
#######################################################
#                                                     #
#                        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 T0335TS168_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS168_4-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          2.01     2.01
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35         5 - 39          1.97     2.02
  LCS_AVERAGE:     96.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        21 - 40          0.79     3.19
  LCS_AVERAGE:     50.62

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     16   35   36     8   12   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K       6     K       6     16   35   36     8   13   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I       7     I       7     16   35   36     8   13   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A       8     A       8     16   35   36     8   13   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R       9     R       9     16   35   36     8   13   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      10     I      10     16   35   36     8   13   15   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     N      11     N      11     16   35   36     8   13   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      12     E      12     16   35   36     8   13   19   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      13     L      13     16   35   36     7   13   15   17   29   33   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      14     A      14     16   35   36     7   13   15   16   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      15     A      15     16   35   36     7   13   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      16     K      16     16   35   36     5   13   15   16   29   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      17     A      17     16   35   36     5   13   15   15   16   16   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      18     K      18     16   35   36     5   13   15   20   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      19     A      19     16   35   36     5   11   15   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      20     G      20     16   35   36     3    3    3   13   26   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     V      21     V      21     20   35   36     6   12   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     I      22     I      22     20   35   36     4   16   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     T      23     T      23     20   35   36     7   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      24     E      24     20   35   36     6   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      25     E      25     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      26     E      26     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      27     K      27     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     A      28     A      28     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      29     E      29     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      30     Q      30     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      31     Q      31     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      32     K      32     20   35   36     4   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      33     L      33     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     R      34     R      34     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Q      35     Q      35     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     E      36     E      36     20   35   36     8   17   21   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     Y      37     Y      37     20   35   36     8   17   20   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     L      38     L      38     20   35   36     8   17   20   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     K      39     K      39     20   35   36     8   17   20   25   31   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_GDT     G      40     G      40     20   27   36     8   10   20   22   30   34   35   36   36   36   36   36   36   36   36   36   36   36   36   36 
LCS_AVERAGE  LCS_A:  82.41  (  50.62   96.60  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      8     17     21     25     31     34     35     36     36     36     36     36     36     36     36     36     36     36     36     36 
GDT PERCENT_CA  22.22  47.22  58.33  69.44  86.11  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    0.20   0.64   1.04   1.26   1.60   1.84   1.91   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01
GDT RMS_ALL_CA   3.33   3.23   2.38   2.23   2.10   2.03   2.02   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01   2.01

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.164
LGA    K       6      K       6          1.248
LGA    I       7      I       7          1.057
LGA    A       8      A       8          0.844
LGA    R       9      R       9          1.562
LGA    I      10      I      10          1.656
LGA    N      11      N      11          1.037
LGA    E      12      E      12          1.401
LGA    L      13      L      13          2.798
LGA    A      14      A      14          2.195
LGA    A      15      A      15          0.890
LGA    K      16      K      16          2.597
LGA    A      17      A      17          3.770
LGA    K      18      K      18          1.966
LGA    A      19      A      19          1.816
LGA    G      20      G      20          3.237
LGA    V      21      V      21          2.218
LGA    I      22      I      22          2.531
LGA    T      23      T      23          1.898
LGA    E      24      E      24          2.048
LGA    E      25      E      25          1.210
LGA    E      26      E      26          1.952
LGA    K      27      K      27          2.002
LGA    A      28      A      28          1.072
LGA    E      29      E      29          1.119
LGA    Q      30      Q      30          2.064
LGA    Q      31      Q      31          2.173
LGA    K      32      K      32          1.969
LGA    L      33      L      33          1.682
LGA    R      34      R      34          2.085
LGA    Q      35      Q      35          1.712
LGA    E      36      E      36          1.995
LGA    Y      37      Y      37          2.769
LGA    L      38      L      38          2.585
LGA    K      39      K      39          2.656
LGA    G      40      G      40          3.543

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   36   36    4.0     36    2.01    79.167    88.320     1.702

LGA_LOCAL      RMSD =  2.015  Number of atoms =   36  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.086  Number of atoms =   36 
Std_ALL_ATOMS  RMSD =  2.015  (standard rmsd on all 36 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.135363 * X  +   0.574446 * Y  +   0.807273 * Z  +   4.465652
  Y_new =   0.453942 * X  +  -0.760183 * Y  +   0.464821 * Z  +   1.459448
  Z_new =   0.880689 * X  +   0.303535 * Y  +  -0.363666 * Z  +  -6.287219 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.446074   -0.695518  [ DEG:   140.1497    -39.8503 ]
  Theta =  -1.077315   -2.064277  [ DEG:   -61.7256   -118.2744 ]
  Phi   =   1.280997   -1.860596  [ DEG:    73.3957   -106.6043 ]
 
# 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: T0335TS168_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS168_4-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   2.01  88.320     2.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS168_4-D1
PFRMAT TS
TARGET T0335
MODEL 4
PARENT N/A
ATOM      5  CA  ALA     5       0.064 -10.683  -6.115  1.00 25.00           C
ATOM      6  CA  LYS     6       1.510  -7.137  -6.077  1.00 25.00           C
ATOM      7  CA  ILE     7      -1.818  -5.738  -7.355  1.00 25.00           C
ATOM      8  CA  ALA     8      -3.699  -7.656  -4.625  1.00 25.00           C
ATOM      9  CA  ARG     9      -1.308  -6.275  -1.972  1.00 25.00           C
ATOM     10  CA  ILE    10      -1.847  -2.724  -3.298  1.00 25.00           C
ATOM     11  CA  ASN    11      -5.641  -3.224  -3.167  1.00 25.00           C
ATOM     12  CA  GLU    12      -5.374  -4.489   0.438  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.262  -1.434   1.378  1.00 25.00           C
ATOM     14  CA  ALA    14      -5.853   0.882  -0.230  1.00 25.00           C
ATOM     15  CA  ALA    15      -8.655  -0.862   1.713  1.00 25.00           C
ATOM     16  CA  LYS    16      -6.681  -0.460   4.970  1.00 25.00           C
ATOM     17  CA  ALA    17      -6.156   3.259   4.220  1.00 25.00           C
ATOM     18  CA  LYS    18      -9.901   3.679   3.547  1.00 25.00           C
ATOM     19  CA  ALA    19     -10.717   1.928   6.855  1.00 25.00           C
ATOM     20  CA  GLY    20     -10.699   4.492   9.712  1.00 25.00           C
ATOM     21  CA  VAL    21      -8.508   2.084  11.785  1.00 25.00           C
ATOM     22  CA  ILE    22      -5.077   1.852  10.067  1.00 25.00           C
ATOM     23  CA  THR    23      -2.183   3.259  12.150  1.00 25.00           C
ATOM     24  CA  GLU    24       0.882   5.456  11.861  1.00 25.00           C
ATOM     25  CA  GLU    25       3.796   3.058  11.214  1.00 25.00           C
ATOM     26  CA  GLU    26       1.417   0.588   9.508  1.00 25.00           C
ATOM     27  CA  LYS    27       0.021   3.406   7.323  1.00 25.00           C
ATOM     28  CA  ALA    28       3.576   4.458   6.364  1.00 25.00           C
ATOM     29  CA  GLU    29       4.429   0.836   5.457  1.00 25.00           C
ATOM     30  CA  GLN    30       1.269   0.603   3.307  1.00 25.00           C
ATOM     31  CA  GLN    31       2.204   3.867   1.535  1.00 25.00           C
ATOM     32  CA  LYS    32       5.732   2.527   0.876  1.00 25.00           C
ATOM     33  CA  LEU    33       4.262  -0.711  -0.548  1.00 25.00           C
ATOM     34  CA  ARG    34       1.937   1.315  -2.819  1.00 25.00           C
ATOM     35  CA  GLN    35       4.905   3.411  -4.030  1.00 25.00           C
ATOM     36  CA  GLU    36       6.891   0.219  -4.763  1.00 25.00           C
ATOM     37  CA  TYR    37       3.924  -1.208  -6.721  1.00 25.00           C
ATOM     38  CA  LEU    38       3.660   2.041  -8.733  1.00 25.00           C
ATOM     39  CA  LYS    39       7.410   1.900  -9.500  1.00 25.00           C
ATOM     40  CA  GLY    40       7.063  -1.738 -10.646  1.00 25.00           C
TER
END
