
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0358AL333_2-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   27 , name T0358_D1.pdb
# PARAMETERS: T0358AL333_2-D1.T0358_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:    26        10 - 38          4.82     5.02
  LCS_AVERAGE:     38.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        12 - 25          1.86     7.36
  LCS_AVERAGE:     12.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        16 - 25          0.62     9.68
  LCS_AVERAGE:      9.63

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:   65
LCS_GDT     G      10     G      10      3    9   26     3    3    6    7   10   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     P      11     P      11      3    9   26     3    3    6    7   10   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     F      12     F      12      3   11   26     3    3    6    7   11   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     Q      16     Q      16     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     A      17     A      17     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     Q      18     Q      18     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     A      19     A      19     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     V      20     V      20     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     T      21     T      21     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     T      22     T      22     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     T      23     T      23     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     Y      24     Y      24     10   11   26     9    9   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     S      25     S      25     10   11   26     4    8   10   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     N      26     N      26      4    5   26     4    4    4    4    6    6    9   11   15   16   17   19   23   24   25   26   26   27   27   27 
LCS_GDT     I      27     I      27      4    5   26     4    4    4    4    4    5    8    8   10   11   17   20   23   24   25   26   26   27   27   27 
LCS_GDT     T      28     T      28      3    3   26     3    3    3    3    5    9   12   15   17   18   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     L      29     L      29      4    4   26     3    3    6   11   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     E      30     E      30      4    4   26     3    3    6    7   11   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     D      31     D      31      4    4   26     3    3    6    9   12   13   16   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     D      32     D      32      4    4   26     3    3    5    6    6    6   12   13   15   16   17   18   19   22   24   25   26   27   27   27 
LCS_GDT     Q      33     Q      33      5    7   26     4    5    6    6    7    7    7    8    9   10   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     G      34     G      34      5    7   26     4    5    6    6    7   10   12   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     S      35     S      35      5    7   26     4    5    6    6    7    7   14   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     H      36     H      36      5    7   26     4    5    6    6    7    7    8    9   14   18   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     F      37     F      37      5    7   26     3    5    5    6    7    7   10   16   17   19   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     R      38     R      38      4    7   26     3    4    6    6    7    7    7    8    9   18   20   21   23   24   25   26   26   27   27   27 
LCS_GDT     L      39     L      39      4    7    8     3    4    6    6    7    7    7    8    9    9   11   16   21   22   24   26   26   27   27   27 
LCS_AVERAGE  LCS_A:  20.32  (   9.63   12.36   38.97 )

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      9     10     11     12     13     16     16     17     19     20     21     23     24     25     26     26     27     27     27 
GDT PERCENT_CA  13.85  13.85  15.38  16.92  18.46  20.00  24.62  24.62  26.15  29.23  30.77  32.31  35.38  36.92  38.46  40.00  40.00  41.54  41.54  41.54
GDT RMS_LOCAL    0.26   0.26   0.62   1.35   1.56   2.14   2.39   2.39   2.71   3.21   3.33   3.65   4.04   4.34   4.54   4.75   4.75   5.01   5.01   5.01
GDT RMS_ALL_CA   9.23   9.23   9.68   7.78   7.12   5.61   5.74   5.74   5.73   5.26   5.35   5.30   5.22   5.07   5.05   5.04   5.04   5.01   5.01   5.01

#      Molecule1      Molecule2       DISTANCE
LGA    G      10      G      10          3.537
LGA    P      11      P      11          3.137
LGA    F      12      F      12          2.522
LGA    Q      16      Q      16          2.589
LGA    A      17      A      17          2.374
LGA    Q      18      Q      18          0.502
LGA    A      19      A      19          2.218
LGA    V      20      V      20          3.170
LGA    T      21      T      21          1.604
LGA    T      22      T      22          1.957
LGA    T      23      T      23          3.371
LGA    Y      24      Y      24          2.183
LGA    S      25      S      25          1.894
LGA    N      26      N      26          7.209
LGA    I      27      I      27          8.017
LGA    T      28      T      28          5.244
LGA    L      29      L      29          2.039
LGA    E      30      E      30          1.959
LGA    D      31      D      31          2.743
LGA    D      32      D      32          9.034
LGA    Q      33      Q      33         12.035
LGA    G      34      G      34          7.593
LGA    S      35      S      35          5.423
LGA    H      36      H      36          9.171
LGA    F      37      F      37          7.869
LGA    R      38      R      38          9.500
LGA    L      39      L      39         10.301

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   65    4.0     16    2.39    23.846    21.229     0.641

LGA_LOCAL      RMSD =  2.394  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.766  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  5.006  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.082615 * X  +   0.457462 * Y  +   0.885383 * Z  + -178.030991
  Y_new =   0.836219 * X  +  -0.515118 * Y  +   0.188125 * Z  +  -3.099637
  Z_new =   0.542137 * X  +   0.724832 * Y  +  -0.425095 * Z  +  -9.186513 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.101210   -1.040382  [ DEG:   120.3905    -59.6095 ]
  Theta =  -0.572978   -2.568614  [ DEG:   -32.8292   -147.1708 ]
  Phi   =   1.472320   -1.669272  [ DEG:    84.3577    -95.6423 ]
 
# 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: T0358AL333_2-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0358AL333_2-D1.T0358_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   65   4.0   16   2.39  21.229     5.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL333_2-D1
REMARK Aligment from pdb entry: 2fok_A
ATOM     37  N   GLY    10       9.533  -0.201   4.182  1.00  0.00              
ATOM     38  CA  GLY    10      10.238   1.071   4.114  1.00  0.00              
ATOM     39  C   GLY    10       9.669   1.923   2.984  1.00  0.00              
ATOM     40  O   GLY    10       8.453   2.115   2.914  1.00  0.00              
ATOM     41  N   PRO    11      10.535   2.444   2.112  1.00  0.00              
ATOM     42  CA  PRO    11      10.093   3.248   0.969  1.00  0.00              
ATOM     43  C   PRO    11       9.615   2.245  -0.088  1.00  0.00              
ATOM     44  O   PRO    11      10.312   1.270  -0.391  1.00  0.00              
ATOM     45  N   PHE    12       8.434   2.483  -0.651  1.00  0.00              
ATOM     46  CA  PHE    12       7.858   1.556  -1.624  1.00  0.00              
ATOM     47  C   PHE    12       7.285   2.234  -2.871  1.00  0.00              
ATOM     48  O   PHE    12       6.911   3.407  -2.843  1.00  0.00              
ATOM     49  N   GLN    16       7.214   1.478  -3.966  1.00  0.00              
ATOM     50  CA  GLN    16       6.639   1.974  -5.212  1.00  0.00              
ATOM     51  C   GLN    16       5.230   1.374  -5.311  1.00  0.00              
ATOM     52  O   GLN    16       5.027   0.202  -4.988  1.00  0.00              
ATOM     53  N   ALA    17       4.259   2.174  -5.749  1.00  0.00              
ATOM     54  CA  ALA    17       2.880   1.704  -5.854  1.00  0.00              
ATOM     55  C   ALA    17       2.786   0.320  -6.469  1.00  0.00              
ATOM     56  O   ALA    17       1.893  -0.452  -6.130  1.00  0.00              
ATOM     57  N   GLN    18       3.713   0.005  -7.369  1.00  0.00              
ATOM     58  CA  GLN    18       3.727  -1.298  -8.029  1.00  0.00              
ATOM     59  C   GLN    18       4.127  -2.414  -7.062  1.00  0.00              
ATOM     60  O   GLN    18       3.691  -3.563  -7.199  1.00  0.00              
ATOM     61  N   ALA    19       4.961  -2.079  -6.082  1.00  0.00              
ATOM     62  CA  ALA    19       5.375  -3.065  -5.090  1.00  0.00              
ATOM     63  C   ALA    19       4.231  -3.235  -4.074  1.00  0.00              
ATOM     64  O   ALA    19       3.959  -4.336  -3.599  1.00  0.00              
ATOM     65  N   VAL    20       3.554  -2.135  -3.754  1.00  0.00              
ATOM     66  CA  VAL    20       2.430  -2.186  -2.826  1.00  0.00              
ATOM     67  C   VAL    20       1.336  -3.014  -3.477  1.00  0.00              
ATOM     68  O   VAL    20       0.705  -3.845  -2.827  1.00  0.00              
ATOM     69  N   THR    21       1.116  -2.775  -4.766  1.00  0.00              
ATOM     70  CA  THR    21       0.095  -3.497  -5.517  1.00  0.00              
ATOM     71  C   THR    21       0.507  -4.952  -5.563  1.00  0.00              
ATOM     72  O   THR    21      -0.326  -5.857  -5.474  1.00  0.00              
ATOM     73  N   THR    22       1.812  -5.160  -5.708  1.00  0.00              
ATOM     74  CA  THR    22       2.393  -6.496  -5.748  1.00  0.00              
ATOM     75  C   THR    22       2.160  -7.218  -4.417  1.00  0.00              
ATOM     76  O   THR    22       1.657  -8.344  -4.392  1.00  0.00              
ATOM     77  N   THR    23       2.535  -6.563  -3.316  1.00  0.00              
ATOM     78  CA  THR    23       2.372  -7.132  -1.979  1.00  0.00              
ATOM     79  C   THR    23       0.897  -7.388  -1.692  1.00  0.00              
ATOM     80  O   THR    23       0.539  -8.358  -1.022  1.00  0.00              
ATOM     81  N   TYR    24       0.045  -6.506  -2.207  1.00  0.00              
ATOM     82  CA  TYR    24      -1.395  -6.629  -2.042  1.00  0.00              
ATOM     83  C   TYR    24      -1.908  -7.871  -2.774  1.00  0.00              
ATOM     84  O   TYR    24      -2.708  -8.646  -2.240  1.00  0.00              
ATOM     85  N   SER    25      -1.457  -8.048  -4.010  1.00  0.00              
ATOM     86  CA  SER    25      -1.889  -9.192  -4.810  1.00  0.00              
ATOM     87  C   SER    25      -1.582 -10.526  -4.111  1.00  0.00              
ATOM     88  O   SER    25      -2.389 -11.451  -4.140  1.00  0.00              
ATOM     89  N   ASN    26      -0.418 -10.618  -3.480  1.00  0.00              
ATOM     90  CA  ASN    26      -0.046 -11.840  -2.787  1.00  0.00              
ATOM     91  C   ASN    26      -1.126 -12.231  -1.781  1.00  0.00              
ATOM     92  O   ASN    26      -1.369 -13.416  -1.558  1.00  0.00              
ATOM     93  N   ILE    27      -1.771 -11.232  -1.181  1.00  0.00              
ATOM     94  CA  ILE    27      -2.812 -11.477  -0.192  1.00  0.00              
ATOM     95  C   ILE    27      -4.165 -11.817  -0.800  1.00  0.00              
ATOM     96  O   ILE    27      -5.139 -12.013  -0.083  1.00  0.00              
ATOM     97  N   THR    28      -6.602   2.623  -7.724  1.00  0.00              
ATOM     98  CA  THR    28      -7.549   2.350  -6.652  1.00  0.00              
ATOM     99  C   THR    28      -6.707   2.414  -5.382  1.00  0.00              
ATOM    100  O   THR    28      -7.129   2.969  -4.369  1.00  0.00              
ATOM    101  N   LEU    29      -5.505   1.846  -5.462  1.00  0.00              
ATOM    102  CA  LEU    29      -4.563   1.832  -4.349  1.00  0.00              
ATOM    103  C   LEU    29      -4.116   3.257  -4.020  1.00  0.00              
ATOM    104  O   LEU    29      -3.931   3.600  -2.850  1.00  0.00              
ATOM    105  N   GLU    30      -3.957   4.085  -5.049  1.00  0.00              
ATOM    106  CA  GLU    30      -3.552   5.482  -4.864  1.00  0.00              
ATOM    107  C   GLU    30      -4.659   6.277  -4.163  1.00  0.00              
ATOM    108  O   GLU    30      -4.381   7.128  -3.323  1.00  0.00              
ATOM    109  N   ASP    31      -5.916   6.006  -4.512  1.00  0.00              
ATOM    110  CA  ASP    31      -7.034   6.718  -3.891  1.00  0.00              
ATOM    111  C   ASP    31      -7.223   6.260  -2.452  1.00  0.00              
ATOM    112  O   ASP    31      -7.628   7.037  -1.585  1.00  0.00              
ATOM    113  N   ASP    32      -6.924   4.993  -2.205  1.00  0.00              
ATOM    114  CA  ASP    32      -7.030   4.428  -0.866  1.00  0.00              
ATOM    115  C   ASP    32      -5.973   5.072   0.040  1.00  0.00              
ATOM    116  O   ASP    32      -6.175   5.213   1.233  1.00  0.00              
ATOM    117  N   GLN    33       7.521  10.883  -2.174  1.00  0.00              
ATOM    118  CA  GLN    33       8.624  11.578  -2.824  1.00  0.00              
ATOM    119  C   GLN    33       8.770  11.017  -4.227  1.00  0.00              
ATOM    120  O   GLN    33       9.336   9.938  -4.427  1.00  0.00              
ATOM    121  N   GLY    34       8.245  11.749  -5.202  1.00  0.00              
ATOM    122  CA  GLY    34       8.317  11.284  -6.568  1.00  0.00              
ATOM    123  C   GLY    34       7.494  10.020  -6.704  1.00  0.00              
ATOM    124  O   GLY    34       6.281  10.039  -6.497  1.00  0.00              
ATOM    125  N   SER    35       8.153   8.917  -7.032  1.00  0.00              
ATOM    126  CA  SER    35       7.471   7.639  -7.207  1.00  0.00              
ATOM    127  C   SER    35       7.482   6.755  -5.962  1.00  0.00              
ATOM    128  O   SER    35       7.036   5.615  -6.022  1.00  0.00              
ATOM    129  N   HIS    36       7.967   7.275  -4.836  1.00  0.00              
ATOM    130  CA  HIS    36       8.052   6.464  -3.625  1.00  0.00              
ATOM    131  C   HIS    36       7.233   6.926  -2.433  1.00  0.00              
ATOM    132  O   HIS    36       7.180   8.114  -2.109  1.00  0.00              
ATOM    133  N   PHE    37       6.596   5.966  -1.776  1.00  0.00              
ATOM    134  CA  PHE    37       5.788   6.241  -0.602  1.00  0.00              
ATOM    135  C   PHE    37       6.509   5.672   0.618  1.00  0.00              
ATOM    136  O   PHE    37       7.181   4.641   0.536  1.00  0.00              
ATOM    137  N   ARG    38       6.364   6.342   1.752  1.00  0.00              
ATOM    138  CA  ARG    38       6.968   5.863   2.981  1.00  0.00              
ATOM    139  C   ARG    38       6.218   6.376   4.192  1.00  0.00              
ATOM    140  O   ARG    38       6.167   7.581   4.423  1.00  0.00              
ATOM    141  N   LEU    39       5.629   5.463   4.961  1.00  0.00              
ATOM    142  CA  LEU    39       4.898   5.858   6.164  1.00  0.00              
ATOM    143  C   LEU    39       5.877   6.336   7.241  1.00  0.00              
ATOM    144  O   LEU    39       6.874   5.676   7.520  1.00  0.00              
END
