
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0372AL333_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   34 , name T0372_D1.pdb
# PARAMETERS: T0372AL333_3-D1.T0372_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:    17        71 - 87          1.56    16.96
  LONGEST_CONTINUOUS_SEGMENT:    17        72 - 95          4.95    16.62
  LCS_AVERAGE:     12.04

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        71 - 87          1.56    16.96
  LCS_AVERAGE:      9.92

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        72 - 87          0.62    16.99
  LCS_AVERAGE:      8.73

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:  126
LCS_GDT     F      31     F      31      0    0    0     0    0    0    0    0    0    1    4    4    4    6    7    8    8    9    9   10   11   12   13 
LCS_GDT     S      32     S      32      0    0    0     0    0    0    0    0    0    0    0    2    2    6    7    8    8    8    9    9   11   11   11 
LCS_GDT     G      71     G      71      3   17   17     3    3    3    5    6    9   10   12   17   17   17   17   17   17   19   19   20   21   22   25 
LCS_GDT     D      72     D      72     16   17   17     9   15   16   16   16   16   16   16   17   17   17   17   17   17   19   19   22   24   24   26 
LCS_GDT     L      73     L      73     16   17   17    10   15   16   16   16   16   16   16   17   17   17   17   17   17   19   19   20   21   23   25 
LCS_GDT     K      74     K      74     16   17   17    10   15   16   16   16   16   16   16   17   17   17   17   17   17   19   22   23   24   24   26 
LCS_GDT     A      75     A      75     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     V      76     V      76     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     L      77     L      77     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     R      78     R      78     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     K      79     K      79     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     L      80     L      80     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     I      81     I      81     16   17   17    10   15   16   16   16   16   16   16   17   17   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     E      82     E      82     16   17   17    10   15   16   16   16   16   16   16   17   17   17   17   17   17   19   21   23   24   24   26 
LCS_GDT     D      83     D      83     16   17   17    10   15   16   16   16   16   16   16   17   17   17   17   17   17   19   19   21   24   24   26 
LCS_GDT     A      84     A      84     16   17   17     9   15   16   16   16   16   16   16   17   17   17   17   17   17   19   19   21   24   24   26 
LCS_GDT     D      85     D      85     16   17   17    10   15   16   16   16   16   16   16   17   17   17   17   17   17   19   19   21   24   24   26 
LCS_GDT     K      86     K      86     16   17   17     9   15   16   16   16   16   16   16   17   17   17   17   17   17   19   19   20   21   22   24 
LCS_GDT     E      87     E      87     16   17   17     9   14   16   16   16   16   16   16   17   17   17   17   17   17   19   19   20   20   22   24 
LCS_GDT     G      95     G      95      3    3   17     3    3    4    7    7    8    9   12   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     V      96     V      96      3    4   15     3    3    3    4    4    5    5    9   10   12   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     C      97     C      97      3    4   15     3    3    4    4    7    7    9   12   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     S      98     S      98      3    4   15     3    3    3    4    5    5    8    9   14   14   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     N      99     N      99      3   11   15     3    3    3    4    5    8   10   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     M     100     M     100     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     R     101     R     101     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     A     102     A     102     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     D     103     D     103     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     L     104     L     104     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     E     105     E     105     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     A     106     A     106     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     I     107     I     107     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     L     108     L     108     10   11   15     9    9   10   11   11   12   12   14   14   15   17   19   22   22   22   22   23   24   24   26 
LCS_GDT     P     109     P     109     10   11   15     0    3   10   11   11   12   12   14   14   14   15   17   22   22   22   22   23   24   24   26 
LCS_AVERAGE  LCS_A:  10.23  (   8.73    9.92   12.04 )

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     10     15     16     16     16     16     16     16     17     17     17     19     22     22     22     22     23     24     24     26 
GDT PERCENT_CA   7.94  11.90  12.70  12.70  12.70  12.70  12.70  12.70  13.49  13.49  13.49  15.08  17.46  17.46  17.46  17.46  18.25  19.05  19.05  20.63
GDT RMS_LOCAL    0.30   0.54   0.62   0.62   0.62   0.62   0.62   0.62   1.56   1.56   1.56   4.17   4.58   4.58   4.58   4.58   4.93   5.34   5.34   6.18
GDT RMS_ALL_CA  17.30  17.14  16.99  16.99  16.99  16.99  16.99  16.99  16.96  16.96  16.96  12.66  12.70  12.70  12.70  12.70  12.67  12.55  12.55  12.48

#      Molecule1      Molecule2       DISTANCE
LGA    F      31      F      31         26.924
LGA    S      32      S      32         30.278
LGA    G      71      G      71          6.771
LGA    D      72      D      72          0.909
LGA    L      73      L      73          0.424
LGA    K      74      K      74          0.611
LGA    A      75      A      75          0.624
LGA    V      76      V      76          0.753
LGA    L      77      L      77          0.745
LGA    R      78      R      78          0.116
LGA    K      79      K      79          0.315
LGA    L      80      L      80          0.607
LGA    I      81      I      81          0.396
LGA    E      82      E      82          0.424
LGA    D      83      D      83          0.251
LGA    A      84      A      84          0.461
LGA    D      85      D      85          0.339
LGA    K      86      K      86          0.821
LGA    E      87      E      87          1.141
LGA    G      95      G      95         22.353
LGA    V      96      V      96         23.743
LGA    C      97      C      97         26.773
LGA    S      98      S      98         25.804
LGA    N      99      N      99         25.805
LGA    M     100      M     100         20.972
LGA    R     101      R     101         18.319
LGA    A     102      A     102         24.095
LGA    D     103      D     103         23.854
LGA    L     104      L     104         18.586
LGA    E     105      E     105         21.797
LGA    A     106      A     106         26.177
LGA    I     107      I     107         23.001
LGA    L     108      L     108         19.934
LGA    P     109      P     109         25.472

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  126    4.0     16    0.62    13.690    12.745     2.234

LGA_LOCAL      RMSD =  0.616  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.987  Number of atoms =   34 
Std_ALL_ATOMS  RMSD = 11.511  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.342966 * X  +  -0.916147 * Y  +   0.207482 * Z  +  -4.318631
  Y_new =   0.906509 * X  +   0.380694 * Y  +   0.182522 * Z  +  33.979588
  Z_new =  -0.246204 * X  +   0.125486 * Y  +   0.961060 * Z  +  -2.658710 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.129836   -3.011757  [ DEG:     7.4390   -172.5610 ]
  Theta =   0.248762    2.892831  [ DEG:    14.2530    165.7470 ]
  Phi   =   1.209103   -1.932490  [ DEG:    69.2765   -110.7235 ]
 
# 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: T0372AL333_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_3-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  126   4.0   16   0.62  12.745    11.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_3-D1
REMARK Aligment from pdb entry: 1lva_A
ATOM      1  N   PHE    31      23.938  63.603  -3.027  1.00  0.00              
ATOM      2  CA  PHE    31      25.336  63.693  -2.610  1.00  0.00              
ATOM      3  C   PHE    31      25.907  65.091  -2.783  1.00  0.00              
ATOM      4  O   PHE    31      25.382  65.900  -3.537  1.00  0.00              
ATOM      5  N   SER    32      26.998  65.357  -2.079  1.00  0.00              
ATOM      6  CA  SER    32      27.692  66.627  -2.180  1.00  0.00              
ATOM      7  C   SER    32      28.677  66.412  -3.328  1.00  0.00              
ATOM      8  O   SER    32      28.988  65.267  -3.666  1.00  0.00              
ATOM      9  N   GLY    71      29.167  67.492  -3.928  1.00  0.00              
ATOM     10  CA  GLY    71      30.111  67.362  -5.030  1.00  0.00              
ATOM     11  C   GLY    71      31.350  66.558  -4.640  1.00  0.00              
ATOM     12  O   GLY    71      31.943  65.893  -5.483  1.00  0.00              
ATOM     13  N   ASP    72      31.736  66.614  -3.366  1.00  0.00              
ATOM     14  CA  ASP    72      32.881  65.853  -2.887  1.00  0.00              
ATOM     15  C   ASP    72      32.532  64.364  -2.839  1.00  0.00              
ATOM     16  O   ASP    72      33.357  63.510  -3.172  1.00  0.00              
ATOM     17  N   LEU    73      31.305  64.060  -2.424  1.00  0.00              
ATOM     18  CA  LEU    73      30.851  62.678  -2.361  1.00  0.00              
ATOM     19  C   LEU    73      30.780  62.118  -3.781  1.00  0.00              
ATOM     20  O   LEU    73      31.181  60.974  -4.032  1.00  0.00              
ATOM     21  N   LYS    74      30.279  62.937  -4.706  1.00  0.00              
ATOM     22  CA  LYS    74      30.159  62.521  -6.096  1.00  0.00              
ATOM     23  C   LYS    74      31.518  62.179  -6.690  1.00  0.00              
ATOM     24  O   LYS    74      31.657  61.177  -7.390  1.00  0.00              
ATOM     25  N   ALA    75      32.523  63.002  -6.407  1.00  0.00              
ATOM     26  CA  ALA    75      33.846  62.746  -6.950  1.00  0.00              
ATOM     27  C   ALA    75      34.423  61.449  -6.406  1.00  0.00              
ATOM     28  O   ALA    75      34.973  60.642  -7.156  1.00  0.00              
ATOM     29  N   VAL    76      34.298  61.252  -5.100  1.00  0.00              
ATOM     30  CA  VAL    76      34.805  60.044  -4.466  1.00  0.00              
ATOM     31  C   VAL    76      34.145  58.786  -5.058  1.00  0.00              
ATOM     32  O   VAL    76      34.798  57.750  -5.231  1.00  0.00              
ATOM     33  N   LEU    77      32.854  58.876  -5.372  1.00  0.00              
ATOM     34  CA  LEU    77      32.153  57.736  -5.953  1.00  0.00              
ATOM     35  C   LEU    77      32.711  57.473  -7.342  1.00  0.00              
ATOM     36  O   LEU    77      32.895  56.316  -7.748  1.00  0.00              
ATOM     37  N   ARG    78      32.991  58.563  -8.058  1.00  0.00              
ATOM     38  CA  ARG    78      33.556  58.513  -9.405  1.00  0.00              
ATOM     39  C   ARG    78      34.976  57.932  -9.376  1.00  0.00              
ATOM     40  O   ARG    78      35.273  56.968 -10.090  1.00  0.00              
ATOM     41  N   LYS    79      35.849  58.502  -8.551  1.00  0.00              
ATOM     42  CA  LYS    79      37.214  57.996  -8.458  1.00  0.00              
ATOM     43  C   LYS    79      37.240  56.551  -7.986  1.00  0.00              
ATOM     44  O   LYS    79      38.055  55.738  -8.445  1.00  0.00              
ATOM     45  N   LEU    80      36.341  56.243  -7.059  1.00  0.00              
ATOM     46  CA  LEU    80      36.255  54.908  -6.507  1.00  0.00              
ATOM     47  C   LEU    80      35.899  53.916  -7.607  1.00  0.00              
ATOM     48  O   LEU    80      36.556  52.883  -7.763  1.00  0.00              
ATOM     49  N   ILE    81      34.863  54.230  -8.375  1.00  0.00              
ATOM     50  CA  ILE    81      34.457  53.343  -9.456  1.00  0.00              
ATOM     51  C   ILE    81      35.560  53.191 -10.505  1.00  0.00              
ATOM     52  O   ILE    81      35.772  52.101 -11.053  1.00  0.00              
ATOM     53  N   GLU    82      36.258  54.281 -10.795  1.00  0.00              
ATOM     54  CA  GLU    82      37.311  54.217 -11.795  1.00  0.00              
ATOM     55  C   GLU    82      38.475  53.334 -11.360  1.00  0.00              
ATOM     56  O   GLU    82      39.047  52.618 -12.180  1.00  0.00              
ATOM     57  N   ASP    83      38.832  53.371 -10.078  1.00  0.00              
ATOM     58  CA  ASP    83      39.930  52.532  -9.608  1.00  0.00              
ATOM     59  C   ASP    83      39.602  51.065  -9.863  1.00  0.00              
ATOM     60  O   ASP    83      40.458  50.294 -10.308  1.00  0.00              
ATOM     61  N   ALA    84      38.363  50.673  -9.581  1.00  0.00              
ATOM     62  CA  ALA    84      37.974  49.290  -9.813  1.00  0.00              
ATOM     63  C   ALA    84      37.882  49.012 -11.315  1.00  0.00              
ATOM     64  O   ALA    84      38.286  47.947 -11.776  1.00  0.00              
ATOM     65  N   ASP    85      37.368  49.969 -12.082  1.00  0.00              
ATOM     66  CA  ASP    85      37.266  49.785 -13.525  1.00  0.00              
ATOM     67  C   ASP    85      38.645  49.545 -14.134  1.00  0.00              
ATOM     68  O   ASP    85      38.836  48.598 -14.884  1.00  0.00              
ATOM     69  N   LYS    86      39.602  50.406 -13.807  1.00  0.00              
ATOM     70  CA  LYS    86      40.957  50.275 -14.330  1.00  0.00              
ATOM     71  C   LYS    86      41.606  48.966 -13.881  1.00  0.00              
ATOM     72  O   LYS    86      42.325  48.325 -14.639  1.00  0.00              
ATOM     73  N   GLU    87      41.346  48.571 -12.642  1.00  0.00              
ATOM     74  CA  GLU    87      41.912  47.344 -12.113  1.00  0.00              
ATOM     75  C   GLU    87      41.471  46.083 -12.861  1.00  0.00              
ATOM     76  O   GLU    87      42.169  45.067 -12.837  1.00  0.00              
ATOM     77  N   GLY    95      40.310  46.160 -13.507  1.00  0.00              
ATOM     78  CA  GLY    95      39.728  45.045 -14.257  1.00  0.00              
ATOM     79  C   GLY    95      39.675  43.735 -13.466  1.00  0.00              
ATOM     80  O   GLY    95      38.891  43.620 -12.519  1.00  0.00              
ATOM     81  N   VAL    96      40.509  42.761 -13.833  1.00  0.00              
ATOM     82  CA  VAL    96      40.496  41.456 -13.166  1.00  0.00              
ATOM     83  C   VAL    96      41.536  41.288 -12.059  1.00  0.00              
ATOM     84  O   VAL    96      41.839  40.169 -11.626  1.00  0.00              
ATOM     85  N   CYS    97      42.094  42.407 -11.617  1.00  0.00              
ATOM     86  CA  CYS    97      43.060  42.409 -10.526  1.00  0.00              
ATOM     87  C   CYS    97      42.628  43.562  -9.608  1.00  0.00              
ATOM     88  O   CYS    97      43.378  44.510  -9.376  1.00  0.00              
ATOM     89  N   SER    98      41.391  43.491  -9.083  1.00  0.00              
ATOM     90  CA  SER    98      40.869  44.534  -8.201  1.00  0.00              
ATOM     91  C   SER    98      41.713  44.756  -6.971  1.00  0.00              
ATOM     92  O   SER    98      42.313  43.833  -6.430  1.00  0.00              
ATOM     93  N   ASN    99      41.780  46.002  -6.516  1.00  0.00              
ATOM     94  CA  ASN    99      42.569  46.280  -5.322  1.00  0.00              
ATOM     95  C   ASN    99      41.753  45.702  -4.169  1.00  0.00              
ATOM     96  O   ASN    99      40.525  45.559  -4.288  1.00  0.00              
ATOM     97  N   MET   100      42.402  45.358  -3.065  1.00  0.00              
ATOM     98  CA  MET   100      41.659  44.817  -1.921  1.00  0.00              
ATOM     99  C   MET   100      41.021  45.964  -1.133  1.00  0.00              
ATOM    100  O   MET   100      41.295  47.132  -1.395  1.00  0.00              
ATOM    101  N   ARG   101      40.163  45.622  -0.176  1.00  0.00              
ATOM    102  CA  ARG   101      39.493  46.611   0.664  1.00  0.00              
ATOM    103  C   ARG   101      40.542  47.470   1.382  1.00  0.00              
ATOM    104  O   ARG   101      40.479  48.701   1.358  1.00  0.00              
ATOM    105  N   ALA   102      41.508  46.817   2.022  1.00  0.00              
ATOM    106  CA  ALA   102      42.564  47.536   2.733  1.00  0.00              
ATOM    107  C   ALA   102      43.349  48.450   1.804  1.00  0.00              
ATOM    108  O   ALA   102      43.635  49.594   2.154  1.00  0.00              
ATOM    109  N   ASP   103      43.700  47.948   0.620  1.00  0.00              
ATOM    110  CA  ASP   103      44.446  48.741  -0.353  1.00  0.00              
ATOM    111  C   ASP   103      43.702  50.030  -0.687  1.00  0.00              
ATOM    112  O   ASP   103      44.263  51.123  -0.609  1.00  0.00              
ATOM    113  N   LEU   104      42.438  49.897  -1.070  1.00  0.00              
ATOM    114  CA  LEU   104      41.630  51.062  -1.411  1.00  0.00              
ATOM    115  C   LEU   104      41.544  51.994  -0.207  1.00  0.00              
ATOM    116  O   LEU   104      41.629  53.214  -0.342  1.00  0.00              
ATOM    117  N   GLU   105      41.368  51.408   0.971  1.00  0.00              
ATOM    118  CA  GLU   105      41.270  52.187   2.196  1.00  0.00              
ATOM    119  C   GLU   105      42.477  53.108   2.338  1.00  0.00              
ATOM    120  O   GLU   105      42.335  54.301   2.605  1.00  0.00              
ATOM    121  N   ALA   106      43.667  52.542   2.158  1.00  0.00              
ATOM    122  CA  ALA   106      44.884  53.325   2.279  1.00  0.00              
ATOM    123  C   ALA   106      45.030  54.383   1.198  1.00  0.00              
ATOM    124  O   ALA   106      45.261  55.560   1.485  1.00  0.00              
ATOM    125  N   ILE   107      44.887  53.955  -0.051  1.00  0.00              
ATOM    126  CA  ILE   107      45.010  54.841  -1.198  1.00  0.00              
ATOM    127  C   ILE   107      44.185  56.114  -1.037  1.00  0.00              
ATOM    128  O   ILE   107      44.717  57.219  -1.125  1.00  0.00              
ATOM    129  N   LEU   108      42.889  55.958  -0.801  1.00  0.00              
ATOM    130  CA  LEU   108      41.996  57.102  -0.635  1.00  0.00              
ATOM    131  C   LEU   108      41.999  57.584   0.810  1.00  0.00              
ATOM    132  O   LEU   108      41.283  58.518   1.169  1.00  0.00              
ATOM    133  N   PRO   109      42.801  56.927   1.635  1.00  0.00              
ATOM    134  CA  PRO   109      42.895  57.255   3.049  1.00  0.00              
ATOM    135  C   PRO   109      41.524  57.465   3.684  1.00  0.00              
ATOM    136  O   PRO   109      41.153  58.584   4.050  1.00  0.00              
END
