
#######################################################
#                                                     #
#                        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 T0335TS393_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS393_3-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          1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36         5 - 40          1.81     1.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        22 - 40          0.73     2.72
  LCS_AVERAGE:     47.53

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     15   36   36     8   12   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K       6     K       6     15   36   36     8   13   18   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I       7     I       7     15   36   36     8   13   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A       8     A       8     15   36   36     8   13   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R       9     R       9     15   36   36     8   13   18   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      10     I      10     15   36   36     8   13   17   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     N      11     N      11     15   36   36     8   13   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      12     E      12     15   36   36     8   13   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      13     L      13     15   36   36     7   13   15   23   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      14     A      14     15   36   36     7   13   15   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      15     A      15     15   36   36     7   13   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      16     K      16     15   36   36     6   13   15   21   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      17     A      17     15   36   36     5   13   15   15   16   27   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      18     K      18     15   36   36     5   13   17   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      19     A      19     15   36   36     5   11   18   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      20     G      20     15   36   36     7   14   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     V      21     V      21     15   36   36     3    3   10   23   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      22     I      22     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     T      23     T      23     19   36   36     3   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      24     E      24     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      25     E      25     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      26     E      26     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      27     K      27     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      28     A      28     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      29     E      29     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      30     Q      30     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      31     Q      31     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      32     K      32     19   36   36     4   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      33     L      33     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R      34     R      34     19   36   36    10   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      35     Q      35     19   36   36     8   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      36     E      36     19   36   36     8   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Y      37     Y      37     19   36   36     8   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      38     L      38     19   36   36     8   17   20   27   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      39     K      39     19   36   36     8   17   20   25   31   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      40     G      40     19   36   36     8   16   19   23   27   34   36   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  82.51  (  47.53  100.00  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     10     17     20     27     31     34     36     36     36     36     36     36     36     36     36     36     36     36     36     36 
GDT PERCENT_CA  27.78  47.22  55.56  75.00  86.11  94.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.61   0.94   1.28   1.47   1.65   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81
GDT RMS_ALL_CA   2.52   2.55   2.16   1.91   1.86   1.82   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81   1.81

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.745
LGA    K       6      K       6          1.862
LGA    I       7      I       7          1.312
LGA    A       8      A       8          0.895
LGA    R       9      R       9          1.952
LGA    I      10      I      10          2.018
LGA    N      11      N      11          1.189
LGA    E      12      E      12          1.559
LGA    L      13      L      13          2.993
LGA    A      14      A      14          2.300
LGA    A      15      A      15          1.137
LGA    K      16      K      16          2.641
LGA    A      17      A      17          3.679
LGA    K      18      K      18          1.906
LGA    A      19      A      19          2.088
LGA    G      20      G      20          1.676
LGA    V      21      V      21          2.671
LGA    I      22      I      22          1.577
LGA    T      23      T      23          1.723
LGA    E      24      E      24          1.045
LGA    E      25      E      25          0.268
LGA    E      26      E      26          0.770
LGA    K      27      K      27          0.977
LGA    A      28      A      28          0.501
LGA    E      29      E      29          0.881
LGA    Q      30      Q      30          1.485
LGA    Q      31      Q      31          1.074
LGA    K      32      K      32          1.467
LGA    L      33      L      33          1.464
LGA    R      34      R      34          1.054
LGA    Q      35      Q      35          0.824
LGA    E      36      E      36          1.953
LGA    Y      37      Y      37          1.894
LGA    L      38      L      38          0.850
LGA    K      39      K      39          2.413
LGA    G      40      G      40          3.256

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36   36    4.0     36    1.81    80.556    89.510     1.885

LGA_LOCAL      RMSD =  1.810  Number of atoms =   36  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.810  Number of atoms =   36 
Std_ALL_ATOMS  RMSD =  1.810  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.303709 * X  +   0.281693 * Y  +   0.910170 * Z  +   4.958743
  Y_new =   0.947286 * X  +  -0.191578 * Y  +  -0.256802 * Z  +   1.727187
  Z_new =   0.102030 * X  +   0.940185 * Y  +  -0.325028 * Z  +  -6.806008 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.903641   -1.237952  [ DEG:   109.0706    -70.9294 ]
  Theta =  -0.102207   -3.039385  [ DEG:    -5.8561   -174.1440 ]
  Phi   =   1.260540   -1.881052  [ DEG:    72.2236   -107.7764 ]
 
# 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: T0335TS393_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_3-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   36   1.81  89.510     1.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_3-D1
PFRMAT TS
TARGET T0335
MODEL 3
PARENT N/A
ATOM      5  CA  ALA     5       0.283 -10.380  -6.685  1.00 25.00           C
ATOM      6  CA  LYS     6       1.579  -6.778  -6.617  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.847  -5.497  -7.750  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.551  -7.549  -5.003  1.00 25.00           C
ATOM      9  CA  ARG     9      -1.129  -6.122  -2.401  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.864  -2.570  -3.631  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.627  -3.236  -3.383  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.183  -4.561   0.182  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.170  -1.440   1.118  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.910   0.797  -0.350  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.568  -1.106   1.646  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.502  -0.687   4.844  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.158   3.065   4.159  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.941   3.338   3.621  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.567   1.486   6.914  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.285   0.505  10.578  1.00 25.00           C
ATOM     21  CA  VAL    21      -6.827   2.089  10.554  1.00 25.00           C
ATOM     22  CA  ILE    22      -4.926   5.262   9.956  1.00 25.00           C
ATOM     23  CA  THR    23      -2.166   4.994  12.535  1.00 25.00           C
ATOM     24  CA  GLU    24       1.124   6.328  11.099  1.00 25.00           C
ATOM     25  CA  GLU    25       3.016   3.036  10.601  1.00 25.00           C
ATOM     26  CA  GLU    26       0.169   1.703   8.414  1.00 25.00           C
ATOM     27  CA  LYS    27       0.233   4.915   6.330  1.00 25.00           C
ATOM     28  CA  ALA    28       4.025   4.589   5.898  1.00 25.00           C
ATOM     29  CA  GLU    29       3.611   0.947   4.791  1.00 25.00           C
ATOM     30  CA  GLN    30       0.930   1.994   2.265  1.00 25.00           C
ATOM     31  CA  GLN    31       3.242   4.730   0.908  1.00 25.00           C
ATOM     32  CA  LYS    32       6.087   2.189   0.563  1.00 25.00           C
ATOM     33  CA  LEU    33       3.753  -0.207  -1.303  1.00 25.00           C
ATOM     34  CA  ARG    34       2.686   2.623  -3.651  1.00 25.00           C
ATOM     35  CA  GLN    35       6.357   3.493  -4.311  1.00 25.00           C
ATOM     36  CA  GLU    36       7.116  -0.182  -5.075  1.00 25.00           C
ATOM     37  CA  TYR    37       4.149  -0.319  -7.492  1.00 25.00           C
ATOM     38  CA  LEU    38       5.386   2.860  -9.230  1.00 25.00           C
ATOM     39  CA  LYS    39       8.891   1.350  -9.552  1.00 25.00           C
ATOM     40  CA  GLY    40       7.402  -1.848 -11.043  1.00 25.00           C
TER
END
