
#######################################################
#                                                     #
#                        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   76 (   76),  selected   62 , name T0309TS599_5
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS599_5.T0309.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:    30        25 - 54          4.99    15.82
  LCS_AVERAGE:     36.45

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        34 - 50          1.97    16.95
  LCS_AVERAGE:     16.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        34 - 43          0.74    20.07
  LONGEST_CONTINUOUS_SEGMENT:    10        35 - 44          0.88    20.09
  LCS_AVERAGE:     10.04

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:   62
LCS_GDT     A       2     A       2      3    3    9     0    3    3    3    3    4    5    5    6    7    8   10   10   10   11   12   13   13   15   29 
LCS_GDT     S       3     S       3      3    3    9     0    3    3    3    3    4    5    5    6    7    8   10   10   18   21   26   27   27   27   29 
LCS_GDT     K       4     K       4      3    3   10     0    3    3    3    3    4    5    5    6   10   11   18   21   22   24   26   27   27   28   30 
LCS_GDT     K       5     K       5      3    3   10     1    3    3    4    4    4    5    5    7    7    8   10   11   19   21   26   27   27   27   29 
LCS_GDT     V       6     V       6      3    3   11     0    3    3    4    4    7   12   16   17   19   21   21   23   25   28   29   30   30   34   37 
LCS_GDT     H       7     H       7      3    3   16     1    3    3    4    4    4    4    5    7    9   21   23   25   28   29   33   34   35   36   37 
LCS_GDT     Q       8     Q       8      6    7   16     3    6    6    6    6    7    8   10   12   14   17   17   25   28   30   33   34   35   36   37 
LCS_GDT     I       9     I       9      6    7   16     4    6    6    6    7    7   10   14   15   18   21   26   28   31   32   33   34   35   36   37 
LCS_GDT     N      10     N      10      6    7   16     4    6    6    6    7    7   13   17   17   19   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     V      11     V      11      6    8   16     4    6    6    6    7    8   10   14   15   18   20   23   28   31   32   33   34   35   36   37 
LCS_GDT     K      12     K      12      6    8   16     4    6    6    6    8    8   10   11   13   14   17   17   17   19   20   21   22   24   25   31 
LCS_GDT     G      13     G      13      6    8   16     3    6    6    6    8    8   10   11   13   14   17   17   17   17   18   19   20   23   24   24 
LCS_GDT     F      14     F      14      5    8   16     3    4    6    6    8    8   10   11   13   14   17   17   18   19   20   21   22   23   24   25 
LCS_GDT     F      15     F      15      5    8   16     3    4    6    6    8    8   10   11   13   14   17   17   18   19   20   21   22   23   24   25 
LCS_GDT     D      16     D      16      5    8   16     3    4    6    6    8    8   10   11   13   14   17   17   18   19   20   21   22   23   25   26 
LCS_GDT     M      17     M      17      5    8   16     3    4    6    6    8    8   10   11   13   14   17   17   18   19   20   21   22   23   25   26 
LCS_GDT     D      18     D      18      5    8   16     3    4    6    6    8    8   10   11   13   14   17   17   18   19   20   21   22   23   25   26 
LCS_GDT     V      19     V      19      3    8   16     3    3    3    3    8    8    8   11   13   14   17   17   18   19   20   21   22   23   25   26 
LCS_GDT     M      20     M      20      3    4   16     3    3    3    3    5    5    7    9   13   14   17   17   17   19   20   21   22   23   25   26 
LCS_GDT     E      21     E      21      3    4   16     3    3    3    4    5    5    7    9   13   14   17   17   18   19   21   21   26   26   26   26 
LCS_GDT     V      22     V      22      3    4   16     1    3    3    3    5    5   12   14   15   15   18   18   21   22   23   26   28   30   33   36 
LCS_GDT     T      23     T      23      3    3   16     0    3    3    3    4    4   12   14   15   15   18   18   21   22   24   26   29   31   34   36 
LCS_GDT     E      24     E      24      3    3   25     3    4    5    6   10   10   11   14   15   18   20   22   27   30   32   33   34   35   36   37 
LCS_GDT     Q      25     Q      25      3    4   30     3    4    4    4    4    7    8   11   14   18   23   27   28   31   32   33   34   35   36   37 
LCS_GDT     T      26     T      26      4   12   30     3    4    7   10   11   13   14   17   18   19   20   26   28   31   32   33   34   35   36   37 
LCS_GDT     K      27     K      27      4   14   30     3    4    7   10   12   13   14   17   18   19   20   21   28   31   32   33   34   35   36   37 
LCS_GDT     E      28     E      28      4   14   30     3    4    7   11   12   13   15   17   18   19   20   22   26   30   32   33   33   35   36   37 
LCS_GDT     A      29     A      29      7   14   30     3    4    8   11   11   13   14   16   18   19   19   21   22   25   30   32   33   35   35   36 
LCS_GDT     E      30     E      30      7   14   30     4    6    8   11   12   13   15   17   18   19   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     Y      31     Y      31      7   14   30     4    6    8   11   12   13   15   17   18   19   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     T      32     T      32      7   14   30     4    6    8   11   12   13   17   21   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     Y      33     Y      33      9   16   30     4    6    8   11   12   13   19   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     D      34     D      34     10   17   30     4    8   10   12   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     F      35     F      35     10   17   30     6    9   10   12   15   17   19   22   23   23   23   27   28   31   32   33   34   35   36   37 
LCS_GDT     K      36     K      36     10   17   30     6    9   10   12   15   17   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     E      37     E      37     10   17   30     6    9   10   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     I      38     I      38     10   17   30     6    9   10   12   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     L      39     L      39     10   17   30     6    9   10   12   15   17   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     S      40     S      40     10   17   30     6    9   10   12   16   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     E      41     E      41     10   17   30     3    9   10   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     F      42     F      42     10   17   30     3    9   10   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     N      43     N      43     10   17   30     4    9   10   12   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     G      44     G      44     10   17   30     4    6   10   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     K      45     K      45      9   17   30     4    6    9   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     N      46     N      46      9   17   30     4    8    9   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     V      47     V      47      9   17   30     4    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     S      48     S      48      9   17   30     4    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     I      49     I      49      9   17   30     4    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     T      50     T      50      9   17   30     3    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     V      51     V      51      9   15   30     4    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     K      52     K      52      9   15   30     3    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     E      53     E      53      9   15   30     3    8    8   14   17   18   20   22   23   23   24   27   28   31   32   33   34   35   36   37 
LCS_GDT     E      54     E      54      5   15   30     3    5    8   14   17   18   20   22   23   23   23   27   28   31   32   33   34   35   36   37 
LCS_GDT     N      55     N      55      4    6   29     3    3    4    5    6    8    9   10   10   12   22   24   24   24   30   33   34   35   36   37 
LCS_GDT     E      56     E      56      4    6   28     3    4    5    5    6    8    9   10   10   10   10   11   19   24   25   28   29   34   35   37 
LCS_GDT     L      57     L      57      4    6   26     3    4    5    5    6    8    9   10   10   10   10   11   11   11   13   17   17   19   20   27 
LCS_GDT     P      58     P      58      4    6   12     3    4    5    5    6    8    9   10   10   10   10   11   11   11   13   17   17   19   20   23 
LCS_GDT     V      59     V      59      5    6   12     3    5    5    5    5    8    9   10   10   10   10   11   11   11   13   17   17   19   20   23 
LCS_GDT     K      60     K      60      5    6   12     3    5    5    5    6    8    9   10   10   10   10   11   11   11   12   17   17   19   19   23 
LCS_GDT     G      61     G      61      5    5   12     3    5    5    5    5    8    9   10   10   10   10   11   11   11   12   13   13   14   16   19 
LCS_GDT     V      62     V      62      5    5   12     3    5    5    5    5    6    9   10   10   10   10   11   11   11   12   13   13   14   16   17 
LCS_GDT     E      63     E      63      5    5   12     3    5    5    5    5    5    7   10   10   10   10   11   11   11   12   12   13   13   15   17 
LCS_AVERAGE  LCS_A:  21.09  (  10.04   16.78   36.45 )

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      6      9     10     14     17     18     20     22     23     23     24     27     28     31     32     33     34     35     36     37 
GDT PERCENT_CA   9.68  14.52  16.13  22.58  27.42  29.03  32.26  35.48  37.10  37.10  38.71  43.55  45.16  50.00  51.61  53.23  54.84  56.45  58.06  59.68
GDT RMS_LOCAL    0.19   0.61   0.74   1.52   1.82   1.92   2.25   2.48   2.65   2.65   3.70   4.06   4.26   4.82   4.98   5.15   5.41   5.56   5.68   5.94
GDT RMS_ALL_CA  20.73  20.34  20.07  16.46  16.52  16.44  16.39  16.49  16.37  16.37  15.93  15.83  15.80  15.69  15.72  15.69  15.61  15.71  15.58  15.59

#      Molecule1      Molecule2       DISTANCE
LGA    A       2      A       2         19.200
LGA    S       3      S       3         16.196
LGA    K       4      K       4         16.811
LGA    K       5      K       5         17.916
LGA    V       6      V       6         11.013
LGA    H       7      H       7         12.117
LGA    Q       8      Q       8         12.327
LGA    I       9      I       9         10.173
LGA    N      10      N      10          9.994
LGA    V      11      V      11         11.039
LGA    K      12      K      12         16.941
LGA    G      13      G      13         19.016
LGA    F      14      F      14         18.968
LGA    F      15      F      15         20.798
LGA    D      16      D      16         24.805
LGA    M      17      M      17         26.047
LGA    D      18      D      18         31.918
LGA    V      19      V      19         31.237
LGA    M      20      M      20         28.368
LGA    E      21      E      21         22.408
LGA    V      22      V      22         17.520
LGA    T      23      T      23         18.788
LGA    E      24      E      24         14.049
LGA    Q      25      Q      25         12.450
LGA    T      26      T      26         13.331
LGA    K      27      K      27         14.713
LGA    E      28      E      28         14.253
LGA    A      29      A      29         15.068
LGA    E      30      E      30         10.228
LGA    Y      31      Y      31          8.924
LGA    T      32      T      32          5.332
LGA    Y      33      Y      33          3.944
LGA    D      34      D      34          1.062
LGA    F      35      F      35          3.965
LGA    K      36      K      36          3.979
LGA    E      37      E      37          1.677
LGA    I      38      I      38          2.266
LGA    L      39      L      39          3.664
LGA    S      40      S      40          2.675
LGA    E      41      E      41          1.275
LGA    F      42      F      42          1.567
LGA    N      43      N      43          2.152
LGA    G      44      G      44          0.349
LGA    K      45      K      45          0.970
LGA    N      46      N      46          2.519
LGA    V      47      V      47          2.272
LGA    S      48      S      48          1.836
LGA    I      49      I      49          1.928
LGA    T      50      T      50          2.011
LGA    V      51      V      51          2.295
LGA    K      52      K      52          2.782
LGA    E      53      E      53          3.044
LGA    E      54      E      54          2.023
LGA    N      55      N      55          7.846
LGA    E      56      E      56         11.363
LGA    L      57      L      57         17.625
LGA    P      58      P      58         21.196
LGA    V      59      V      59         27.428
LGA    K      60      K      60         33.798
LGA    G      61      G      61         35.501
LGA    V      62      V      62         33.384
LGA    E      63      E      63         37.803

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   76   62    4.0     22    2.48    31.452    28.134     0.852

LGA_LOCAL      RMSD =  2.482  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.486  Number of atoms =   62 
Std_ALL_ATOMS  RMSD = 14.082  (standard rmsd on all 62 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.532056 * X  +  -0.210504 * Y  +  -0.820125 * Z  +  -4.448827
  Y_new =  -0.227796 * X  +   0.968477 * Y  +  -0.100799 * Z  + -19.232712
  Z_new =   0.815491 * X  +   0.133191 * Y  +  -0.563236 * Z  +  -3.517640 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.909384   -0.232208  [ DEG:   166.6954    -13.3046 ]
  Theta =  -0.953577   -2.188015  [ DEG:   -54.6359   -125.3641 ]
  Phi   =  -2.737062    0.404530  [ DEG:  -156.8221     23.1779 ]
 
# 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: T0309TS599_5                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309TS599_5.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   76   62   4.0   22   2.48  28.134    14.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS599_5
PFRMAT TS                                                                       
TARGET T0309                                                                    
MODEL  5                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -3.075 -32.523   0.061  1.00  0.00              
ATOM      2  CA  ALA     2      -1.101 -31.602  -2.796  1.00  0.00              
ATOM      3  CA  SER     3      -3.862 -30.552  -0.764  1.00  0.00              
ATOM      4  CA  LYS     4      -0.782 -30.784   2.119  1.00  0.00              
ATOM      5  CA  LYS     5       0.619 -27.791   0.210  1.00  0.00              
ATOM      6  CA  VAL     6      -2.783 -26.059   0.361  1.00  0.00              
ATOM      7  CA  HIS     7      -2.966 -26.288   4.150  1.00  0.00              
ATOM      8  CA  GLN     8       0.585 -24.834   4.494  1.00  0.00              
ATOM      9  CA  ILE     9      -0.652 -21.809   2.626  1.00  0.00              
ATOM     10  CA  ASN    10      -4.030 -20.924   3.985  1.00  0.00              
ATOM     11  CA  VAL    11      -6.431 -19.045   1.831  1.00  0.00              
ATOM     12  CA  LYS    12      -9.799 -18.453   3.086  1.00  0.00              
ATOM     13  CA  GLY    13     -11.060 -15.649   0.788  1.00  0.00              
ATOM     14  CA  PHE    14      -9.666 -17.096  -2.412  1.00  0.00              
ATOM     15  CA  PHE    15     -10.653 -20.778  -1.937  1.00  0.00              
ATOM     16  CA  ASP    16     -11.745 -22.850  -4.928  1.00  0.00              
ATOM     17  CA  MET    17      -9.509 -25.838  -4.252  1.00  0.00              
ATOM     18  CA  ASP    18      -9.719 -28.681  -6.714  1.00  0.00              
ATOM     19  CA  VAL    19      -6.495 -30.531  -5.827  1.00  0.00              
ATOM     20  CA  MET    20      -5.222 -31.064  -9.371  1.00  0.00              
ATOM     21  CA  GLU    21      -5.899 -27.392 -10.262  1.00  0.00              
ATOM     22  CA  VAL    22      -4.152 -25.945  -7.212  1.00  0.00              
ATOM     23  CA  THR    23      -1.000 -28.075  -7.758  1.00  0.00              
ATOM     24  CA  GLU    24      -0.575 -27.226 -11.408  1.00  0.00              
ATOM     25  CA  GLN    25      -1.088 -23.459 -10.837  1.00  0.00              
ATOM     26  CA  THR    26       1.401 -23.351  -7.988  1.00  0.00              
ATOM     27  CA  LYS    27       4.161 -25.208  -9.934  1.00  0.00              
ATOM     28  CA  GLU    28       4.043 -22.596 -12.669  1.00  0.00              
ATOM     29  CA  ALA    29       4.016 -19.576 -10.329  1.00  0.00              
ATOM     30  CA  GLU    30       1.402 -17.370 -11.986  1.00  0.00              
ATOM     31  CA  TYR    31      -0.775 -15.291  -9.824  1.00  0.00              
ATOM     32  CA  THR    32      -1.895 -11.755 -10.598  1.00  0.00              
ATOM     33  CA  TYR    33      -3.010  -9.344  -7.823  1.00  0.00              
ATOM     34  CA  ASP    34      -4.837  -6.109  -8.351  1.00  0.00              
ATOM     35  CA  PHE    35      -4.398  -3.984  -5.205  1.00  0.00              
ATOM     36  CA  LYS    36      -8.089  -3.164  -4.844  1.00  0.00              
ATOM     37  CA  GLU    37      -8.962  -6.831  -5.346  1.00  0.00              
ATOM     38  CA  ILE    38      -6.418  -7.906  -2.736  1.00  0.00              
ATOM     39  CA  LEU    39      -7.671  -5.331  -0.307  1.00  0.00              
ATOM     40  CA  SER    40     -11.248  -6.336  -0.758  1.00  0.00              
ATOM     41  CA  GLU    41     -10.478 -10.002  -0.175  1.00  0.00              
ATOM     42  CA  PHE    42      -8.513  -9.184   2.997  1.00  0.00              
ATOM     43  CA  ASN    43     -11.141  -6.950   4.658  1.00  0.00              
ATOM     44  CA  GLY    44     -10.499  -8.018   8.269  1.00  0.00              
ATOM     45  CA  LYS    45     -10.242 -11.721   7.733  1.00  0.00              
ATOM     46  CA  ASN    46      -6.875 -13.346   8.059  1.00  0.00              
ATOM     47  CA  VAL    47      -5.485 -15.023   4.889  1.00  0.00              
ATOM     48  CA  SER    48      -2.013 -16.516   5.148  1.00  0.00              
ATOM     49  CA  ILE    49       0.144 -16.863   2.110  1.00  0.00              
ATOM     50  CA  THR    50       3.603 -18.564   2.213  1.00  0.00              
ATOM     51  CA  VAL    51       5.805 -17.933  -0.820  1.00  0.00              
ATOM     52  CA  LYS    52       8.171 -20.705  -1.692  1.00  0.00              
ATOM     53  CA  GLU    53      11.247 -19.818  -3.694  1.00  0.00              
ATOM     54  CA  GLU    54      10.619 -22.066  -6.710  1.00  0.00              
ATOM     55  CA  ASN    55       7.078 -20.852  -7.133  1.00  0.00              
ATOM     56  CA  GLU    56       7.723 -17.221  -6.563  1.00  0.00              
ATOM     57  CA  LEU    57       5.236 -15.660  -4.330  1.00  0.00              
ATOM     58  CA  PRO    58       6.150 -13.017  -1.804  1.00  0.00              
ATOM     59  CA  VAL    59       4.201 -13.438   1.460  1.00  0.00              
ATOM     60  CA  LYS    60       2.453 -10.051   1.962  1.00  0.00              
ATOM     61  CA  GLY    61       1.515  -9.464  -1.696  1.00  0.00              
ATOM     62  CA  VAL    62       0.303 -12.863  -2.914  1.00  0.00              
ATOM     63  CA  GLU    63      -2.865 -12.426  -4.990  1.00  0.00              
ATOM     64  CA  MET    64      -4.406 -15.006  -7.222  1.00  0.00              
ATOM     65  CA  ALA    65      -6.656 -13.810  -9.970  1.00  0.00              
ATOM     66  CA  GLY    66      -7.712 -16.909 -11.772  1.00  0.00              
ATOM     67  CA  ASP    67     -11.259 -17.223 -10.341  1.00  0.00              
ATOM     68  CA  PRO    68     -11.225 -20.694  -8.824  1.00  0.00              
ATOM     69  CA  LEU    69     -14.478 -22.187  -9.996  1.00  0.00              
ATOM     70  CA  GLU    70     -16.051 -23.790  -6.968  1.00  0.00              
ATOM     71  CA  HIS    71     -18.851 -26.170  -8.153  1.00  0.00              
ATOM     72  CA  HIS    72     -20.962 -26.362  -5.045  1.00  0.00              
ATOM     73  CA  HIS    73     -22.523 -29.864  -4.805  1.00  0.00              
ATOM     74  CA  HIS    74     -19.275 -31.254  -7.071  1.00  0.00              
ATOM     75  CA  HIS    75     -15.836 -33.608  -6.357  1.00  0.00              
ATOM     76  CA  HIS    76     -11.673 -33.710  -6.331  1.00  0.00              
TER                                                                             
END
