
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0382AL381_2
# Molecule2: number of CA atoms  121 (  929),  selected   25 , name T0382.pdb
# PARAMETERS: T0382AL381_2.T0382.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:    25        83 - 107         4.75     4.75
  LCS_AVERAGE:     20.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        83 - 99          1.84    10.22
  LCS_AVERAGE:     11.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        86 - 99          0.48     9.49
  LCS_AVERAGE:      7.83

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:  121
LCS_GDT     A      83     A      83      3   17   25     3    4    6   10   16   16   17   17   17   18   18   20   20   22   22   22   25   25   25   25 
LCS_GDT     V      84     V      84      3   17   25     3    4    6   10   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     A      85     A      85      3   17   25     3    4    7   10   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     P      86     P      86     14   17   25     4   12   14   14   14   14   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     V      87     V      87     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     K      88     K      88     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     A      89     A      89     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     R      90     R      90     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     E      91     E      91     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     Q      92     Q      92     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     L      93     L      93     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     E      94     E      94     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     A      95     A      95     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     I      96     I      96     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     V      97     V      97     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     S      98     S      98     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     S      99     S      99     14   17   25    13   13   14   14   16   16   17   17   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     K     100     K     100      4   15   25     3    4    5    6    8   10   12   15   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     W     101     W     101      4    6   25     3    4    5    6    8   10   12   14   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     F     102     F     102      4    6   25     3    3    4    6    7    7   11   14   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     P     103     P     103      4    6   25     3    4    5    6    7    7   11   14   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     Q     104     Q     104      4    5   25     4    4    4    4    5    9   12   14   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     A     105     A     105      4    5   25     4    4    4    4    4    5    5    7    7    8   10   10   13   14   24   24   25   25   25   25 
LCS_GDT     G     106     G     106      4    5   25     4    4    4    4    4    5    9   14   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_GDT     D     107     D     107      4    5   25     4    4    5    5    8   10   12   14   17   18   20   21   22   23   24   24   25   25   25   25 
LCS_AVERAGE  LCS_A:  13.27  (   7.83   11.31   20.66 )

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     13     14     14     16     16     17     17     17     18     20     21     22     23     24     24     25     25     25     25 
GDT PERCENT_CA  10.74  10.74  11.57  11.57  13.22  13.22  14.05  14.05  14.05  14.88  16.53  17.36  18.18  19.01  19.83  19.83  20.66  20.66  20.66  20.66
GDT RMS_LOCAL    0.25   0.25   0.48   0.48   1.61   1.61   1.84   1.84   1.84   2.43   3.73   3.86   4.01   4.23   4.41   4.41   4.75   4.75   4.75   4.75
GDT RMS_ALL_CA   9.49   9.49   9.49   9.49  10.10  10.10  10.22  10.22  10.22   9.63   5.19   5.10   5.02   4.83   4.82   4.82   4.75   4.75   4.75   4.75

#      Molecule1      Molecule2       DISTANCE
LGA    A      83      A      83          2.777
LGA    V      84      V      84          2.688
LGA    A      85      A      85          2.387
LGA    P      86      P      86          3.756
LGA    V      87      V      87          0.453
LGA    K      88      K      88          1.884
LGA    A      89      A      89          2.203
LGA    R      90      R      90          1.168
LGA    E      91      E      91          0.567
LGA    Q      92      Q      92          1.177
LGA    L      93      L      93          1.269
LGA    E      94      E      94          1.168
LGA    A      95      A      95          1.083
LGA    I      96      I      96          0.762
LGA    V      97      V      97          1.552
LGA    S      98      S      98          1.840
LGA    S      99      S      99          0.771
LGA    K     100      K     100          7.642
LGA    W     101      W     101         12.278
LGA    F     102      F     102         16.602
LGA    P     103      P     103         21.984
LGA    Q     104      Q     104         19.682
LGA    A     105      A     105         19.194
LGA    G     106      G     106         22.022
LGA    D     107      D     107         18.564

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25  121    4.0     17    1.84    14.050    13.549     0.876

LGA_LOCAL      RMSD =  1.840  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.220  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  4.746  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.018657 * X  +  -0.476857 * Y  +   0.878783 * Z  + -67.347252
  Y_new =   0.541813 * X  +  -0.743514 * Y  +  -0.391952 * Z  +  80.328041
  Z_new =   0.840292 * X  +   0.468823 * Y  +   0.272239 * Z  + -26.438526 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.044700   -2.096892  [ DEG:    59.8569   -120.1431 ]
  Theta =  -0.997822   -2.143771  [ DEG:   -57.1710   -122.8290 ]
  Phi   =   1.605217   -1.536376  [ DEG:    91.9721    -88.0279 ]
 
# 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: T0382AL381_2                                  
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382AL381_2.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25  121   4.0   17   1.84  13.549     4.75
REMARK  ---------------------------------------------------------- 
MOLECULE T0382AL381_2
REMARK Aligment from pdb entry: 1mgrA
ATOM      1  N   ALA    83     -12.822  56.375  -0.097  1.00  0.00              
ATOM      2  CA  ALA    83     -13.177  57.657  -0.650  1.00  0.00              
ATOM      3  C   ALA    83     -14.008  57.583  -1.926  1.00  0.00              
ATOM      4  O   ALA    83     -14.709  58.542  -2.279  1.00  0.00              
ATOM      5  N   VAL    84     -13.967  56.429  -2.587  1.00  0.00              
ATOM      6  CA  VAL    84     -14.608  56.190  -3.848  1.00  0.00              
ATOM      7  C   VAL    84     -15.998  55.522  -3.661  1.00  0.00              
ATOM      8  O   VAL    84     -16.688  55.216  -4.620  1.00  0.00              
ATOM      9  N   ALA    85     -16.391  55.285  -2.430  1.00  0.00              
ATOM     10  CA  ALA    85     -17.717  54.676  -2.216  1.00  0.00              
ATOM     11  C   ALA    85     -18.786  55.770  -2.251  1.00  0.00              
ATOM     12  O   ALA    85     -18.523  56.935  -1.906  1.00  0.00              
ATOM     13  N   PRO    86     -20.017  55.418  -2.593  1.00  0.00              
ATOM     14  CA  PRO    86     -21.123  56.400  -2.527  1.00  0.00              
ATOM     15  C   PRO    86     -21.429  56.824  -1.058  1.00  0.00              
ATOM     16  O   PRO    86     -21.118  56.077  -0.123  1.00  0.00              
ATOM     17  N   VAL    87     -21.982  58.030  -0.866  1.00  0.00              
ATOM     18  CA  VAL    87     -22.168  58.621   0.465  1.00  0.00              
ATOM     19  C   VAL    87     -23.075  57.754   1.360  1.00  0.00              
ATOM     20  O   VAL    87     -22.850  57.667   2.545  1.00  0.00              
ATOM     21  N   LYS    88     -24.070  57.116   0.758  1.00  0.00              
ATOM     22  CA  LYS    88     -24.905  56.113   1.461  1.00  0.00              
ATOM     23  C   LYS    88     -24.080  54.949   2.032  1.00  0.00              
ATOM     24  O   LYS    88     -24.402  54.427   3.105  1.00  0.00              
ATOM     25  N   ALA    89     -23.014  54.512   1.342  1.00  0.00              
ATOM     26  CA  ALA    89     -22.187  53.488   1.918  1.00  0.00              
ATOM     27  C   ALA    89     -21.434  54.042   3.125  1.00  0.00              
ATOM     28  O   ALA    89     -21.144  53.327   4.039  1.00  0.00              
ATOM     29  N   ARG    90     -21.032  55.322   3.078  1.00  0.00              
ATOM     30  CA  ARG    90     -20.408  55.936   4.205  1.00  0.00              
ATOM     31  C   ARG    90     -21.404  55.918   5.386  1.00  0.00              
ATOM     32  O   ARG    90     -21.028  55.542   6.486  1.00  0.00              
ATOM     33  N   GLU    91     -22.643  56.298   5.115  1.00  0.00              
ATOM     34  CA  GLU    91     -23.700  56.230   6.130  1.00  0.00              
ATOM     35  C   GLU    91     -23.811  54.832   6.747  1.00  0.00              
ATOM     36  O   GLU    91     -23.830  54.681   7.947  1.00  0.00              
ATOM     37  N   GLN    92     -23.906  53.794   5.905  1.00  0.00              
ATOM     38  CA  GLN    92     -23.919  52.431   6.424  1.00  0.00              
ATOM     39  C   GLN    92     -22.773  52.087   7.302  1.00  0.00              
ATOM     40  O   GLN    92     -22.939  51.437   8.302  1.00  0.00              
ATOM     41  N   LEU    93     -21.551  52.436   6.886  1.00  0.00              
ATOM     42  CA  LEU    93     -20.394  52.109   7.686  1.00  0.00              
ATOM     43  C   LEU    93     -20.430  52.791   9.054  1.00  0.00              
ATOM     44  O   LEU    93     -20.107  52.159  10.044  1.00  0.00              
ATOM     45  N   GLU    94     -20.880  54.020   9.074  1.00  0.00              
ATOM     46  CA  GLU    94     -21.064  54.799  10.310  1.00  0.00              
ATOM     47  C   GLU    94     -22.098  54.081  11.224  1.00  0.00              
ATOM     48  O   GLU    94     -21.880  53.872  12.428  1.00  0.00              
ATOM     49  N   ALA    95     -23.195  53.634  10.615  1.00  0.00              
ATOM     50  CA  ALA    95     -24.196  52.960  11.395  1.00  0.00              
ATOM     51  C   ALA    95     -23.677  51.655  11.960  1.00  0.00              
ATOM     52  O   ALA    95     -24.023  51.285  13.018  1.00  0.00              
ATOM     53  N   ILE    96     -22.892  50.881  11.213  1.00  0.00              
ATOM     54  CA  ILE    96     -22.349  49.668  11.723  1.00  0.00              
ATOM     55  C   ILE    96     -21.432  49.994  12.935  1.00  0.00              
ATOM     56  O   ILE    96     -21.430  49.273  13.870  1.00  0.00              
ATOM     57  N   VAL    97     -20.663  51.066  12.839  1.00  0.00              
ATOM     58  CA  VAL    97     -19.738  51.446  13.924  1.00  0.00              
ATOM     59  C   VAL    97     -20.537  51.757  15.188  1.00  0.00              
ATOM     60  O   VAL    97     -20.131  51.441  16.293  1.00  0.00              
ATOM     61  N   SER    98     -21.694  52.343  14.980  1.00  0.00              
ATOM     62  CA  SER    98     -22.575  52.764  16.112  1.00  0.00              
ATOM     63  C   SER    98     -23.490  51.672  16.648  1.00  0.00              
ATOM     64  O   SER    98     -23.981  51.754  17.775  1.00  0.00              
ATOM     65  N   SER    99     -23.742  50.633  15.849  1.00  0.00              
ATOM     66  CA  SER    99     -24.580  49.561  16.257  1.00  0.00              
ATOM     67  C   SER    99     -26.057  49.814  15.882  1.00  0.00              
ATOM     68  O   SER    99     -26.903  49.112  16.415  1.00  0.00              
ATOM     69  N   LYS   100     -26.325  50.740  14.979  1.00  0.00              
ATOM     70  CA  LYS   100     -27.677  51.050  14.539  1.00  0.00              
ATOM     71  C   LYS   100     -27.940  52.533  14.695  1.00  0.00              
ATOM     72  O   LYS   100     -27.049  53.249  15.127  1.00  0.00              
ATOM     73  N   TRP   101     -29.140  53.020  14.384  1.00  0.00              
ATOM     74  CA  TRP   101     -30.282  52.205  13.919  1.00  0.00              
ATOM     75  C   TRP   101     -30.231  51.879  12.461  1.00  0.00              
ATOM     76  O   TRP   101     -29.736  52.711  11.710  1.00  0.00              
ATOM     77  N   PHE   102     -30.771  50.713  12.080  1.00  0.00              
ATOM     78  CA  PHE   102     -30.748  50.279  10.694  1.00  0.00              
ATOM     79  C   PHE   102     -32.141  50.324  10.137  1.00  0.00              
ATOM     80  O   PHE   102     -33.100  50.059  10.852  1.00  0.00              
ATOM     81  N   PRO   103     -32.225  50.673   8.869  1.00  0.00              
ATOM     82  CA  PRO   103     -33.532  50.851   8.224  1.00  0.00              
ATOM     83  C   PRO   103     -34.305  49.580   7.873  1.00  0.00              
ATOM     84  O   PRO   103     -35.569  49.645   7.835  1.00  0.00              
ATOM     85  N   GLN   104     -33.629  48.445   7.722  1.00  0.00              
ATOM     86  CA  GLN   104     -34.269  47.219   7.276  1.00  0.00              
ATOM     87  C   GLN   104     -34.082  46.109   8.242  1.00  0.00              
ATOM     88  O   GLN   104     -33.049  46.011   8.922  1.00  0.00              
ATOM     89  N   ALA   105     -35.030  45.188   8.265  1.00  0.00              
ATOM     90  CA  ALA   105     -34.996  44.115   9.200  1.00  0.00              
ATOM     91  C   ALA   105     -33.804  43.193   8.955  1.00  0.00              
ATOM     92  O   ALA   105     -33.337  42.591   9.876  1.00  0.00              
ATOM     93  N   GLY   106     -33.368  43.067   7.702  1.00  0.00              
ATOM     94  CA  GLY   106     -32.278  42.163   7.402  1.00  0.00              
ATOM     95  C   GLY   106     -30.922  42.750   7.747  1.00  0.00              
ATOM     96  O   GLY   106     -29.903  42.059   7.671  1.00  0.00              
ATOM     97  N   ASP   107     -30.882  43.998   8.126  1.00  0.00              
ATOM     98  CA  ASP   107     -29.553  44.623   8.439  1.00  0.00              
ATOM     99  C   ASP   107     -29.020  44.028   9.699  1.00  0.00              
ATOM    100  O   ASP   107     -29.651  44.071  10.759  1.00  0.00              
END
