
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0335TS307_2u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   32 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_2u-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:    32         5 - 40          3.88     3.88
  LCS_AVERAGE:     88.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19         5 - 23          1.95     4.76
  LCS_AVERAGE:     39.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15         5 - 19          0.69     5.79
  LCS_AVERAGE:     28.99

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   19   32     8   14   15   15   16   19   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     K       6     K       6     15   19   32     9   14   15   15   16   19   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     I       7     I       7     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     A       8     A       8     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     R       9     R       9     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     I      10     I      10     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     N      11     N      11     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     E      12     E      12     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     L      13     L      13     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     A      14     A      14     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     A      15     A      15     15   19   32     9   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     K      16     K      16     15   19   32     8   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     A      17     A      17     15   19   32     8   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     K      18     K      18     15   19   32     5   14   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     A      19     A      19     15   19   32     4   10   15   15   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     G      20     G      20      3   19   32     3    3    4    4    5   14   19   21   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     V      21     V      21      9   19   32     3    3    9   14   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     I      22     I      22      9   19   32     3    8    9    9   11   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     T      23     T      23      9   19   32     7    8    9   10   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     E      24     E      24      9   10   32     7    8    9    9   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     E      25     E      25      9   10   32     7    8    9    9   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     E      26     E      26      9   10   32     7    8    9    9   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     K      27     K      27      9   10   32     7    8    9   13   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     A      28     A      28      9   10   32     7    8    9   10   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     E      29     E      29      9   10   32     7    8    9   10   16   20   23   24   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     K      32     K      32      4   10   32     4    4    4    4    5    6   10   14   23   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     L      33     L      33      4    5   32     4    4    4    4    5    6   10   11   23   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     R      34     R      34      4    5   32     4    4    4    4    5   11   19   23   25   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     Q      35     Q      35      4    5   32     4    4    4    4    5   10   11   21   22   28   29   30   31   32   32   32   32   32   32   32 
LCS_GDT     L      38     L      38      3    5   32     3    3    3    3    5    6   11   11   14   16   21   26   31   32   32   32   32   32   32   32 
LCS_GDT     K      39     K      39      3    4   32     3    3    3    3    4    4   11   11   14   16   21   30   31   32   32   32   32   32   32   32 
LCS_GDT     G      40     G      40      3    4   32     3    3    3    3    4    4   11   14   17   25   29   30   31   32   32   32   32   32   32   32 
LCS_AVERAGE  LCS_A:  52.58  (  28.99   39.84   88.89 )

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      9     14     15     15     16     20     23     24     25     28     29     30     31     32     32     32     32     32     32     32 
GDT PERCENT_CA  25.00  38.89  41.67  41.67  44.44  55.56  63.89  66.67  69.44  77.78  80.56  83.33  86.11  88.89  88.89  88.89  88.89  88.89  88.89  88.89
GDT RMS_LOCAL    0.25   0.51   0.69   0.69   1.17   2.11   2.31   2.40   2.56   3.20   3.27   3.45   3.66   3.88   3.88   3.88   3.88   3.88   3.88   3.88
GDT RMS_ALL_CA   5.53   5.67   5.79   5.79   5.25   4.37   4.34   4.38   4.33   3.95   3.95   3.91   3.89   3.88   3.88   3.88   3.88   3.88   3.88   3.88

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          3.323
LGA    K       6      K       6          2.916
LGA    I       7      I       7          1.950
LGA    A       8      A       8          1.695
LGA    R       9      R       9          2.166
LGA    I      10      I      10          2.146
LGA    N      11      N      11          1.418
LGA    E      12      E      12          1.063
LGA    L      13      L      13          1.562
LGA    A      14      A      14          1.718
LGA    A      15      A      15          1.141
LGA    K      16      K      16          1.420
LGA    A      17      A      17          2.517
LGA    K      18      K      18          1.850
LGA    A      19      A      19          3.120
LGA    G      20      G      20          4.678
LGA    V      21      V      21          2.073
LGA    I      22      I      22          3.311
LGA    T      23      T      23          2.381
LGA    E      24      E      24          3.048
LGA    E      25      E      25          3.678
LGA    E      26      E      26          3.073
LGA    K      27      K      27          2.342
LGA    A      28      A      28          2.535
LGA    E      29      E      29          3.077
LGA    K      32      K      32          7.443
LGA    L      33      L      33          5.910
LGA    R      34      R      34          6.237
LGA    Q      35      Q      35          7.559
LGA    L      38      L      38         10.049
LGA    K      39      K      39          8.536
LGA    G      40      G      40          8.709

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   36    4.0     24    2.40    59.028    56.245     0.959

LGA_LOCAL      RMSD =  2.402  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.328  Number of atoms =   32 
Std_ALL_ATOMS  RMSD =  3.878  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.974501 * X  +  -0.196342 * Y  +   0.108613 * Z  + -26.614176
  Y_new =  -0.221803 * X  +  -0.769759 * Y  +   0.598561 * Z  + -70.819481
  Z_new =  -0.033917 * X  +  -0.607389 * Y  +  -0.793680 * Z  + 111.847229 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.488383    0.653210  [ DEG:  -142.5738     37.4262 ]
  Theta =   0.033924    3.107669  [ DEG:     1.9437    178.0563 ]
  Phi   =  -0.223794    2.917799  [ DEG:   -12.8225    167.1775 ]
 
# 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: T0335TS307_2u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_2u-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   36   4.0   24   2.40  56.245     3.88
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_2u-D1
PFRMAT   TS
TARGET   T0335
MODEL    2  UNREFINED
PARENT   1ywm_A
ATOM     1   N   ALA     5      -2.529 -11.666  -9.123  1.00                    
ATOM     1   CA  ALA     5      -2.920 -11.875  -7.722  1.00                    
ATOM     1   C   ALA     5      -2.165 -10.930  -6.781  1.00                    
ATOM     1   O   ALA     5      -2.739 -10.397  -5.819  1.00                    
ATOM     1   N   LYS     6      -0.869 -10.747  -7.039  1.00                    
ATOM     1   CA  LYS     6      -0.102  -9.746  -6.304  1.00                    
ATOM     1   C   LYS     6      -0.772  -8.388  -6.390  1.00                    
ATOM     1   O   LYS     6      -0.937  -7.702  -5.362  1.00                    
ATOM     1   N   ILE     7      -1.182  -7.987  -7.592  1.00                    
ATOM     1   CA  ILE     7      -1.764  -6.648  -7.743  1.00                    
ATOM     1   C   ILE     7      -3.095  -6.522  -6.987  1.00                    
ATOM     1   O   ILE     7      -3.376  -5.495  -6.377  1.00                    
ATOM     1   N   ALA     8      -3.893  -7.589  -7.006  1.00                    
ATOM     1   CA  ALA     8      -5.140  -7.627  -6.243  1.00                    
ATOM     1   C   ALA     8      -4.840  -7.542  -4.762  1.00                    
ATOM     1   O   ALA     8      -5.493  -6.794  -4.043  1.00                    
ATOM     1   N   ARG     9      -3.880  -8.337  -4.309  1.00                    
ATOM     1   CA  ARG     9      -3.472  -8.308  -2.900  1.00                    
ATOM     1   C   ARG     9      -3.025  -6.911  -2.467  1.00                    
ATOM     1   O   ARG     9      -3.374  -6.421  -1.371  1.00                    
ATOM     1   N   ILE    10      -2.211  -6.280  -3.296  1.00                    
ATOM     1   CA  ILE    10      -1.771  -4.940  -2.997  1.00                    
ATOM     1   C   ILE    10      -2.948  -3.985  -2.837  1.00                    
ATOM     1   O   ILE    10      -2.956  -3.168  -1.905  1.00                    
ATOM     1   N   ASN    11      -3.945  -4.076  -3.725  1.00                    
ATOM     1   CA  ASN    11      -5.106  -3.165  -3.636  1.00                    
ATOM     1   C   ASN    11      -5.942  -3.467  -2.393  1.00                    
ATOM     1   O   ASN    11      -6.482  -2.552  -1.776  1.00                    
ATOM     1   N   GLU    12      -6.013  -4.734  -2.012  1.00                    
ATOM     1   CA  GLU    12      -6.757  -5.113  -0.795  1.00                    
ATOM     1   C   GLU    12      -6.099  -4.544   0.469  1.00                    
ATOM     1   O   GLU    12      -6.798  -4.011   1.365  1.00                    
ATOM     1   N   LEU    13      -4.769  -4.610   0.538  1.00                    
ATOM     1   CA  LEU    13      -4.050  -4.063   1.706  1.00                    
ATOM     1   C   LEU    13      -4.140  -2.537   1.692  1.00                    
ATOM     1   O   LEU    13      -4.280  -1.906   2.738  1.00                    
ATOM     1   N   ALA    14      -4.032  -1.932   0.510  1.00                    
ATOM     1   CA  ALA    14      -4.182  -0.493   0.385  1.00                    
ATOM     1   C   ALA    14      -5.542  -0.052   0.941  1.00                    
ATOM     1   O   ALA    14      -5.645   0.930   1.707  1.00                    
ATOM     1   N   ALA    15      -6.592  -0.774   0.548  1.00                    
ATOM     1   CA  ALA    15      -7.949  -0.417   0.957  1.00                    
ATOM     1   C   ALA    15      -8.056  -0.537   2.487  1.00                    
ATOM     1   O   ALA    15      -8.557   0.352   3.163  1.00                    
ATOM     1   N   LYS    16      -7.562  -1.646   3.006  1.00                    
ATOM     1   CA  LYS    16      -7.521  -1.855   4.447  1.00                    
ATOM     1   C   LYS    16      -6.747  -0.731   5.162  1.00                    
ATOM     1   O   LYS    16      -7.255  -0.132   6.132  1.00                    
ATOM     1   N   ALA    17      -5.533  -0.446   4.686  1.00                    
ATOM     1   CA  ALA    17      -4.661   0.536   5.324  1.00                    
ATOM     1   C   ALA    17      -5.315   1.922   5.389  1.00                    
ATOM     1   O   ALA    17      -5.047   2.672   6.320  1.00                    
ATOM     1   N   LYS    18      -6.167   2.240   4.415  1.00                    
ATOM     1   CA  LYS    18      -6.817   3.555   4.353  1.00                    
ATOM     1   C   LYS    18      -7.967   3.751   5.336  1.00                    
ATOM     1   O   LYS    18      -8.472   4.863   5.496  1.00                    
ATOM     1   N   ALA    19      -8.323   2.689   6.040  1.00                    
ATOM     1   CA  ALA    19      -9.350   2.783   7.082  1.00                    
ATOM     1   C   ALA    19      -8.840   3.714   8.220  1.00                    
ATOM     1   O   ALA    19      -7.762   3.469   8.759  1.00                    
ATOM     1   N   GLY    20      -9.579   4.762   8.588  1.00                    
ATOM     1   CA  GLY    20      -9.134   5.645   9.665  1.00                    
ATOM     1   C   GLY    20      -8.987   4.988  11.027  1.00                    
ATOM     1   O   GLY    20      -8.441   5.657  11.910  1.00                    
ATOM     1   N   VAL    21      -9.367   3.719  11.203  1.00                    
ATOM     1   CA  VAL    21      -9.143   3.089  12.517  1.00                    
ATOM     1   C   VAL    21      -7.635   2.829  12.823  1.00                    
ATOM     1   O   VAL    21      -7.252   2.626  13.984  1.00                    
ATOM     1   N   ILE    22      -6.804   2.817  11.771  1.00                    
ATOM     1   CA  ILE    22      -5.360   2.592  11.884  1.00                    
ATOM     1   C   ILE    22      -4.629   3.902  12.126  1.00                    
ATOM     1   O   ILE    22      -5.043   4.951  11.636  1.00                    
ATOM     1   N   THR    23      -3.552   3.858  12.906  1.00                    
ATOM     1   CA  THR    23      -2.733   5.051  13.092  1.00                    
ATOM     1   C   THR    23      -2.242   5.580  11.744  1.00                    
ATOM     1   O   THR    23      -1.942   4.802  10.832  1.00                    
ATOM     1   N   GLU    24      -2.124   6.896  11.630  1.00                    
ATOM     1   CA  GLU    24      -1.565   7.446  10.389  1.00                    
ATOM     1   C   GLU    24      -0.117   6.955  10.162  1.00                    
ATOM     1   O   GLU    24       0.285   6.652   9.036  1.00                    
ATOM     1   N   GLU    25       0.653   6.850  11.233  1.00                    
ATOM     1   CA  GLU    25       2.051   6.439  11.128  1.00                    
ATOM     1   C   GLU    25       2.172   5.003  10.571  1.00                    
ATOM     1   O   GLU    25       3.029   4.727   9.709  1.00                    
ATOM     1   N   GLU    26       1.335   4.086  11.060  1.00                    
ATOM     1   CA  GLU    26       1.369   2.732  10.493  1.00                    
ATOM     1   C   GLU    26       0.829   2.675   9.040  1.00                    
ATOM     1   O   GLU    26       1.414   1.975   8.178  1.00                    
ATOM     1   N   LYS    27      -0.255   3.394   8.768  1.00                    
ATOM     1   CA  LYS    27      -0.782   3.469   7.398  1.00                    
ATOM     1   C   LYS    27       0.338   3.890   6.438  1.00                    
ATOM     1   O   LYS    27       0.518   3.306   5.364  1.00                    
ATOM     1   N   ALA    28       1.055   4.938   6.816  1.00                    
ATOM     1   CA  ALA    28       2.054   5.515   5.934  1.00                    
ATOM     1   C   ALA    28       3.184   4.526   5.674  1.00                    
ATOM     1   O   ALA    28       3.671   4.408   4.546  1.00                    
ATOM     1   N   GLU    29       3.604   3.811   6.713  1.00                    
ATOM     1   CA  GLU    29       4.676   2.835   6.542  1.00                    
ATOM     1   C   GLU    29       4.229   1.710   5.627  1.00                    
ATOM     1   O   GLU    29       4.988   1.257   4.766  1.00                    
ATOM     1   N   LYS    32       2.992   1.256   5.811  1.00                    
ATOM     1   CA  LYS    32       2.455   0.178   4.979  1.00                    
ATOM     1   C   LYS    32       2.316   0.648   3.513  1.00                    
ATOM     1   O   LYS    32       2.765  -0.044   2.572  1.00                    
ATOM     1   N   LEU    33       1.745   1.829   3.314  1.00                    
ATOM     1   CA  LEU    33       1.586   2.321   1.920  1.00                    
ATOM     1   C   LEU    33       2.916   2.546   1.238  1.00                    
ATOM     1   O   LEU    33       3.049   2.377  -0.008  1.00                    
ATOM     1   N   ARG    34       3.924   2.949   2.010  1.00                    
ATOM     1   CA  ARG    34       5.254   3.154   1.437  1.00                    
ATOM     1   C   ARG    34       5.798   1.840   0.859  1.00                    
ATOM     1   O   ARG    34       6.392   1.805  -0.238  1.00                    
ATOM     1   N   GLN    35       5.610   0.765   1.611  1.00                    
ATOM     1   CA  GLN    35       6.091  -0.545   1.176  1.00                    
ATOM     1   C   GLN    35       5.313  -1.042  -0.043  1.00                    
ATOM     1   O   GLN    35       5.887  -1.614  -1.008  1.00                    
ATOM     1   N   LEU    38       4.000  -0.868  -0.005  1.00                    
ATOM     1   CA  LEU    38       3.196  -1.215  -1.180  1.00                    
ATOM     1   C   LEU    38       3.613  -0.416  -2.431  1.00                    
ATOM     1   O   LEU    38       3.648  -0.973  -3.539  1.00                    
ATOM     1   N   LYS    39       3.845   0.890  -2.281  1.00                    
ATOM     1   CA  LYS    39       4.285   1.723  -3.400  1.00                    
ATOM     1   C   LYS    39       5.606   1.270  -3.992  1.00                    
ATOM     1   O   LYS    39       5.784   1.307  -5.210  1.00                    
ATOM     1   N   GLY    40       6.522   0.848  -3.137  1.00                    
ATOM     1   CA  GLY    40       7.821   0.359  -3.592  1.00                    
ATOM     1   C   GLY    40       7.658  -0.911  -4.460  1.00                    
ATOM     1   O   GLY    40       8.228  -1.018  -5.572  1.00                    
TER
END
