
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS393_1-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:    22        19 - 40          0.97     2.30
  LCS_AVERAGE:     53.55

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   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K       6     K       6     15   36   36     8   13   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I       7     I       7     15   36   36     8   13   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A       8     A       8     15   36   36     8   13   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R       9     R       9     15   36   36     8   13   20   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      10     I      10     15   36   36     8   13   15   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     N      11     N      11     15   36   36     8   13   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      12     E      12     15   36   36     8   13   22   28   32   34   35   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   22   31   34   35   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   15   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      15     A      15     15   36   36     7   13   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      16     K      16     15   36   36     7   13   15   19   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      17     A      17     15   36   36     7   13   15   15   15   18   34   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      18     K      18     15   36   36     7   13   15   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      19     A      19     22   36   36     7   13   15   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      20     G      20     22   36   36     6   19   20   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     V      21     V      21     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      22     I      22     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     T      23     T      23     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      24     E      24     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      25     E      25     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      26     E      26     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      27     K      27     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      28     A      28     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      29     E      29     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      30     Q      30     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      31     Q      31     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      32     K      32     22   36   36     4   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      33     L      33     22   36   36    12   19   21   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R      34     R      34     22   36   36    12   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      35     Q      35     22   36   36     8   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      36     E      36     22   36   36     8   19   20   27   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Y      37     Y      37     22   36   36     8   19   20   27   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      38     L      38     22   36   36     8   19   22   28   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      39     K      39     22   36   36     8   16   20   25   32   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      40     G      40     22   36   36     8   16   18   21   28   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  84.52  (  53.55  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     12     19     22     28     32     34     35     36     36     36     36     36     36     36     36     36     36     36     36     36 
GDT PERCENT_CA  33.33  52.78  61.11  77.78  88.89  94.44  97.22 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.65   1.11   1.33   1.51   1.64   1.72   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   2.35   2.32   1.94   1.89   1.83   1.82   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

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.824
LGA    K       6      K       6          1.836
LGA    I       7      I       7          1.396
LGA    A       8      A       8          1.184
LGA    R       9      R       9          2.032
LGA    I      10      I      10          2.039
LGA    N      11      N      11          1.387
LGA    E      12      E      12          1.735
LGA    L      13      L      13          3.061
LGA    A      14      A      14          2.309
LGA    A      15      A      15          1.242
LGA    K      16      K      16          2.780
LGA    A      17      A      17          3.795
LGA    K      18      K      18          1.890
LGA    A      19      A      19          2.094
LGA    G      20      G      20          1.578
LGA    V      21      V      21          1.325
LGA    I      22      I      22          1.532
LGA    T      23      T      23          1.544
LGA    E      24      E      24          1.266
LGA    E      25      E      25          0.491
LGA    E      26      E      26          0.692
LGA    K      27      K      27          1.039
LGA    A      28      A      28          0.440
LGA    E      29      E      29          0.773
LGA    Q      30      Q      30          1.506
LGA    Q      31      Q      31          1.102
LGA    K      32      K      32          1.456
LGA    L      33      L      33          1.539
LGA    R      34      R      34          1.226
LGA    Q      35      Q      35          0.733
LGA    E      36      E      36          1.987
LGA    Y      37      Y      37          2.120
LGA    L      38      L      38          0.820
LGA    K      39      K      39          2.291
LGA    G      40      G      40          3.303

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36   36    4.0     36    1.81    82.639    90.582     1.884

LGA_LOCAL      RMSD =  1.811  Number of atoms =   36  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.811  Number of atoms =   36 
Std_ALL_ATOMS  RMSD =  1.811  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.258045 * X  +   0.372925 * Y  +   0.891258 * Z  +   4.412623
  Y_new =   0.887766 * X  +  -0.455473 * Y  +  -0.066452 * Z  +   1.555691
  Z_new =   0.381162 * X  +   0.808376 * Y  +  -0.448602 * Z  +  -6.744076 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.077427   -1.064166  [ DEG:   119.0278    -60.9722 ]
  Theta =  -0.391053   -2.750539  [ DEG:   -22.4057   -157.5943 ]
  Phi   =   1.287923   -1.853670  [ DEG:    73.7925   -106.2075 ]
 
# 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_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS393_1-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  90.582     1.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS393_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT N/A
ATOM      5  CA  ALA     5       0.465 -10.665  -6.660  1.00 25.00           C
ATOM      6  CA  LYS     6       1.857  -7.098  -6.570  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.506  -5.729  -7.787  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.329  -7.727  -5.075  1.00 25.00           C
ATOM      9  CA  ARG     9      -0.932  -6.358  -2.421  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.541  -2.790  -3.675  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.325  -3.354  -3.515  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.001  -4.681   0.063  1.00 25.00           C
ATOM     13  CA  LEU    13      -2.928  -1.612   1.039  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.571   0.693  -0.499  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.325  -1.132   1.439  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.324  -0.759   4.682  1.00 25.00           C
ATOM     17  CA  ALA    17      -5.864   2.981   3.998  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.624   3.354   3.371  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.377   1.529   6.652  1.00 25.00           C
ATOM     20  CA  GLY    20     -11.476   2.330  10.175  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.674   4.152  12.061  1.00 25.00           C
ATOM     22  CA  ILE    22      -5.163   3.999  10.466  1.00 25.00           C
ATOM     23  CA  THR    23      -1.871   4.505  12.384  1.00 25.00           C
ATOM     24  CA  GLU    24       1.446   6.080  11.285  1.00 25.00           C
ATOM     25  CA  GLU    25       3.304   2.792  10.652  1.00 25.00           C
ATOM     26  CA  GLU    26       0.383   1.522   8.524  1.00 25.00           C
ATOM     27  CA  LYS    27       0.398   4.782   6.514  1.00 25.00           C
ATOM     28  CA  ALA    28       4.173   4.449   5.957  1.00 25.00           C
ATOM     29  CA  GLU    29       3.705   0.835   4.779  1.00 25.00           C
ATOM     30  CA  GLN    30       0.952   1.953   2.363  1.00 25.00           C
ATOM     31  CA  GLN    31       3.235   4.709   0.998  1.00 25.00           C
ATOM     32  CA  LYS    32       6.054   2.164   0.506  1.00 25.00           C
ATOM     33  CA  LEU    33       3.652  -0.178  -1.341  1.00 25.00           C
ATOM     34  CA  ARG    34       2.525   2.711  -3.590  1.00 25.00           C
ATOM     35  CA  GLN    35       6.178   3.579  -4.344  1.00 25.00           C
ATOM     36  CA  GLU    36       6.895  -0.080  -5.215  1.00 25.00           C
ATOM     37  CA  TYR    37       3.852  -0.147  -7.540  1.00 25.00           C
ATOM     38  CA  LEU    38       5.051   3.066  -9.243  1.00 25.00           C
ATOM     39  CA  LYS    39       8.536   1.547  -9.709  1.00 25.00           C
ATOM     40  CA  GLY    40       6.986  -1.609 -11.226  1.00 25.00           C
TER
END
