
#######################################################
#                                                     #
#                        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   32 , name T0296AL380_3
# Molecule2: number of CA atoms  414 ( 2974),  selected   32 , name T0296.pdb
# PARAMETERS: T0296AL380_3.T0296.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:    18        27 - 44          4.94    24.14
  LCS_AVERAGE:      3.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        28 - 34          1.84    16.12
  LCS_AVERAGE:      1.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        29 - 33          0.45    17.16
  LONGEST_CONTINUOUS_SEGMENT:     5        36 - 40          0.27    27.10
  LCS_AVERAGE:      0.96

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:  414
LCS_GDT     G      26     G      26      3    3   17     0    3    3    3    5    5    8    8   10   11   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     I      27     I      27      3    3   18     0    3    3    3    3    6    8    8   10   11   13   14   17   19   19   19   19   19   19   19 
LCS_GDT     S      28     S      28      3    7   18     3    3    4    6    6    7    9    9   11   11   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     L      29     L      29      5    7   18     4    5    5    6    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     L      30     L      30      5    7   18     4    5    5    6    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     D      31     D      31      5    7   18     4    5    5    6    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     C      32     C      32      5    7   18     4    5    5    6    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     I      33     I      33      5    7   18     4    5    5    6    6    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     D      34     D      34      4    7   18     4    5    5    5    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     P      35     P      35      4    5   18     4    4    4    4    5    6    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     D      36     D      36      5    5   18     5    5    5    5    5    6    8   10   11   12   13   14   17   19   19   19   19   19   19   19 
LCS_GDT     I      37     I      37      5    5   18     5    5    5    6    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     N      38     N      38      5    5   18     5    5    5    5    5    7    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     R      39     R      39      5    5   18     5    5    5    6    7    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     A      40     A      40      5    5   18     5    5    5    5    5    5    7    7    9   11   12   14   17   19   19   19   19   19   19   19 
LCS_GDT     A      41     A      41      3    4   18     3    3    4    5    6    8    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     E      42     E      42      3    4   18     3    3    4    4    5    6    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     K      43     K      43      3    4   18     3    3    4    4    5    6    9   10   11   12   12   14   16   19   19   19   19   19   19   19 
LCS_GDT     I      44     I      44      3    4   18     0    3    4    4    5    6    9   10   11   12   13   15   17   19   19   19   19   19   19   19 
LCS_GDT     D     428     D     428      3    3   13     3    3    3    3    3    3    4    5    8   10   10   11   12   12   12   13   13   13   13   13 
LCS_GDT     F     429     F     429      3    3   13     3    3    3    3    5    6    8    8    8   10   10   11   12   12   12   13   13   13   13   13 
LCS_GDT     I     430     I     430      3    6   13     3    3    3    3    5    7    8    8    8   10   10   11   12   12   12   13   13   13   13   13 
LCS_GDT     S     431     S     431      3    6   13     3    3    3    3    5    7    8    8    8   10   10   11   12   12   12   13   13   13   13   13 
LCS_GDT     R     432     R     432      4    6   13     3    3    4    4    5    7    8    8    8   10   10   11   12   12   12   13   13   13   13   13 
LCS_GDT     G     433     G     433      4    6   13     3    4    4    4    5    7    8    8    8   10   10   11   12   12   12   13   13   13   18   18 
LCS_GDT     G     434     G     434      4    6   13     3    4    4    4    5    7    8    8    8   10   10   11   12   12   12   14   15   17   18   19 
LCS_GDT     Q     435     Q     435      4    6   13     3    4    4    4    5    7    8    8    8   10   10   11   12   12   12   13   15   17   18   19 
LCS_GDT     I     436     I     436      4    5   13     3    4    4    5    5    7    8    8    8   10   10   11   12   12   12   13   13   17   18   19 
LCS_GDT     P     437     P     437      4    5   13     3    4    4    5    5    5    6    6    8   10   10   11   12   12   12   13   13   17   18   19 
LCS_GDT     A     438     A     438      4    5   13     3    4    4    5    5    5    6    6    7    7    9    9   12   12   12   13   13   13   13   13 
LCS_GDT     P     439     P     439      4    5   13     3    4    4    5    5    5    6    6    7    8    9   11   12   12   12   13   13   13   13   13 
LCS_GDT     I     440     I     440      4    5   13     3    4    4    5    5    5    6    6    7    7    9    9   10   10   12   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   2.03  (   0.96    1.27    3.85 )

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      5      5      5      6      7      8      9     10     11     12     13     15     17     19     19     19     19     19     19     19 
GDT PERCENT_CA   1.21   1.21   1.21   1.45   1.69   1.93   2.17   2.42   2.66   2.90   3.14   3.62   4.11   4.59   4.59   4.59   4.59   4.59   4.59   4.59
GDT RMS_LOCAL    0.27   0.27   0.27   1.10   1.67   1.90   2.22   2.60   2.94   3.28   3.60   4.36   4.69   5.04   5.04   5.04   5.04   5.04   5.04   5.04
GDT RMS_ALL_CA  27.10  27.10  27.10  16.31  17.57  17.46  16.52  18.21  16.90  23.89  21.80  21.37  22.26  23.79  23.79  23.79  23.79  23.79  23.79  23.79

#      Molecule1      Molecule2       DISTANCE
LGA    G      26      G      26         10.667
LGA    I      27      I      27         11.112
LGA    S      28      S      28          6.456
LGA    L      29      L      29          2.547
LGA    L      30      L      30          1.372
LGA    D      31      D      31          2.358
LGA    C      32      C      32          1.021
LGA    I      33      I      33          3.430
LGA    D      34      D      34          2.415
LGA    P      35      P      35          7.090
LGA    D      36      D      36          7.371
LGA    I      37      I      37          1.885
LGA    N      38      N      38          3.952
LGA    R      39      R      39          2.217
LGA    A      40      A      40          6.609
LGA    A      41      A      41          3.295
LGA    E      42      E      42         10.200
LGA    K      43      K      43         12.012
LGA    I      44      I      44          7.703
LGA    D     428      D     428         33.235
LGA    F     429      F     429         32.418
LGA    I     430      I     430         28.805
LGA    S     431      S     431         32.079
LGA    R     432      R     432         32.744
LGA    G     433      G     433         28.093
LGA    G     434      G     434         22.639
LGA    Q     435      Q     435         18.733
LGA    I     436      I     436         20.074
LGA    P     437      P     437         21.771
LGA    A     438      A     438         22.936
LGA    P     439      P     439         26.700
LGA    I     440      I     440         30.938

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  414    4.0     10    2.60     2.415     2.140     0.371

LGA_LOCAL      RMSD =  2.598  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 18.213  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 12.444  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.624839 * X  +  -0.396691 * Y  +  -0.672467 * Z  + 147.990936
  Y_new =   0.129640 * X  +   0.796634 * Y  +  -0.590396 * Z  + -65.623970
  Z_new =   0.769915 * X  +  -0.456081 * Y  +  -0.446341 * Z  +  76.228638 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.345402    0.796191  [ DEG:  -134.3816     45.6184 ]
  Theta =  -0.878708   -2.262884  [ DEG:   -50.3463   -129.6537 ]
  Phi   =   2.937018   -0.204575  [ DEG:   168.2787    -11.7213 ]
 
# 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: T0296AL380_3                                  
REMARK     2: T0296.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0296AL380_3.T0296.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  414   4.0   10   2.60   2.140    12.44
REMARK  ---------------------------------------------------------- 
MOLECULE T0296AL380_3
REMARK Aligment from pdb entry: 1gthC
ATOM      1  N   GLY    26      59.984  31.299  31.095  1.00  0.00              
ATOM      2  CA  GLY    26      61.355  31.724  30.925  1.00  0.00              
ATOM      3  C   GLY    26      61.533  32.939  31.804  1.00  0.00              
ATOM      4  O   GLY    26      60.568  33.432  32.390  1.00  0.00              
ATOM      5  N   ILE    27      62.753  33.438  31.899  1.00  0.00              
ATOM      6  CA  ILE    27      63.001  34.596  32.730  1.00  0.00              
ATOM      7  C   ILE    27      62.281  35.859  32.234  1.00  0.00              
ATOM      8  O   ILE    27      61.954  36.742  33.027  1.00  0.00              
ATOM      9  N   SER    28      62.031  35.956  30.931  1.00  0.00              
ATOM     10  CA  SER    28      61.333  37.132  30.407  1.00  0.00              
ATOM     11  C   SER    28      59.880  37.144  30.884  1.00  0.00              
ATOM     12  O   SER    28      59.303  38.202  31.129  1.00  0.00              
ATOM     13  N   LEU    29      59.298  35.959  31.015  1.00  0.00              
ATOM     14  CA  LEU    29      57.921  35.827  31.466  1.00  0.00              
ATOM     15  C   LEU    29      57.732  36.527  32.813  1.00  0.00              
ATOM     16  O   LEU    29      56.757  37.256  33.019  1.00  0.00              
ATOM     17  N   LEU    30      58.674  36.307  33.724  1.00  0.00              
ATOM     18  CA  LEU    30      58.598  36.900  35.054  1.00  0.00              
ATOM     19  C   LEU    30      58.710  38.420  35.073  1.00  0.00              
ATOM     20  O   LEU    30      58.110  39.074  35.932  1.00  0.00              
ATOM     21  N   ASP    31      59.469  38.993  34.140  1.00  0.00              
ATOM     22  CA  ASP    31      59.578  40.443  34.083  1.00  0.00              
ATOM     23  C   ASP    31      58.291  41.015  33.494  1.00  0.00              
ATOM     24  O   ASP    31      57.934  42.170  33.759  1.00  0.00              
ATOM     25  N   CYS    32      57.606  40.213  32.680  1.00  0.00              
ATOM     26  CA  CYS    32      56.342  40.646  32.091  1.00  0.00              
ATOM     27  C   CYS    32      55.297  40.620  33.196  1.00  0.00              
ATOM     28  O   CYS    32      54.475  41.528  33.306  1.00  0.00              
ATOM     29  N   ILE    33      55.342  39.574  34.016  1.00  0.00              
ATOM     30  CA  ILE    33      54.408  39.414  35.121  1.00  0.00              
ATOM     31  C   ILE    33      54.522  40.574  36.105  1.00  0.00              
ATOM     32  O   ILE    33      53.528  41.229  36.421  1.00  0.00              
ATOM     33  N   ASP    34      55.733  40.830  36.589  1.00  0.00              
ATOM     34  CA  ASP    34      55.945  41.915  37.545  1.00  0.00              
ATOM     35  C   ASP    34      55.674  43.281  36.924  1.00  0.00              
ATOM     36  O   ASP    34      55.178  44.186  37.595  1.00  0.00              
ATOM     37  N   PRO    35      56.003  43.438  35.646  1.00  0.00              
ATOM     38  CA  PRO    35      55.766  44.705  34.975  1.00  0.00              
ATOM     39  C   PRO    35      54.268  44.923  34.784  1.00  0.00              
ATOM     40  O   PRO    35      53.787  46.054  34.822  1.00  0.00              
ATOM     41  N   ASP    36      53.531  43.837  34.578  1.00  0.00              
ATOM     42  CA  ASP    36      52.086  43.939  34.393  1.00  0.00              
ATOM     43  C   ASP    36      51.463  44.588  35.630  1.00  0.00              
ATOM     44  O   ASP    36      50.596  45.461  35.514  1.00  0.00              
ATOM     45  N   ILE    37      51.916  44.168  36.811  1.00  0.00              
ATOM     46  CA  ILE    37      51.405  44.714  38.065  1.00  0.00              
ATOM     47  C   ILE    37      51.599  46.221  38.144  1.00  0.00              
ATOM     48  O   ILE    37      50.739  46.938  38.658  1.00  0.00              
ATOM     49  N   ASN    38      52.727  46.702  37.634  1.00  0.00              
ATOM     50  CA  ASN    38      53.008  48.133  37.658  1.00  0.00              
ATOM     51  C   ASN    38      52.070  48.896  36.738  1.00  0.00              
ATOM     52  O   ASN    38      51.872  50.100  36.903  1.00  0.00              
ATOM     53  N   ARG    39      51.498  48.193  35.765  1.00  0.00              
ATOM     54  CA  ARG    39      50.595  48.824  34.815  1.00  0.00              
ATOM     55  C   ARG    39      49.143  48.851  35.277  1.00  0.00              
ATOM     56  O   ARG    39      48.297  49.478  34.639  1.00  0.00              
ATOM     57  N   ALA    40      48.859  48.180  36.389  1.00  0.00              
ATOM     58  CA  ALA    40      47.506  48.177  36.920  1.00  0.00              
ATOM     59  C   ALA    40      46.800  46.837  36.925  1.00  0.00              
ATOM     60  O   ALA    40      45.631  46.756  37.307  1.00  0.00              
ATOM     61  N   ALA    41      47.494  45.786  36.500  1.00  0.00              
ATOM     62  CA  ALA    41      46.901  44.460  36.469  1.00  0.00              
ATOM     63  C   ALA    41      46.272  44.143  37.817  1.00  0.00              
ATOM     64  O   ALA    41      46.854  44.425  38.865  1.00  0.00              
ATOM     65  N   GLU    42      45.077  43.568  37.782  1.00  0.00              
ATOM     66  CA  GLU    42      44.376  43.197  39.000  1.00  0.00              
ATOM     67  C   GLU    42      44.960  41.879  39.477  1.00  0.00              
ATOM     68  O   GLU    42      45.095  41.635  40.676  1.00  0.00              
ATOM     69  N   LYS    43      45.302  41.025  38.524  1.00  0.00              
ATOM     70  CA  LYS    43      45.895  39.746  38.852  1.00  0.00              
ATOM     71  C   LYS    43      46.718  39.254  37.673  1.00  0.00              
ATOM     72  O   LYS    43      46.412  39.562  36.522  1.00  0.00              
ATOM     73  N   ILE    44      47.775  38.505  37.965  1.00  0.00              
ATOM     74  CA  ILE    44      48.654  37.995  36.926  1.00  0.00              
ATOM     75  C   ILE    44      48.876  36.504  37.066  1.00  0.00              
ATOM     76  O   ILE    44      49.258  36.023  38.138  1.00  0.00              
ATOM     77  N   ASP   428      48.642  35.777  35.978  1.00  0.00              
ATOM     78  CA  ASP   428      48.834  34.335  35.973  1.00  0.00              
ATOM     79  C   ASP   428      49.950  33.965  35.010  1.00  0.00              
ATOM     80  O   ASP   428      49.999  34.453  33.882  1.00  0.00              
ATOM     81  N   PHE   429      50.854  33.112  35.471  1.00  0.00              
ATOM     82  CA  PHE   429      51.952  32.641  34.646  1.00  0.00              
ATOM     83  C   PHE   429      51.572  31.213  34.268  1.00  0.00              
ATOM     84  O   PHE   429      51.526  30.326  35.123  1.00  0.00              
ATOM     85  N   ILE   430      51.275  31.003  32.988  1.00  0.00              
ATOM     86  CA  ILE   430      50.878  29.686  32.508  1.00  0.00              
ATOM     87  C   ILE   430      51.940  29.098  31.592  1.00  0.00              
ATOM     88  O   ILE   430      52.264  29.676  30.555  1.00  0.00              
ATOM     89  N   SER   431      52.477  27.946  31.984  1.00  0.00              
ATOM     90  CA  SER   431      53.503  27.272  31.202  1.00  0.00              
ATOM     91  C   SER   431      53.108  25.839  30.859  1.00  0.00              
ATOM     92  O   SER   431      52.337  25.207  31.581  1.00  0.00              
ATOM     93  N   ARG   432      53.642  25.340  29.748  1.00  0.00              
ATOM     94  CA  ARG   432      53.327  24.002  29.263  1.00  0.00              
ATOM     95  C   ARG   432      53.999  22.855  29.996  1.00  0.00              
ATOM     96  O   ARG   432      53.673  21.697  29.757  1.00  0.00              
ATOM     97  N   GLY   433      54.942  23.156  30.875  1.00  0.00              
ATOM     98  CA  GLY   433      55.605  22.095  31.617  1.00  0.00              
ATOM     99  C   GLY   433      55.365  22.225  33.115  1.00  0.00              
ATOM    100  O   GLY   433      54.505  22.994  33.540  1.00  0.00              
ATOM    101  N   GLY   434      56.114  21.467  33.907  1.00  0.00              
ATOM    102  CA  GLY   434      55.929  21.513  35.346  1.00  0.00              
ATOM    103  C   GLY   434      56.707  22.592  36.070  1.00  0.00              
ATOM    104  O   GLY   434      57.527  23.297  35.479  1.00  0.00              
ATOM    105  N   GLN   435      56.441  22.722  37.364  1.00  0.00              
ATOM    106  CA  GLN   435      57.127  23.708  38.186  1.00  0.00              
ATOM    107  C   GLN   435      58.617  23.408  38.203  1.00  0.00              
ATOM    108  O   GLN   435      59.448  24.315  38.147  1.00  0.00              
ATOM    109  N   ILE   436      58.941  22.123  38.289  1.00  0.00              
ATOM    110  CA  ILE   436      60.322  21.672  38.314  1.00  0.00              
ATOM    111  C   ILE   436      61.035  22.040  37.015  1.00  0.00              
ATOM    112  O   ILE   436      62.259  22.142  36.977  1.00  0.00              
ATOM    113  N   PRO   437      60.262  22.244  35.951  1.00  0.00              
ATOM    114  CA  PRO   437      60.841  22.569  34.654  1.00  0.00              
ATOM    115  C   PRO   437      61.121  24.040  34.421  1.00  0.00              
ATOM    116  O   PRO   437      61.692  24.407  33.389  1.00  0.00              
ATOM    117  N   ALA   438      60.705  24.893  35.351  1.00  0.00              
ATOM    118  CA  ALA   438      60.981  26.310  35.196  1.00  0.00              
ATOM    119  C   ALA   438      62.501  26.415  35.266  1.00  0.00              
ATOM    120  O   ALA   438      63.127  25.930  36.212  1.00  0.00              
ATOM    121  N   PRO   439      63.099  27.027  34.258  1.00  0.00              
ATOM    122  CA  PRO   439      64.548  27.157  34.237  1.00  0.00              
ATOM    123  C   PRO   439      64.994  28.589  34.462  1.00  0.00              
ATOM    124  O   PRO   439      66.177  28.902  34.336  1.00  0.00              
ATOM    125  N   ILE   440      64.036  29.459  34.774  1.00  0.00              
ATOM    126  CA  ILE   440      64.339  30.859  35.059  1.00  0.00              
ATOM    127  C   ILE   440      65.112  30.888  36.385  1.00  0.00              
ATOM    128  O   ILE   440      64.888  30.045  37.256  1.00  0.00              
ATOM    129  N   HIS   441      66.023  31.841  36.538  1.00  0.00              
ATOM    130  CA  HIS   441      66.807  31.928  37.769  1.00  0.00              
ATOM    131  C   HIS   441      65.878  32.054  38.990  1.00  0.00              
ATOM    132  O   HIS   441      64.939  32.852  38.985  1.00  0.00              
END
