
#######################################################
#                                                     #
#                        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   29 (  116),  selected   22 , name T0300AL242_5
# Molecule2: number of CA atoms   89 (  695),  selected   22 , name T0300
# PARAMETERS: T0300AL242_5.T0300  -3  -ie  -d:4  -o1  -sda  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        12 - 40          4.95     4.95
  LCS_AVERAGE:     24.72

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        12 - 31          0.36     5.56
  LCS_AVERAGE:     20.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20        12 - 31          0.36     5.56
  LCS_AVERAGE:     20.43

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:   89
LCS_GDT     E      12     E      12     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     M      13     M      13     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     V      14     V      14     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     K      15     K      15     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     E      16     E      16     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     V      17     V      17     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     E      18     E      18     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     R      19     R      19     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     L      20     L      20     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     K      21     K      21     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     L      22     L      22     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     E      23     E      23     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     N      24     N      24     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     K      25     K      25     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     T      26     T      26     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     L      27     L      27     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     K      28     K      28     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     Q      29     Q      29     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     K      30     K      30     20   20   22    19   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     V      31     V      31     20   20   22     8   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   20   21 
LCS_GDT     S      39     S      39      0    0   22     0    0    1    2    2    4    4    4    4    4    4    6    7    8   10   11   14   17   20   21 
LCS_GDT     D      40     D      40      0    0   22     0    0    0    2    2    4    4    4    4    4    4    5    5    6    7    8    8    9    9    9 
LCS_AVERAGE  LCS_A:  21.86  (  20.43   20.43   24.72 )

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     19     20     20     20     20     20     20     20     20     20     20     20     20     20     20     20     20     20     20     21 
GDT PERCENT_CA  21.35  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  22.47  23.60
GDT RMS_LOCAL    0.29   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   3.11
GDT RMS_ALL_CA   5.58   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.56   5.11

#      Molecule1      Molecule2       DISTANCE
LGA    E      12      E      12          0.346
LGA    M      13      M      13          0.228
LGA    V      14      V      14          0.237
LGA    K      15      K      15          0.294
LGA    E      16      E      16          0.289
LGA    V      17      V      17          0.243
LGA    E      18      E      18          0.553
LGA    R      19      R      19          0.285
LGA    L      20      L      20          0.080
LGA    K      21      K      21          0.259
LGA    L      22      L      22          0.185
LGA    E      23      E      23          0.304
LGA    N      24      N      24          0.386
LGA    K      25      K      25          0.395
LGA    T      26      T      26          0.338
LGA    L      27      L      27          0.205
LGA    K      28      K      28          0.098
LGA    Q      29      Q      29          0.447
LGA    K      30      K      30          0.211
LGA    V      31      V      31          0.879
LGA    S      39      S      39         15.274
LGA    D      40      D      40         21.067

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29   89    4.0     20    0.36    22.472    21.961     4.388

LGA_LOCAL      RMSD =  0.356  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.558  Number of atoms =   22 
Std_ALL_ATOMS  RMSD =  4.947  (standard rmsd on all 22 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.664361 * X  +   0.217763 * Y  +  -0.714985 * Z  +  38.192204
  Y_new =  -0.655904 * X  +   0.288784 * Y  +   0.697419 * Z  + -19.094641
  Z_new =   0.358349 * X  +   0.932300 * Y  +  -0.049025 * Z  + -71.283051 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.623333   -1.518259  [ DEG:    93.0101    -86.9899 ]
  Theta =  -0.366498   -2.775094  [ DEG:   -20.9988   -159.0012 ]
  Phi   =  -2.362600    0.778993  [ DEG:  -135.3670     44.6330 ]
 
# 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: T0300AL242_5                                  
REMARK     2: T0300                                         
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0300AL242_5.T0300 -3 -ie -d:4 -o1 -sda 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29   89   4.0   20   0.36  21.961     4.95
REMARK  ---------------------------------------------------------- 
MOLECULE T0300AL242_5
REMARK Aligment from pdb entry: 1p9i_A
ATOM      1  N   GLU    12      35.169  -4.956  -6.751  1.00  0.00              
ATOM      2  CA  GLU    12      34.521  -4.992  -8.064  1.00  0.00              
ATOM      3  C   GLU    12      35.490  -4.805  -9.206  1.00  0.00              
ATOM      4  O   GLU    12      35.168  -5.028 -10.379  1.00  0.00              
ATOM      5  N   MET    13      36.701  -4.360  -8.941  1.00  0.00              
ATOM      6  CA  MET    13      37.663  -4.225 -10.045  1.00  0.00              
ATOM      7  C   MET    13      38.015  -5.597 -10.609  1.00  0.00              
ATOM      8  O   MET    13      38.084  -5.749 -11.824  1.00  0.00              
ATOM      9  N   VAL    14      38.199  -6.623  -9.762  1.00  0.00              
ATOM     10  CA  VAL    14      38.493  -7.941 -10.313  1.00  0.00              
ATOM     11  C   VAL    14      37.319  -8.450 -11.119  1.00  0.00              
ATOM     12  O   VAL    14      37.524  -9.190 -12.084  1.00  0.00              
ATOM     13  N   LYS    15      36.092  -8.143 -10.750  1.00  0.00              
ATOM     14  CA  LYS    15      34.968  -8.594 -11.563  1.00  0.00              
ATOM     15  C   LYS    15      34.947  -7.926 -12.910  1.00  0.00              
ATOM     16  O   LYS    15      34.624  -8.565 -13.910  1.00  0.00              
ATOM     17  N   GLU    16      35.313  -6.635 -12.959  1.00  0.00              
ATOM     18  CA  GLU    16      35.412  -5.979 -14.276  1.00  0.00              
ATOM     19  C   GLU    16      36.522  -6.610 -15.108  1.00  0.00              
ATOM     20  O   GLU    16      36.339  -6.886 -16.300  1.00  0.00              
ATOM     21  N   VAL    17      37.686  -6.854 -14.510  1.00  0.00              
ATOM     22  CA  VAL    17      38.772  -7.518 -15.211  1.00  0.00              
ATOM     23  C   VAL    17      38.265  -8.867 -15.747  1.00  0.00              
ATOM     24  O   VAL    17      38.516  -9.219 -16.886  1.00  0.00              
ATOM     25  N   GLU    18      37.581  -9.657 -14.919  1.00  0.00              
ATOM     26  CA  GLU    18      37.123 -10.951 -15.320  1.00  0.00              
ATOM     27  C   GLU    18      36.161 -10.869 -16.488  1.00  0.00              
ATOM     28  O   GLU    18      36.189 -11.662 -17.437  1.00  0.00              
ATOM     29  N   ARG    19      35.269  -9.917 -16.457  1.00  0.00              
ATOM     30  CA  ARG    19      34.306  -9.777 -17.532  1.00  0.00              
ATOM     31  C   ARG    19      34.989  -9.385 -18.850  1.00  0.00              
ATOM     32  O   ARG    19      34.700  -9.927 -19.884  1.00  0.00              
ATOM     33  N   LEU    20      35.920  -8.436 -18.758  1.00  0.00              
ATOM     34  CA  LEU    20      36.678  -8.023 -19.918  1.00  0.00              
ATOM     35  C   LEU    20      37.495  -9.172 -20.489  1.00  0.00              
ATOM     36  O   LEU    20      37.598  -9.332 -21.723  1.00  0.00              
ATOM     37  N   LYS    21      38.088  -9.984 -19.599  1.00  0.00              
ATOM     38  CA  LYS    21      38.858 -11.130 -20.058  1.00  0.00              
ATOM     39  C   LYS    21      37.961 -12.135 -20.777  1.00  0.00              
ATOM     40  O   LYS    21      38.317 -12.703 -21.803  1.00  0.00              
ATOM     41  N   LEU    22      36.810 -12.373 -20.186  1.00  0.00              
ATOM     42  CA  LEU    22      35.907 -13.318 -20.825  1.00  0.00              
ATOM     43  C   LEU    22      35.485 -12.803 -22.202  1.00  0.00              
ATOM     44  O   LEU    22      35.417 -13.547 -23.162  1.00  0.00              
ATOM     45  N   GLU    23      35.124 -11.527 -22.291  1.00  0.00              
ATOM     46  CA  GLU    23      34.710 -10.921 -23.549  1.00  0.00              
ATOM     47  C   GLU    23      35.841 -10.995 -24.562  1.00  0.00              
ATOM     48  O   GLU    23      35.586 -11.350 -25.712  1.00  0.00              
ATOM     49  N   ASN    24      37.055 -10.676 -24.099  1.00  0.00              
ATOM     50  CA  ASN    24      38.178 -10.719 -25.037  1.00  0.00              
ATOM     51  C   ASN    24      38.377 -12.112 -25.590  1.00  0.00              
ATOM     52  O   ASN    24      38.681 -12.299 -26.770  1.00  0.00              
ATOM     53  N   LYS    25      38.266 -13.122 -24.725  1.00  0.00              
ATOM     54  CA  LYS    25      38.451 -14.496 -25.223  1.00  0.00              
ATOM     55  C   LYS    25      37.383 -14.835 -26.239  1.00  0.00              
ATOM     56  O   LYS    25      37.675 -15.446 -27.283  1.00  0.00              
ATOM     57  N   THR    26      36.144 -14.458 -25.953  1.00  0.00              
ATOM     58  CA  THR    26      35.046 -14.729 -26.873  1.00  0.00              
ATOM     59  C   THR    26      35.230 -14.037 -28.196  1.00  0.00              
ATOM     60  O   THR    26      35.017 -14.592 -29.295  1.00  0.00              
ATOM     61  N   LEU    27      35.645 -12.779 -28.127  1.00  0.00              
ATOM     62  CA  LEU    27      35.823 -12.022 -29.372  1.00  0.00              
ATOM     63  C   LEU    27      36.946 -12.609 -30.189  1.00  0.00              
ATOM     64  O   LEU    27      36.868 -12.655 -31.407  1.00  0.00              
ATOM     65  N   LYS    28      38.044 -13.025 -29.563  1.00  0.00              
ATOM     66  CA  LYS    28      39.150 -13.632 -30.311  1.00  0.00              
ATOM     67  C   LYS    28      38.648 -14.893 -31.012  1.00  0.00              
ATOM     68  O   LYS    28      39.036 -15.154 -32.144  1.00  0.00              
ATOM     69  N   GLN    29      37.774 -15.667 -30.364  1.00  0.00              
ATOM     70  CA  GLN    29      37.314 -16.889 -30.990  1.00  0.00              
ATOM     71  C   GLN    29      36.370 -16.551 -32.143  1.00  0.00              
ATOM     72  O   GLN    29      36.352 -17.222 -33.188  1.00  0.00              
ATOM     73  N   LYS    30      35.578 -15.495 -31.945  1.00  0.00              
ATOM     74  CA  LYS    30      34.681 -15.075 -33.020  1.00  0.00              
ATOM     75  C   LYS    30      35.478 -14.572 -34.225  1.00  0.00              
ATOM     76  O   LYS    30      35.116 -14.857 -35.374  1.00  0.00              
ATOM     77  N   VAL    31      36.547 -13.847 -33.956  1.00  0.00              
ATOM     78  CA  VAL    31      37.427 -13.453 -35.065  1.00  0.00              
ATOM     79  C   VAL    31      37.952 -14.690 -35.780  1.00  0.00              
ATOM     80  O   VAL    31      37.962 -14.711 -37.008  1.00  0.00              
ATOM     81  N   LYS    32      38.363 -15.727 -35.066  1.00  0.00              
ATOM     82  CA  LYS    32      38.911 -16.933 -35.675  1.00  0.00              
ATOM     83  C   LYS    32      37.856 -17.588 -36.545  1.00  0.00              
ATOM     84  O   LYS    32      38.125 -18.044 -37.655  1.00  0.00              
ATOM     85  N   SER    33      36.626 -17.629 -36.047  1.00  0.00              
ATOM     86  CA  SER    33      35.521 -18.216 -36.792  1.00  0.00              
ATOM     87  C   SER    33      35.302 -17.431 -38.065  1.00  0.00              
ATOM     88  O   SER    33      35.188 -17.972 -39.171  1.00  0.00              
ATOM     89  N   SER    34      35.211 -16.098 -37.943  1.00  0.00              
ATOM     90  CA  SER    34      34.883 -15.287 -39.119  1.00  0.00              
ATOM     91  C   SER    34      35.998 -15.242 -40.128  1.00  0.00              
ATOM     92  O   SER    34      35.755 -15.250 -41.316  1.00  0.00              
ATOM     93  N   GLY    35      37.247 -15.255 -39.686  1.00  0.00              
ATOM     94  CA  GLY    35      38.384 -15.432 -40.584  1.00  0.00              
ATOM     95  C   GLY    35      38.277 -16.681 -41.439  1.00  0.00              
ATOM     96  O   GLY    35      38.460 -16.700 -42.648  1.00  0.00              
ATOM     97  N   ALA    36      37.968 -17.754 -40.711  1.00  0.00              
ATOM     98  CA  ALA    36      37.824 -19.053 -41.428  1.00  0.00              
ATOM     99  C   ALA    36      36.683 -18.989 -42.396  1.00  0.00              
ATOM    100  O   ALA    36      36.717 -19.550 -43.519  1.00  0.00              
ATOM    101  N   VAL    37      35.595 -18.292 -42.077  1.00  0.00              
ATOM    102  CA  VAL    37      34.486 -18.163 -42.984  1.00  0.00              
ATOM    103  C   VAL    37      34.864 -17.312 -44.198  1.00  0.00              
ATOM    104  O   VAL    37      34.455 -17.614 -45.316  1.00  0.00              
ATOM    105  N   SER    38      35.656 -16.263 -43.999  1.00  0.00              
ATOM    106  CA  SER    38      36.109 -15.429 -45.098  1.00  0.00              
ATOM    107  C   SER    38      36.922 -16.287 -46.057  1.00  0.00              
ATOM    108  O   SER    38      36.865 -16.129 -47.270  1.00  0.00              
ATOM    109  N   SER    39      37.688 -17.256 -45.509  1.00  0.00              
ATOM    110  CA  SER    39      38.492 -18.115 -46.382  1.00  0.00              
ATOM    111  C   SER    39      37.624 -19.027 -47.221  1.00  0.00              
ATOM    112  O   SER    39      38.186 -19.644 -48.152  1.00  0.00              
ATOM    113  N   ASP    40      36.327 -19.120 -46.973  1.00  0.00              
ATOM    114  CA  ASP    40      35.461 -19.907 -47.896  1.00  0.00              
ATOM    115  C   ASP    40      35.117 -19.073 -49.099  1.00  0.00              
ATOM    116  O   ASP    40      35.233 -17.835 -49.087  1.00  0.00              
END
 1.00  0.00              
ATOM    104  O   VAL    37      34.455 -17.614 -45.316  1.00  0.00              
ATOM    105  N   SER    38      35.656 -16.263 -43.999  1.00  0.00              
ATOM    106  CA  SER    38      36.109 -15.429 -45.098  1.00  0.00              
ATOM    107  C   SER    38      36.922 -16.287 -46.057  1.00  0.00              
ATOM    108  O   SER    38      36.865 -16.129 -47.270  1.00  0.00              
ATOM    109  N   SER    39      37.688 -17.256 -45.509  1.00  0.00              
ATOM    110  CA  SER    39      38.492 -18.115 -46.382  1.00  0.00              
ATOM    111  C   SER    39      37.624 -19.027 -47.221  1.00  0.00              
ATOM    112  O   SER    39      38.186 -19.644 -48.152  1.00  0.00              
ATOM    113  N   ASP    40      36.327 -19.120 -46.973  1.00  0.00              
ATOM    114  CA  ASP    40      35.461 -19.907 -47.896  1.00  0.00              
ATOM    115  C   ASP    40      35.117 -19.073 -49.099  1.00  0.00              
ATOM    116  O   ASP    40      35.233 -17.835 -49.087  1.00  0.00              
END
