
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0328AL381_5
# Molecule2: number of CA atoms  307 ( 2453),  selected   30 , name T0328.pdb
# PARAMETERS: T0328AL381_5.T0328.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:    17        66 - 82          4.93    13.04
  LONGEST_CONTINUOUS_SEGMENT:    17        67 - 83          4.80    14.42
  LCS_AVERAGE:      5.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        58 - 64          1.90    19.39
  LONGEST_CONTINUOUS_SEGMENT:     7        63 - 69          1.85    14.20
  LONGEST_CONTINUOUS_SEGMENT:     7        75 - 81          1.99    21.65
  LONGEST_CONTINUOUS_SEGMENT:     7        79 - 85          1.99    14.84
  LONGEST_CONTINUOUS_SEGMENT:     7        80 - 86          1.90    12.86
  LCS_AVERAGE:      2.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        63 - 68          0.60    15.09
  LCS_AVERAGE:      1.55

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:  307
LCS_GDT     S      57     S      57      5    6   13     0    3    5    5    6    7    8    8    8    8   10   10   10   11   11   12   13   22   22   23 
LCS_GDT     A      58     A      58      5    7   13     4    4    5    5    6    7    8    8   10   11   12   16   17   18   19   20   22   24   26   26 
LCS_GDT     F      59     F      59      5    7   14     4    4    5    5    6    7    9   10   12   13   15   16   17   18   19   20   22   24   26   26 
LCS_GDT     N      60     N      60      5    7   14     4    4    5    5    6    8    9   10   12   13   15   16   17   18   19   20   22   24   26   26 
LCS_GDT     G      61     G      61      5    7   14     4    4    5    6    6    8    9   10   12   13   15   16   17   18   19   20   22   24   26   26 
LCS_GDT     F      62     F      62      4    7   14     3    3    4    6    6    8    9   10   12   13   15   16   17   18   19   20   22   24   26   26 
LCS_GDT     V      63     V      63      6    7   14     4    6    6    6    6    7    9    9   11   12   12   14   14   16   19   20   22   24   26   26 
LCS_GDT     A      64     A      64      6    7   14     4    6    6    6    6    8    9   10   12   12   15   16   17   18   19   20   22   24   26   26 
LCS_GDT     I      65     I      65      6    7   14     4    6    6    6    6    8    9   10   13   13   15   16   17   18   19   20   22   24   26   26 
LCS_GDT     G      66     G      66      6    7   17     4    6    6    6    6    7   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     A      67     A      67      6    7   17     4    6    6    6    6    7    9   10   12   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     N      68     N      68      6    7   17     4    6    6    6    6    6    8    8    9   12   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     Y      69     Y      69      3    7   17     3    3    4    4    5    6    9   10   11   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     W      70     W      70      3    5   17     3    3    4    4    4    7    9   10   12   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     D      71     D      71      4    5   17     4    4    5    6    8    8   10   10   12   13   15   16   17   19   19   20   22   24   26   26 
LCS_GDT     S      72     S      72      4    5   17     4    4    5    6    8    8   10   10   12   13   13   16   17   18   19   20   21   22   24   25 
LCS_GDT     L      73     L      73      4    5   17     4    4    5    5    6    8   10   10   12   13   13   15   17   19   19   20   21   22   22   23 
LCS_GDT     Y      74     Y      74      4    5   17     4    4    5    5    5    7    9   10   12   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     P      75     P      75      4    7   17     3    4    4    5    6    8   10   10   12   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     E      76     E      76      4    7   17     3    4    5    6    8    9   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     S      77     S      77      5    7   17     0    4    5    6    8    9   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     R      78     R      78      5    7   17     3    4    5    6    8    9   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     P      79     P      79      5    7   17     3    4    5    6    8    8   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     E      80     E      80      5    7   17     3    4    5    6    8    8   10   11   13   13   13   15   18   19   19   20   22   24   26   26 
LCS_GDT     M      81     M      81      5    7   17     3    4    5    6    8    9   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     L      82     L      82      5    7   17     3    4    5    6    6    9   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     K      83     K      83      5    7   17     3    4    5    6    6    9   10   11   13   13   16   16   18   19   19   20   22   24   26   26 
LCS_GDT     P      84     P      84      5    7   14     3    4    5    6    6    9   10   11   13   13   16   16   18   19   19   20   20   23   26   26 
LCS_GDT     F      85     F      85      5    7   14     3    4    5    6    6    9   10   11   13   13   13   15   18   18   19   20   20   21   26   26 
LCS_GDT     P      86     P      86      3    7   14     3    3    4    4    4    9   10   11   13   13   16   16   18   19   19   20   20   21   21   22 
LCS_AVERAGE  LCS_A:   2.95  (   1.55    2.16    5.12 )

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      4      6      6      6      8      9     10     11     13     13     16     16     18     19     19     20     22     24     26     26 
GDT PERCENT_CA   1.30   1.95   1.95   1.95   2.61   2.93   3.26   3.58   4.23   4.23   5.21   5.21   5.86   6.19   6.19   6.51   7.17   7.82   8.47   8.47
GDT RMS_LOCAL    0.11   0.60   0.60   0.60   1.74   2.07   2.28   2.57   2.94   2.94   4.33   4.33   4.60   5.01   4.89   5.17   6.24   6.59   7.08   7.08
GDT RMS_ALL_CA  27.25  15.09  15.09  15.09  21.73  12.15  12.03  12.52  12.21  12.21  12.40  12.40  11.93  12.59  11.82  12.07   8.35   8.31   8.13   8.13

#      Molecule1      Molecule2       DISTANCE
LGA    S      57      S      57         25.021
LGA    A      58      A      58         22.768
LGA    F      59      F      59         24.836
LGA    N      60      N      60         21.382
LGA    G      61      G      61         19.665
LGA    F      62      F      62         16.015
LGA    V      63      V      63         13.731
LGA    A      64      A      64          8.074
LGA    I      65      I      65          4.746
LGA    G      66      G      66          4.540
LGA    A      67      A      67          6.664
LGA    N      68      N      68         10.990
LGA    Y      69      Y      69         13.136
LGA    W      70      W      70         11.301
LGA    D      71      D      71         13.841
LGA    S      72      S      72         19.176
LGA    L      73      L      73         16.739
LGA    Y      74      Y      74          9.800
LGA    P      75      P      75          8.521
LGA    E      76      E      76          2.697
LGA    S      77      S      77          1.420
LGA    R      78      R      78          3.010
LGA    P      79      P      79          3.960
LGA    E      80      E      80          3.713
LGA    M      81      M      81          0.434
LGA    L      82      L      82          2.843
LGA    K      83      K      83          1.278
LGA    P      84      P      84          1.519
LGA    F      85      F      85          1.988
LGA    P      86      P      86          2.910

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30  307    4.0     11    2.57     3.502     3.275     0.413

LGA_LOCAL      RMSD =  2.566  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.523  Number of atoms =   30 
Std_ALL_ATOMS  RMSD =  7.964  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.097772 * X  +  -0.483316 * Y  +  -0.869969 * Z  +  73.550369
  Y_new =  -0.703355 * X  +  -0.584884 * Y  +   0.403983 * Z  +   0.558565
  Z_new =  -0.704082 * X  +   0.651396 * Y  +  -0.282757 * Z  + -35.158100 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.980332   -1.161261  [ DEG:   113.4647    -66.5353 ]
  Theta =   0.781130    2.360463  [ DEG:    44.7554    135.2446 ]
  Phi   =  -1.708920    1.432673  [ DEG:   -97.9139     82.0861 ]
 
# 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: T0328AL381_5                                  
REMARK     2: T0328.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0328AL381_5.T0328.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30  307   4.0   11   2.57   3.275     7.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0328AL381_5
REMARK Aligment from pdb entry: 1p3hA
ATOM      1  N   SER    57      18.586  25.801  31.076  1.00  0.00              
ATOM      2  CA  SER    57      19.916  26.350  30.833  1.00  0.00              
ATOM      3  C   SER    57      20.056  27.692  31.556  1.00  0.00              
ATOM      4  O   SER    57      19.053  28.284  31.944  1.00  0.00              
ATOM      5  N   ALA    58      21.296  28.159  31.749  1.00  0.00              
ATOM      6  CA  ALA    58      21.534  29.433  32.418  1.00  0.00              
ATOM      7  C   ALA    58      22.580  30.285  31.736  1.00  0.00              
ATOM      8  O   ALA    58      23.218  29.881  30.771  1.00  0.00              
ATOM      9  N   PHE    59      22.740  31.488  32.265  1.00  0.00              
ATOM     10  CA  PHE    59      23.729  32.413  31.753  1.00  0.00              
ATOM     11  C   PHE    59      24.654  32.761  32.927  1.00  0.00              
ATOM     12  O   PHE    59      24.205  32.979  34.053  1.00  0.00              
ATOM     13  N   ASN    60      25.953  32.792  32.669  1.00  0.00              
ATOM     14  CA  ASN    60      26.887  33.122  33.729  1.00  0.00              
ATOM     15  C   ASN    60      28.214  33.601  33.191  1.00  0.00              
ATOM     16  O   ASN    60      28.360  33.821  31.998  1.00  0.00              
ATOM     17  N   GLY    61      29.186  33.751  34.066  1.00  0.00              
ATOM     18  CA  GLY    61      30.505  34.203  33.653  1.00  0.00              
ATOM     19  C   GLY    61      31.573  33.171  33.983  1.00  0.00              
ATOM     20  O   GLY    61      31.631  32.660  35.084  1.00  0.00              
ATOM     21  N   PHE    62      32.414  32.867  33.008  1.00  0.00              
ATOM     22  CA  PHE    62      33.488  31.922  33.216  1.00  0.00              
ATOM     23  C   PHE    62      34.491  32.551  34.169  1.00  0.00              
ATOM     24  O   PHE    62      35.018  33.622  33.919  1.00  0.00              
ATOM     25  N   VAL    63      34.755  31.870  35.266  1.00  0.00              
ATOM     26  CA  VAL    63      35.686  32.363  36.264  1.00  0.00              
ATOM     27  C   VAL    63      37.043  31.663  36.196  1.00  0.00              
ATOM     28  O   VAL    63      38.081  32.274  36.471  1.00  0.00              
ATOM     29  N   ALA    64      37.038  30.387  35.844  1.00  0.00              
ATOM     30  CA  ALA    64      38.258  29.608  35.754  1.00  0.00              
ATOM     31  C   ALA    64      38.053  28.474  34.763  1.00  0.00              
ATOM     32  O   ALA    64      36.976  27.916  34.678  1.00  0.00              
ATOM     33  N   ILE    65      39.089  28.138  34.010  1.00  0.00              
ATOM     34  CA  ILE    65      38.973  27.065  33.043  1.00  0.00              
ATOM     35  C   ILE    65      40.030  25.997  33.265  1.00  0.00              
ATOM     36  O   ILE    65      41.144  26.279  33.690  1.00  0.00              
ATOM     37  N   GLY    66      39.673  24.762  32.974  1.00  0.00              
ATOM     38  CA  GLY    66      40.619  23.691  33.144  1.00  0.00              
ATOM     39  C   GLY    66      41.621  23.688  32.015  1.00  0.00              
ATOM     40  O   GLY    66      41.478  24.414  31.036  1.00  0.00              
ATOM     41  N   ALA    67      42.670  22.879  32.136  1.00  0.00              
ATOM     42  CA  ALA    67      43.676  22.826  31.075  1.00  0.00              
ATOM     43  C   ALA    67      43.093  22.260  29.786  1.00  0.00              
ATOM     44  O   ALA    67      43.495  22.640  28.695  1.00  0.00              
ATOM     45  N   ASN    68      42.142  21.348  29.927  1.00  0.00              
ATOM     46  CA  ASN    68      41.518  20.720  28.777  1.00  0.00              
ATOM     47  C   ASN    68      41.730  19.221  28.869  1.00  0.00              
ATOM     48  O   ASN    68      42.516  18.760  29.685  1.00  0.00              
ATOM     49  N   TYR    69      41.035  18.454  28.045  1.00  0.00              
ATOM     50  CA  TYR    69      41.200  17.005  28.064  1.00  0.00              
ATOM     51  C   TYR    69      42.345  16.521  27.150  1.00  0.00              
ATOM     52  O   TYR    69      42.580  17.072  26.061  1.00  0.00              
ATOM     53  N   TRP    70      43.050  15.483  27.591  1.00  0.00              
ATOM     54  CA  TRP    70      44.158  14.942  26.826  1.00  0.00              
ATOM     55  C   TRP    70      43.612  14.240  25.618  1.00  0.00              
ATOM     56  O   TRP    70      42.568  13.604  25.708  1.00  0.00              
ATOM     57  N   ASP    71      44.320  14.347  24.499  1.00  0.00              
ATOM     58  CA  ASP    71      43.905  13.676  23.263  1.00  0.00              
ATOM     59  C   ASP    71      44.066  12.145  23.397  1.00  0.00              
ATOM     60  O   ASP    71      44.472  11.636  24.442  1.00  0.00              
ATOM     61  N   SER    72      43.719  11.415  22.343  1.00  0.00              
ATOM     62  CA  SER    72      43.814   9.951  22.331  1.00  0.00              
ATOM     63  C   SER    72      45.121   9.442  22.924  1.00  0.00              
ATOM     64  O   SER    72      45.130   8.767  23.964  1.00  0.00              
ATOM     65  N   LEU    73      46.209   9.748  22.216  1.00  0.00              
ATOM     66  CA  LEU    73      47.560   9.357  22.596  1.00  0.00              
ATOM     67  C   LEU    73      47.934   9.943  23.981  1.00  0.00              
ATOM     68  O   LEU    73      48.347   9.224  24.888  1.00  0.00              
ATOM     69  N   TYR    74      47.779  11.254  24.140  1.00  0.00              
ATOM     70  CA  TYR    74      48.106  11.894  25.409  1.00  0.00              
ATOM     71  C   TYR    74      49.254  12.903  25.334  1.00  0.00              
ATOM     72  O   TYR    74      49.888  13.210  26.349  1.00  0.00              
ATOM     73  N   PRO    75      49.523  13.422  24.136  1.00  0.00              
ATOM     74  CA  PRO    75      50.602  14.387  23.958  1.00  0.00              
ATOM     75  C   PRO    75      50.146  15.818  23.773  1.00  0.00              
ATOM     76  O   PRO    75      50.975  16.721  23.700  1.00  0.00              
ATOM     77  N   GLU    76      48.836  16.015  23.680  1.00  0.00              
ATOM     78  CA  GLU    76      48.265  17.347  23.530  1.00  0.00              
ATOM     79  C   GLU    76      46.935  17.546  24.247  1.00  0.00              
ATOM     80  O   GLU    76      46.067  16.671  24.205  1.00  0.00              
ATOM     81  N   SER    77      46.775  18.711  24.878  1.00  0.00              
ATOM     82  CA  SER    77      45.516  19.055  25.547  1.00  0.00              
ATOM     83  C   SER    77      44.709  19.846  24.517  1.00  0.00              
ATOM     84  O   SER    77      45.168  20.878  24.003  1.00  0.00              
ATOM     85  N   ARG    78      43.515  19.372  24.208  1.00  0.00              
ATOM     86  CA  ARG    78      42.686  20.098  23.276  1.00  0.00              
ATOM     87  C   ARG    78      42.160  21.310  24.031  1.00  0.00              
ATOM     88  O   ARG    78      41.295  21.173  24.895  1.00  0.00              
ATOM     89  N   PRO    79      42.642  22.525  23.694  1.00  0.00              
ATOM     90  CA  PRO    79      42.226  23.784  24.348  1.00  0.00              
ATOM     91  C   PRO    79      40.703  23.954  24.325  1.00  0.00              
ATOM     92  O   PRO    79      40.061  23.547  23.364  1.00  0.00              
ATOM     93  N   GLU    80      40.155  24.639  25.328  1.00  0.00              
ATOM     94  CA  GLU    80      38.708  24.791  25.426  1.00  0.00              
ATOM     95  C   GLU    80      38.308  25.984  24.590  1.00  0.00              
ATOM     96  O   GLU    80      39.168  26.752  24.157  1.00  0.00              
ATOM     97  N   MET    81      37.016  26.154  24.357  1.00  0.00              
ATOM     98  CA  MET    81      36.587  27.282  23.545  1.00  0.00              
ATOM     99  C   MET    81      36.015  28.413  24.361  1.00  0.00              
ATOM    100  O   MET    81      35.301  29.259  23.837  1.00  0.00              
ATOM    101  N   LEU    82      36.320  28.419  25.649  1.00  0.00              
ATOM    102  CA  LEU    82      35.847  29.480  26.525  1.00  0.00              
ATOM    103  C   LEU    82      37.032  29.990  27.306  1.00  0.00              
ATOM    104  O   LEU    82      38.032  29.289  27.461  1.00  0.00              
ATOM    105  N   LYS    83      36.927  31.220  27.783  1.00  0.00              
ATOM    106  CA  LYS    83      38.006  31.831  28.537  1.00  0.00              
ATOM    107  C   LYS    83      37.416  32.625  29.668  1.00  0.00              
ATOM    108  O   LYS    83      36.223  32.880  29.698  1.00  0.00              
ATOM    109  N   PRO    84      38.261  33.026  30.601  1.00  0.00              
ATOM    110  CA  PRO    84      37.782  33.788  31.734  1.00  0.00              
ATOM    111  C   PRO    84      37.145  35.048  31.224  1.00  0.00              
ATOM    112  O   PRO    84      37.631  35.643  30.275  1.00  0.00              
ATOM    113  N   PHE    85      36.041  35.436  31.847  1.00  0.00              
ATOM    114  CA  PHE    85      35.354  36.650  31.436  1.00  0.00              
ATOM    115  C   PHE    85      34.248  36.404  30.430  1.00  0.00              
ATOM    116  O   PHE    85      33.321  37.212  30.317  1.00  0.00              
ATOM    117  N   PRO    86      34.348  35.305  29.686  1.00  0.00              
ATOM    118  CA  PRO    86      33.330  34.986  28.705  1.00  0.00              
ATOM    119  C   PRO    86      32.006  34.777  29.383  1.00  0.00              
ATOM    120  O   PRO    86      31.927  34.182  30.450  1.00  0.00              
END
