N      11     20   32   36     9   15   21   24   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      12     E      12     20   32   36     9   15   21   24   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      13     L      13     20   32   36     9   15   21   24   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      14     A      14     20   32   36     9   15   21   24   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      15     A      15     20   32   36     9   15   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      16     K      16     21   32   36     9   15   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      17     A      17     24   32   36     6   15   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      18     K      18     24   32   36     5   15   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      19     A      19     24   32   36    11   19   22   25   27   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      20     G      20     24   32   36     3   14   22   25   27   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     V      21     V      21     24   32   36     6   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      22     I      22     24   32   36     3   19   22   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     T      23     T      23     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      24     E      24     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      25     E      25     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      26     E      26     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      27     K      27     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      28     A      28     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      29     E      29     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      30     Q      30     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      31     Q      31     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      32     K      32     24   32   36    10   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      33     L      33     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R      34     R      34     24   32   36    11   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      35     Q      35     24   32   36     8   19   23   25   28   30   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      36     E      36     24   32   36     8   19   23   25   28   29   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Y      37     Y      37     24   32   36     8   19   23   25   28   29   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      38     L      38     24   32   36     8   19   23   25   28   29   31   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      39     K      39     24   32   36     8   18   23   25   28   29   32   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      40     G      40     24   32   36     8   11   23   25   28   29   31   34   35   36   36   36   36   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  83.98  (  63.04   88.89  100.00 )

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     11     19     23     25     28     30     32     34     35     36     36     36     36     36     36     36     36     36     36     36 
GDT PERCENT_CA  30.56  52.78  63.89  69.44  77.78  83.33  88.89  94.44  97.22 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.66   0.97   1.05   1.53   1.81   2.05   2.18   2.28   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39
GDT RMS_ALL_CA   4.08   4.44   3.68   4.13   2.92   2.79   2.44   2.46   2.41   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39   2.39

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          5.879
LGA    K       6      K       6          4.681
LGA    I       7      I       7          3.978
LGA    A       8      A       8          3.520
LGA    R       9      R       9          3.321
LGA    I      10      I      10          2.575
LGA    N      11      N      11          1.763
LGA    E      12      E      12          1.471
LGA    L      13      L      13          1.867
LGA    A      14      A      14          1.186
LGA    A      15      A      15          1.359
LGA    K      16      K      16          1.744
LGA    A      17      A      17          1.112
LGA    K      18      K      18          1.887
LGA    A      19      A      19          3.882
LGA    G      20      G      20          3.493
LGA    V      21      V      21          1.140
LGA    I      22      I      22          1.346
LGA    T      23      T      23          0.993
LGA    E      24      E      24          1.812
LGA    E      25      E      25          2.434
LGA    E      26      E      26          1.593
LGA    K      27      K      27          1.021
LGA    A      28      A      28          2.008
LGA    E      29      E      29          1.965
LGA    Q      30      Q      30          1.109
LGA    Q      31      Q      31          1.201
LGA    K      32      K      32          1.609
LGA    L      33      L      33          1.576
LGA    R      34      R      34          1.092
LGA    Q      35      Q      35          0.828
LGA    E      36      E      36          1.271
LGA    Y      37      Y      37          2.668
LGA    L      38      L      38          2.855
LGA    K      39      K      39          2.273
LGA    G      40      G      40          3.521

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36   36    4.0     34    2.18    79.167    85.112     1.490

LGA_LOCAL      RMSD =  2.182  Number of atoms =   34  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.463  Number of atoms =   36 
Std_ALL_ATOMS  RMSD =  2.392  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.076933 * X  +   0.494320 * Y  +   0.865869 * Z  +   4.679461
  Y_new =   0.531729 * X  +  -0.754975 * Y  +   0.383767 * Z  +  -3.006273
  Z_new =   0.843413 * X  +   0.430883 * Y  +  -0.320927 * Z  + -19.121172 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.210968   -0.930624  [ DEG:   126.6792    -53.3208 ]
  Theta =  -1.003605   -2.137988  [ DEG:   -57.5023   -122.4977 ]
  Phi   =   1.427109   -1.714484  [ DEG:    81.7673    -98.2327 ]
 
# 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: T0335TS599_2-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS599_2-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   36   36   4.0   34   2.18  85.112     2.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS599_2-D1
PFRMAT TS                                                                       
TARGET T0335                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      5  CA  ALA     5      -2.630  -7.729 -10.151  1.00  0.00              
ATOM      6  CA  LYS     6      -0.599  -4.972  -8.583  1.00  0.00              
ATOM      7  CA  ILE     7      -3.521  -2.544  -8.808  1.00  0.00              
ATOM      8  CA  ALA     8      -5.895  -5.099  -7.244  1.00  0.00              
ATOM      9  CA  ARG     9      -3.457  -5.724  -4.408  1.00  0.00              
ATOM     10  CA  ILE    10      -2.985  -1.973  -3.714  1.00  0.00              
ATOM     11  CA  ASN    11      -6.724  -1.587  -3.579  1.00  0.00              
ATOM     12  CA  GLU    12      -7.132  -4.445  -1.161  1.00  0.00              
ATOM     13  CA  LEU    13      -4.410  -3.026   1.147  1.00  0.00              
ATOM     14  CA  ALA    14      -6.033   0.409   1.096  1.00  0.00              
ATOM     15  CA  ALA    15      -9.356  -1.137   2.085  1.00  0.00              
ATOM     16  CA  LYS    16      -7.685  -3.131   4.906  1.00  0.00              
ATOM     17  CA  ALA    17      -6.032   0.030   6.104  1.00  0.00              
ATOM     18  CA  LYS    18      -9.342   1.991   6.036  1.00  0.00              
ATOM     19  CA  ALA    19     -11.079  -0.675   8.073  1.00  0.00              
ATOM     20  CA  GLY    20      -8.318  -0.679  10.659  1.00  0.00              
ATOM     21  CA  VAL    21      -7.977   3.121  10.864  1.00  0.00              
ATOM     22  CA  ILE    22      -4.447   3.300   9.619  1.00  0.00              
ATOM     23  CA  THR    23      -1.972   5.305  11.587  1.00  0.00              
ATOM     24  CA  GLU    24       0.268   7.871   9.978  1.00  0.00              
ATOM     25  CA  GLU    25       3.176   5.370  10.103  1.00  0.00              
ATOM     26  CA  GLU    26       1.089   2.726   8.363  1.00  0.00              
ATOM     27  CA  LYS    27       0.198   5.304   5.656  1.00  0.00              
ATOM     28  CA  ALA    28       3.853   6.236   5.110  1.00  0.00              
ATOM     29  CA  GLU    29       4.828   2.549   4.811  1.00  0.00              
ATOM     30  CA  GLN    30       2.108   1.894   2.324  1.00  0.00              
ATOM     31  CA  GLN    31       3.143   4.815   0.205  1.00  0.00              
ATOM     32  CA  LYS    32       6.785   3.629   0.199  1.00  0.00              
ATOM     33  CA  LEU    33       5.800   0.098  -0.791  1.00  0.00              
ATOM     34  CA  ARG    34       3.590   1.335  -3.567  1.00  0.00              
ATOM     35  CA  GLN    35       6.406   3.448  -4.954  1.00  0.00              
ATOM     36  CA  GLU    36       8.939   0.546  -4.871  1.00  0.00              
ATOM     37  CA  TYR    37       6.527  -1.848  -6.573  1.00  0.00              
ATOM     38  CA  LEU    38       5.730   0.734  -9.245  1.00  0.00              
ATOM     39  CA  LYS    39       9.430   1.415  -9.891  1.00  0.00              
ATOM     40  CA  GLY    40      10.118  -2.314 -10.263  1.00  0.00              
TER                                                                             
END
