
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0347AL380_1
# Molecule2: number of CA atoms  196 ( 1574),  selected   33 , name T0347.pdb
# PARAMETERS: T0347AL380_1.T0347.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:    33        57 - 89          1.39     1.39
  LCS_AVERAGE:     16.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33        57 - 89          1.39     1.39
  LCS_AVERAGE:     16.84

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29        61 - 89          0.97     1.43
  LCS_AVERAGE:     13.51

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:  196
LCS_GDT     A      57     A      57      3   33   33     3    3    3   19   21   29   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G      58     G      58      3   33   33     3    3    4    7   22   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     P      59     P      59      3   33   33     3    3    4   11   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     K      60     K      60     24   33   33     3    9   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     D      61     D      61     29   33   33     4    9   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     R      62     R      62     29   33   33     3    9   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     A      63     A      63     29   33   33     4   19   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     Y      64     Y      64     29   33   33     4   20   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L      65     L      65     29   33   33     4   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     I      66     I      66     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     D      67     D      67     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     H      68     H      68     29   33   33    12   20   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     H      69     H      69     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     H      70     H      70     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L      71     L      71     29   33   33    11   20   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V      72     V      72     29   33   33    12   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L      73     L      73     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     A      74     A      74     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L      75     L      75     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S      76     S      76     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     K      77     K      77     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     E      78     E      78     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     G      79     G      79     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V      80     V      80     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     E      81     E      81     29   33   33    12   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     H      82     H      82     29   33   33     5   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V      83     V      83     29   33   33     5   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     L      84     L      84     29   33   33     5   13   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     T      85     T      85     29   33   33     5   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     S      86     S      86     29   33   33     3   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     E      87     E      87     29   33   33     4   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     V      88     V      88     29   33   33    10   20   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_GDT     A      89     A      89     29   33   33    13   21   29   30   31   32   33   33   33   33   33   33   33   33   33   33   33   33   33   33 
LCS_AVERAGE  LCS_A:  15.73  (  13.51   16.84   16.84 )

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     13     21     29     30     31     32     33     33     33     33     33     33     33     33     33     33     33     33     33     33 
GDT PERCENT_CA   6.63  10.71  14.80  15.31  15.82  16.33  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84  16.84
GDT RMS_LOCAL    0.34   0.66   0.97   1.01   1.09   1.20   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39
GDT RMS_ALL_CA   1.54   1.58   1.43   1.43   1.42   1.41   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39

#      Molecule1      Molecule2       DISTANCE
LGA    A      57      A      57          3.989
LGA    G      58      G      58          2.917
LGA    P      59      P      59          2.366
LGA    K      60      K      60          1.880
LGA    D      61      D      61          1.839
LGA    R      62      R      62          1.693
LGA    A      63      A      63          1.283
LGA    Y      64      Y      64          1.176
LGA    L      65      L      65          0.917
LGA    I      66      I      66          0.880
LGA    D      67      D      67          1.127
LGA    H      68      H      68          1.241
LGA    H      69      H      69          0.428
LGA    H      70      H      70          0.911
LGA    L      71      L      71          1.234
LGA    V      72      V      72          0.896
LGA    L      73      L      73          0.420
LGA    A      74      A      74          0.564
LGA    L      75      L      75          0.728
LGA    S      76      S      76          0.635
LGA    K      77      K      77          0.287
LGA    E      78      E      78          0.480
LGA    G      79      G      79          0.737
LGA    V      80      V      80          0.735
LGA    E      81      E      81          0.506
LGA    H      82      H      82          0.621
LGA    V      83      V      83          0.894
LGA    L      84      L      84          1.570
LGA    T      85      T      85          1.465
LGA    S      86      S      86          1.548
LGA    E      87      E      87          1.188
LGA    V      88      V      88          0.585
LGA    A      89      A      89          0.851

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  196    4.0     33    1.39    14.923    15.995     2.207

LGA_LOCAL      RMSD =  1.395  Number of atoms =   33  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.396  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  1.395  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.192708 * X  +  -0.639324 * Y  +  -0.744398 * Z  +  43.180244
  Y_new =   0.636217 * X  +   0.496147 * Y  +  -0.590817 * Z  +  38.129848
  Z_new =   0.747055 * X  +  -0.587454 * Y  +   0.311138 * Z  +  10.454740 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.083721    2.057872  [ DEG:   -62.0926    117.9074 ]
  Theta =  -0.843621   -2.297972  [ DEG:   -48.3359   -131.6641 ]
  Phi   =   1.864908   -1.276685  [ DEG:   106.8514    -73.1486 ]
 
# 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: T0347AL380_1                                  
REMARK     2: T0347.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347AL380_1.T0347.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  196   4.0   33   1.39  15.995     1.39
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL380_1
REMARK Aligment from pdb entry: 1vk1A
ATOM      1  N   ALA    57       1.687  29.927  -0.746  1.00  0.00              
ATOM      2  CA  ALA    57       0.910  30.237   0.451  1.00  0.00              
ATOM      3  C   ALA    57       0.073  28.987   0.790  1.00  0.00              
ATOM      4  O   ALA    57      -0.718  28.532  -0.025  1.00  0.00              
ATOM      5  N   GLY    58       0.257  28.414   1.990  1.00  0.00              
ATOM      6  CA  GLY    58      -0.464  27.175   2.346  1.00  0.00              
ATOM      7  C   GLY    58      -1.980  27.270   2.179  1.00  0.00              
ATOM      8  O   GLY    58      -2.581  28.307   2.475  1.00  0.00              
ATOM      9  N   PRO    59      -2.576  26.192   1.686  1.00  0.00              
ATOM     10  CA  PRO    59      -4.012  26.132   1.471  1.00  0.00              
ATOM     11  C   PRO    59      -4.512  26.855   0.224  1.00  0.00              
ATOM     12  O   PRO    59      -5.723  26.933   0.001  1.00  0.00              
ATOM     13  N   LYS    60      -3.587  27.387  -0.592  1.00  0.00              
ATOM     14  CA  LYS    60      -3.941  28.076  -1.821  1.00  0.00              
ATOM     15  C   LYS    60      -3.080  27.590  -2.944  1.00  0.00              
ATOM     16  O   LYS    60      -2.084  26.903  -2.729  1.00  0.00              
ATOM     17  N   ASP    61      -3.428  28.010  -4.156  1.00  0.00              
ATOM     18  CA  ASP    61      -2.524  27.879  -5.288  1.00  0.00              
ATOM     19  C   ASP    61      -1.919  29.253  -5.673  1.00  0.00              
ATOM     20  O   ASP    61      -1.605  29.509  -6.825  1.00  0.00              
ATOM     21  N   ARG    62      -1.729  30.102  -4.678  1.00  0.00              
ATOM     22  CA  ARG    62      -1.141  31.421  -4.847  1.00  0.00              
ATOM     23  C   ARG    62       0.247  31.424  -4.206  1.00  0.00              
ATOM     24  O   ARG    62       0.570  30.549  -3.392  1.00  0.00              
ATOM     25  N   ALA    63       1.041  32.430  -4.557  1.00  0.00              
ATOM     26  CA  ALA    63       2.410  32.548  -4.105  1.00  0.00              
ATOM     27  C   ALA    63       2.670  33.870  -3.418  1.00  0.00              
ATOM     28  O   ALA    63       2.252  34.933  -3.894  1.00  0.00              
ATOM     29  N   TYR    64       3.385  33.794  -2.305  1.00  0.00              
ATOM     30  CA  TYR    64       4.050  34.929  -1.712  1.00  0.00              
ATOM     31  C   TYR    64       5.196  35.354  -2.595  1.00  0.00              
ATOM     32  O   TYR    64       6.039  34.543  -2.938  1.00  0.00              
ATOM     33  N   LEU    65       5.251  36.643  -2.938  1.00  0.00              
ATOM     34  CA  LEU    65       6.438  37.207  -3.541  1.00  0.00              
ATOM     35  C   LEU    65       7.470  37.333  -2.425  1.00  0.00              
ATOM     36  O   LEU    65       7.288  38.085  -1.497  1.00  0.00              
ATOM     37  N   ILE    66       8.559  36.592  -2.549  1.00  0.00              
ATOM     38  CA  ILE    66       9.681  36.679  -1.607  1.00  0.00              
ATOM     39  C   ILE    66      10.578  37.823  -2.078  1.00  0.00              
ATOM     40  O   ILE    66      10.912  38.700  -1.321  1.00  0.00              
ATOM     41  N   ASP    67      10.954  37.788  -3.351  1.00  0.00              
ATOM     42  CA  ASP    67      11.762  38.814  -3.964  1.00  0.00              
ATOM     43  C   ASP    67      11.261  39.079  -5.365  1.00  0.00              
ATOM     44  O   ASP    67      11.023  38.149  -6.123  1.00  0.00              
ATOM     45  N   HIS    68      11.127  40.355  -5.699  1.00  0.00              
ATOM     46  CA  HIS    68      10.735  40.773  -7.042  1.00  0.00              
ATOM     47  C   HIS    68       9.466  41.596  -7.143  1.00  0.00              
ATOM     48  O   HIS    68       8.824  41.602  -8.186  1.00  0.00              
ATOM     49  N   HIS    69       9.113  42.354  -6.112  1.00  0.00              
ATOM     50  CA  HIS    69       7.922  43.192  -6.164  1.00  0.00              
ATOM     51  C   HIS    69       7.933  44.175  -7.320  1.00  0.00              
ATOM     52  O   HIS    69       6.925  44.349  -7.996  1.00  0.00              
ATOM     53  N   HIS    70       9.060  44.837  -7.551  1.00  0.00              
ATOM     54  CA  HIS    70       9.131  45.834  -8.606  1.00  0.00              
ATOM     55  C   HIS    70       9.095  45.199  -9.978  1.00  0.00              
ATOM     56  O   HIS    70       8.490  45.766 -10.907  1.00  0.00              
ATOM     57  N   LEU    71       9.710  44.026 -10.117  1.00  0.00              
ATOM     58  CA  LEU    71       9.638  43.248 -11.358  1.00  0.00              
ATOM     59  C   LEU    71       8.224  42.783 -11.669  1.00  0.00              
ATOM     60  O   LEU    71       7.723  42.961 -12.783  1.00  0.00              
ATOM     61  N   VAL    72       7.538  42.234 -10.670  1.00  0.00              
ATOM     62  CA  VAL    72       6.144  41.817 -10.821  1.00  0.00              
ATOM     63  C   VAL    72       5.247  42.988 -11.181  1.00  0.00              
ATOM     64  O   VAL    72       4.471  42.922 -12.144  1.00  0.00              
ATOM     65  N   LEU    73       5.364  44.079 -10.441  1.00  0.00              
ATOM     66  CA  LEU    73       4.500  45.217 -10.660  1.00  0.00              
ATOM     67  C   LEU    73       4.798  45.876 -12.008  1.00  0.00              
ATOM     68  O   LEU    73       3.880  46.325 -12.698  1.00  0.00              
ATOM     69  N   ALA    74       6.073  45.938 -12.392  1.00  0.00              
ATOM     70  CA  ALA    74       6.433  46.502 -13.679  1.00  0.00              
ATOM     71  C   ALA    74       5.906  45.673 -14.834  1.00  0.00              
ATOM     72  O   ALA    74       5.372  46.211 -15.809  1.00  0.00              
ATOM     73  N   LEU    75       6.025  44.361 -14.722  1.00  0.00              
ATOM     74  CA  LEU    75       5.490  43.478 -15.736  1.00  0.00              
ATOM     75  C   LEU    75       3.971  43.594 -15.833  1.00  0.00              
ATOM     76  O   LEU    75       3.421  43.586 -16.935  1.00  0.00              
ATOM     77  N   SER    76       3.289  43.670 -14.701  1.00  0.00              
ATOM     78  CA  SER    76       1.843  43.857 -14.729  1.00  0.00              
ATOM     79  C   SER    76       1.490  45.168 -15.406  1.00  0.00              
ATOM     80  O   SER    76       0.580  45.209 -16.245  1.00  0.00              
ATOM     81  N   LYS    77       2.217  46.233 -15.089  1.00  0.00              
ATOM     82  CA  LYS    77       1.956  47.547 -15.701  1.00  0.00              
ATOM     83  C   LYS    77       2.156  47.498 -17.213  1.00  0.00              
ATOM     84  O   LYS    77       1.413  48.157 -17.970  1.00  0.00              
ATOM     85  N   GLU    78       3.133  46.717 -17.669  1.00  0.00              
ATOM     86  CA  GLU    78       3.410  46.567 -19.100  1.00  0.00              
ATOM     87  C   GLU    78       2.409  45.660 -19.821  1.00  0.00              
ATOM     88  O   GLU    78       2.416  45.581 -21.054  1.00  0.00              
ATOM     89  N   GLY    79       1.564  44.970 -19.075  1.00  0.00              
ATOM     90  CA  GLY    79       0.571  44.067 -19.641  1.00  0.00              
ATOM     91  C   GLY    79       1.044  42.636 -19.863  1.00  0.00              
ATOM     92  O   GLY    79       0.397  41.893 -20.582  1.00  0.00              
ATOM     93  N   VAL    80       2.137  42.223 -19.211  1.00  0.00              
ATOM     94  CA  VAL    80       2.624  40.872 -19.337  1.00  0.00              
ATOM     95  C   VAL    80       1.744  39.913 -18.550  1.00  0.00              
ATOM     96  O   VAL    80       0.898  40.345 -17.756  1.00  0.00              
ATOM     97  N   GLU    81       1.975  38.627 -18.753  1.00  0.00              
ATOM     98  CA  GLU    81       1.180  37.573 -18.149  1.00  0.00              
ATOM     99  C   GLU    81       1.916  36.685 -17.172  1.00  0.00              
ATOM    100  O   GLU    81       1.296  36.159 -16.268  1.00  0.00              
ATOM    101  N   HIS    82       3.219  36.476 -17.374  1.00  0.00              
ATOM    102  CA  HIS    82       3.957  35.496 -16.600  1.00  0.00              
ATOM    103  C   HIS    82       5.359  35.999 -16.326  1.00  0.00              
ATOM    104  O   HIS    82       5.820  36.938 -16.981  1.00  0.00              
ATOM    105  N   VAL    83       6.035  35.370 -15.368  1.00  0.00              
ATOM    106  CA  VAL    83       7.436  35.662 -15.146  1.00  0.00              
ATOM    107  C   VAL    83       8.162  34.398 -14.718  1.00  0.00              
ATOM    108  O   VAL    83       7.624  33.583 -13.967  1.00  0.00              
ATOM    109  N   LEU    84       9.417  34.237 -15.151  1.00  0.00              
ATOM    110  CA  LEU    84      10.245  33.140 -14.661  1.00  0.00              
ATOM    111  C   LEU    84      10.526  33.283 -13.170  1.00  0.00              
ATOM    112  O   LEU    84      10.864  34.373 -12.711  1.00  0.00              
ATOM    113  N   THR    85      10.377  32.179 -12.456  1.00  0.00              
ATOM    114  CA  THR    85      10.347  32.160 -11.019  1.00  0.00              
ATOM    115  C   THR    85      11.080  30.946 -10.447  1.00  0.00              
ATOM    116  O   THR    85      11.096  29.871 -11.030  1.00  0.00              
ATOM    117  N   SER    86      11.636  31.143  -9.263  1.00  0.00              
ATOM    118  CA  SER    86      12.190  30.066  -8.461  1.00  0.00              
ATOM    119  C   SER    86      11.251  29.906  -7.285  1.00  0.00              
ATOM    120  O   SER    86      10.968  30.878  -6.593  1.00  0.00              
ATOM    121  N   GLU    87      10.779  28.687  -7.057  1.00  0.00              
ATOM    122  CA  GLU    87       9.846  28.381  -5.988  1.00  0.00              
ATOM    123  C   GLU    87      10.624  27.817  -4.784  1.00  0.00              
ATOM    124  O   GLU    87      11.325  26.820  -4.914  1.00  0.00              
ATOM    125  N   VAL    88      10.508  28.482  -3.647  1.00  0.00              
ATOM    126  CA  VAL    88      11.213  28.184  -2.415  1.00  0.00              
ATOM    127  C   VAL    88      10.259  27.572  -1.396  1.00  0.00              
ATOM    128  O   VAL    88       9.043  27.814  -1.439  1.00  0.00              
ATOM    129  N   ALA    89      10.812  26.793  -0.464  1.00  0.00              
ATOM    130  CA  ALA    89      10.113  26.464   0.773  1.00  0.00              
ATOM    131  C   ALA    89      10.470  27.580   1.746  1.00  0.00              
ATOM    132  O   ALA    89      11.592  27.645   2.219  1.00  0.00              
END
