
#######################################################
#                                                     #
#                        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 T0304AL333_4-D1
# Molecule2: number of CA atoms  101 (  799),  selected   34 , name T0304_D1.pdb
# PARAMETERS: T0304AL333_4-D1.T0304_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:    14        17 - 30          4.18    20.76
  LONGEST_CONTINUOUS_SEGMENT:    14        21 - 34          4.89    14.56
  LONGEST_CONTINUOUS_SEGMENT:    14        30 - 43          4.85    15.68
  LONGEST_CONTINUOUS_SEGMENT:    14        31 - 44          4.39    16.43
  LONGEST_CONTINUOUS_SEGMENT:    14        35 - 48          4.94    19.40
  LONGEST_CONTINUOUS_SEGMENT:    14        36 - 49          4.77    20.92
  LONGEST_CONTINUOUS_SEGMENT:    14        37 - 50          4.98    22.60
  LCS_AVERAGE:     13.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        23 - 30          1.74    15.21
  LONGEST_CONTINUOUS_SEGMENT:     8        31 - 38          1.83    18.30
  LCS_AVERAGE:      6.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        31 - 36          0.90    17.98
  LONGEST_CONTINUOUS_SEGMENT:     6        44 - 49          0.94    24.56
  LCS_AVERAGE:      4.46

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:  101
LCS_GDT     R      17     R      17      3    3   14     0    3    3    3    4    5    7    9   10   11   13   14   14   14   15   15   17   18   19   19 
LCS_GDT     P      18     P      18      3    3   14     0    3    3    3    4    5    7    9   10   11   13   14   14   14   15   15   17   18   19   19 
LCS_GDT     W      19     W      19      3    3   14     1    3    3    3    3    4    4    8    8   11   13   14   14   14   15   15   17   18   19   19 
LCS_GDT     W      20     W      20      3    3   14     0    3    3    3    3    4    4    6    8   10   13   14   14   14   15   15   17   18   19   19 
LCS_GDT     G      21     G      21      4    4   14     3    4    4    4    5    7    7    9   10   11   13   14   14   14   16   16   17   19   20   21 
LCS_GDT     L      22     L      22      4    4   14     3    4    4    4    4    6    6    9   10   11   13   14   14   15   16   17   18   19   20   21 
LCS_GDT     P      23     P      23      4    8   14     3    4    5    7    8    9    9    9   10   11   13   14   14   15   16   17   18   19   20   21 
LCS_GDT     C      24     C      24      5    8   14     3    5    5    6    8    9    9    9   10   11   13   14   14   15   16   17   18   19   20   21 
LCS_GDT     T      25     T      25      5    8   14     3    5    5    7    8    9    9    9   10   11   13   14   14   15   16   17   18   19   20   21 
LCS_GDT     V      26     V      26      5    8   14     3    5    5    7    8    9    9    9   10   11   13   14   14   15   16   17   18   19   20   21 
LCS_GDT     T      27     T      27      5    8   14     3    5    5    7    8    9    9    9   10   11   13   14   14   15   16   17   18   19   19   21 
LCS_GDT     P      28     P      28      5    8   14     3    5    5    7    8    9    9    9   10   11   13   14   14   15   16   17   18   19   19   21 
LCS_GDT     C      29     C      29      4    8   14     3    4    5    7    8    9    9    9   10   11   13   14   14   15   16   17   18   19   20   21 
LCS_GDT     F      30     F      30      4    8   14     3    4    5    7    8    9    9    9   10   11   12   14   14   15   16   17   18   19   20   21 
LCS_GDT     G      31     G      31      6    8   14     3    5    6    6    7    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     A      32     A      32      6    8   14     3    5    6    7    8    9    9   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     R      33     R      33      6    8   14     3    5    6    6    7    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     L      34     L      34      6    8   14     3    5    6    6    7    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     V      35     V      35      6    8   14     3    5    6    6    7    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     Q      36     Q      36      6    8   14     3    3    6    6    6    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     E      37     E      37      3    8   14     3    4    4    5    7    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     G      38     G      38      3    8   14     3    3    4    5    7    8    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     N      39     N      39      3    5   14     3    4    4    4    5    7    7    9    9   10   10   11   12   14   16   16   18   19   20   21 
LCS_GDT     R      40     R      40      3    5   14     3    4    4    4    4    6    7   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     L      41     L      41      3    5   14     0    4    4    5    5    7    8   10   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     H      42     H      42      3    3   14     1    3    4    5    5    5    8    9   10   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     Y      43     Y      43      3    6   14     1    3    5    5    6    7    8    9   11   12   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     L      44     L      44      6    6   14     4    5    5    6    6    6    7    9    9   11   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     A      45     A      45      6    6   14     4    5    5    6    6    6    6    8    9   11   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     D      46     D      46      6    6   14     4    5    5    6    6    6    6    8    9   11   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     R      47     R      47      6    6   14     4    5    5    6    6    6    6    8    9   11   12   13   16   17   17   17   18   19   20   21 
LCS_GDT     A      48     A      48      6    6   14     3    5    5    6    6    6    6    8    9   11   11   13   13   17   17   17   18   18   19   20 
LCS_GDT     G      49     G      49      6    6   14     0    3    5    6    6    6    6    8    9   11   11   13   13   13   16   16   18   18   19   19 
LCS_GDT     I      50     I      50      3    4   14     0    3    3    3    4    4    5    6    7    8    8   11   11   13   16   16   16   17   17   18 
LCS_AVERAGE  LCS_A:   8.16  (   4.46    6.17   13.86 )

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      4      5      6      7      8      9      9     10     11     12     13     14     16     17     17     17     18     19     20     21 
GDT PERCENT_CA   3.96   4.95   5.94   6.93   7.92   8.91   8.91   9.90  10.89  11.88  12.87  13.86  15.84  16.83  16.83  16.83  17.82  18.81  19.80  20.79
GDT RMS_LOCAL    0.28   0.48   0.90   1.49   1.69   1.87   1.87   2.65   2.96   3.10   4.00   4.18   4.87   5.15   5.15   5.15   5.62   6.08   6.35   6.65
GDT RMS_ALL_CA  24.95  24.15  17.98  15.10  14.98  14.94  14.94  17.28  16.86  16.72  21.41  20.76  17.12  17.41  17.41  17.41  17.96  14.86  14.87  14.47

#      Molecule1      Molecule2       DISTANCE
LGA    R      17      R      17         31.729
LGA    P      18      P      18         28.282
LGA    W      19      W      19         22.372
LGA    W      20      W      20         19.713
LGA    G      21      G      21         12.224
LGA    L      22      L      22         12.324
LGA    P      23      P      23         16.256
LGA    C      24      C      24         22.680
LGA    T      25      T      25         25.191
LGA    V      26      V      26         26.950
LGA    T      27      T      27         26.916
LGA    P      28      P      28         25.433
LGA    C      29      C      29         18.268
LGA    F      30      F      30         13.295
LGA    G      31      G      31          1.974
LGA    A      32      A      32          1.554
LGA    R      33      R      33          0.437
LGA    L      34      L      34          1.738
LGA    V      35      V      35          3.187
LGA    Q      36      Q      36          2.477
LGA    E      37      E      37          3.252
LGA    G      38      G      38          3.220
LGA    N      39      N      39          7.015
LGA    R      40      R      40          3.912
LGA    L      41      L      41          3.811
LGA    H      42      H      42          5.809
LGA    Y      43      Y      43          5.576
LGA    L      44      L      44         12.408
LGA    A      45      A      45         16.571
LGA    D      46      D      46         17.373
LGA    R      47      R      47         16.017
LGA    A      48      A      48         17.918
LGA    G      49      G      49         22.439
LGA    I      50      I      50         25.729

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  101    4.0     10    2.65     9.653     9.082     0.363

LGA_LOCAL      RMSD =  2.655  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.875  Number of atoms =   34 
Std_ALL_ATOMS  RMSD = 11.401  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.325705 * X  +   0.614354 * Y  +  -0.718669 * Z  +  71.898689
  Y_new =  -0.898098 * X  +  -0.438626 * Y  +   0.032065 * Z  +  86.394386
  Z_new =  -0.295528 * X  +   0.655879 * Y  +   0.694613 * Z  +  63.982655 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.756725   -2.384868  [ DEG:    43.3571   -136.6429 ]
  Theta =   0.300008    2.841585  [ DEG:    17.1892    162.8108 ]
  Phi   =  -1.918706    1.222887  [ DEG:  -109.9338     70.0662 ]
 
# 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: T0304AL333_4-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0304AL333_4-D1.T0304_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  101   4.0   10   2.65   9.082    11.40
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL333_4-D1
REMARK Aligment from pdb entry: 1glq_A
ATOM     65  N   ARG    17      42.423  43.708  55.431  1.00  0.00              
ATOM     66  CA  ARG    17      42.016  43.426  56.809  1.00  0.00              
ATOM     67  C   ARG    17      40.516  43.685  56.978  1.00  0.00              
ATOM     68  O   ARG    17      39.849  42.971  57.704  1.00  0.00              
ATOM     69  N   PRO    18      39.927  44.649  56.270  1.00  0.00              
ATOM     70  CA  PRO    18      38.501  44.935  56.336  1.00  0.00              
ATOM     71  C   PRO    18      37.727  43.720  55.880  1.00  0.00              
ATOM     72  O   PRO    18      36.841  43.243  56.588  1.00  0.00              
ATOM     73  N   TRP    19      38.062  43.162  54.697  1.00  0.00              
ATOM     74  CA  TRP    19      37.453  41.931  54.226  1.00  0.00              
ATOM     75  C   TRP    19      37.680  40.818  55.235  1.00  0.00              
ATOM     76  O   TRP    19      36.683  40.196  55.609  1.00  0.00              
ATOM     77  N   TRP    20      38.913  40.586  55.733  1.00  0.00              
ATOM     78  CA  TRP    20      39.166  39.505  56.662  1.00  0.00              
ATOM     79  C   TRP    20      38.269  39.643  57.877  1.00  0.00              
ATOM     80  O   TRP    20      37.624  38.659  58.283  1.00  0.00              
ATOM     81  N   GLY    21      36.195  29.302  56.123  1.00  0.00              
ATOM     82  CA  GLY    21      36.381  28.334  55.057  1.00  0.00              
ATOM     83  C   GLY    21      37.840  27.891  54.965  1.00  0.00              
ATOM     84  O   GLY    21      38.178  26.953  54.223  1.00  0.00              
ATOM     85  N   LEU    22      38.744  28.590  55.654  1.00  0.00              
ATOM     86  CA  LEU    22      40.155  28.254  55.684  1.00  0.00              
ATOM     87  C   LEU    22      40.336  27.092  56.637  1.00  0.00              
ATOM     88  O   LEU    22      39.825  27.160  57.757  1.00  0.00              
ATOM     89  N   PRO    23      41.061  26.036  56.244  1.00  0.00              
ATOM     90  CA  PRO    23      41.195  24.827  57.071  1.00  0.00              
ATOM     91  C   PRO    23      41.582  25.102  58.521  1.00  0.00              
ATOM     92  O   PRO    23      40.946  24.630  59.461  1.00  0.00              
ATOM     93  N   CYS    24      42.665  25.847  58.705  1.00  0.00              
ATOM     94  CA  CYS    24      43.101  26.194  60.048  1.00  0.00              
ATOM     95  C   CYS    24      42.700  27.639  60.424  1.00  0.00              
ATOM     96  O   CYS    24      43.360  28.235  61.289  1.00  0.00              
ATOM     97  N   THR    25      41.737  28.266  59.728  1.00  0.00              
ATOM     98  CA  THR    25      41.302  29.657  59.931  1.00  0.00              
ATOM     99  C   THR    25      42.350  30.710  59.585  1.00  0.00              
ATOM    100  O   THR    25      42.255  31.850  60.035  1.00  0.00              
ATOM    101  N   VAL    26      43.374  30.425  58.774  1.00  0.00              
ATOM    102  CA  VAL    26      44.440  31.394  58.523  1.00  0.00              
ATOM    103  C   VAL    26      44.838  31.356  57.075  1.00  0.00              
ATOM    104  O   VAL    26      44.451  30.418  56.363  1.00  0.00              
ATOM    105  N   THR    27      45.594  32.375  56.650  1.00  0.00              
ATOM    106  CA  THR    27      46.153  32.487  55.319  1.00  0.00              
ATOM    107  C   THR    27      47.679  32.335  55.412  1.00  0.00              
ATOM    108  O   THR    27      48.196  32.636  56.489  1.00  0.00              
ATOM    109  N   PRO    28      48.493  31.955  54.407  1.00  0.00              
ATOM    110  CA  PRO    28      48.072  31.805  52.995  1.00  0.00              
ATOM    111  C   PRO    28      47.176  30.642  52.577  1.00  0.00              
ATOM    112  O   PRO    28      47.111  29.604  53.235  1.00  0.00              
ATOM    113  N   CYS    29      46.423  30.859  51.513  1.00  0.00              
ATOM    114  CA  CYS    29      45.659  29.803  50.887  1.00  0.00              
ATOM    115  C   CYS    29      46.282  29.730  49.494  1.00  0.00              
ATOM    116  O   CYS    29      46.623  30.774  48.912  1.00  0.00              
ATOM    117  N   PHE    30      46.496  28.543  48.918  1.00  0.00              
ATOM    118  CA  PHE    30      47.157  28.418  47.623  1.00  0.00              
ATOM    119  C   PHE    30      46.354  27.456  46.748  1.00  0.00              
ATOM    120  O   PHE    30      45.903  26.422  47.246  1.00  0.00              
ATOM    121  N   GLY    31      43.518  22.097  40.691  1.00  0.00              
ATOM    122  CA  GLY    31      42.543  21.342  41.469  1.00  0.00              
ATOM    123  C   GLY    31      42.810  21.270  42.981  1.00  0.00              
ATOM    124  O   GLY    31      41.916  20.973  43.776  1.00  0.00              
ATOM    125  N   ALA    32      44.069  21.458  43.365  1.00  0.00              
ATOM    126  CA  ALA    32      44.526  21.314  44.738  1.00  0.00              
ATOM    127  C   ALA    32      44.564  22.642  45.508  1.00  0.00              
ATOM    128  O   ALA    32      45.227  23.605  45.108  1.00  0.00              
ATOM    129  N   ARG    33      43.872  22.668  46.638  1.00  0.00              
ATOM    130  CA  ARG    33      43.865  23.822  47.508  1.00  0.00              
ATOM    131  C   ARG    33      44.696  23.409  48.704  1.00  0.00              
ATOM    132  O   ARG    33      44.474  22.359  49.311  1.00  0.00              
ATOM    133  N   LEU    34      45.698  24.211  49.009  1.00  0.00              
ATOM    134  CA  LEU    34      46.577  23.948  50.124  1.00  0.00              
ATOM    135  C   LEU    34      46.559  25.121  51.089  1.00  0.00              
ATOM    136  O   LEU    34      46.225  26.263  50.716  1.00  0.00              
ATOM    137  N   VAL    35      46.822  24.788  52.349  1.00  0.00              
ATOM    138  CA  VAL    35      47.052  25.773  53.408  1.00  0.00              
ATOM    139  C   VAL    35      48.418  25.392  53.947  1.00  0.00              
ATOM    140  O   VAL    35      48.924  24.302  53.637  1.00  0.00              
ATOM    141  N   GLN    36      48.966  26.266  54.808  1.00  0.00              
ATOM    142  CA  GLN    36      50.269  26.153  55.467  1.00  0.00              
ATOM    143  C   GLN    36      51.418  26.519  54.531  1.00  0.00              
ATOM    144  O   GLN    36      51.795  25.739  53.633  1.00  0.00              
ATOM    145  N   GLU    37      52.069  27.690  54.748  1.00  0.00              
ATOM    146  CA  GLU    37      53.108  28.184  53.864  1.00  0.00              
ATOM    147  C   GLU    37      54.254  27.215  53.607  1.00  0.00              
ATOM    148  O   GLU    37      54.731  27.110  52.471  1.00  0.00              
ATOM    149  N   GLY    38      54.705  26.432  54.586  1.00  0.00              
ATOM    150  CA  GLY    38      55.807  25.518  54.303  1.00  0.00              
ATOM    151  C   GLY    38      55.336  24.276  53.565  1.00  0.00              
ATOM    152  O   GLY    38      56.122  23.693  52.831  1.00  0.00              
ATOM    153  N   ASN    39      54.063  23.881  53.722  1.00  0.00              
ATOM    154  CA  ASN    39      53.514  22.774  52.938  1.00  0.00              
ATOM    155  C   ASN    39      53.438  23.192  51.468  1.00  0.00              
ATOM    156  O   ASN    39      53.714  22.410  50.565  1.00  0.00              
ATOM    157  N   ARG    40      53.044  24.442  51.194  1.00  0.00              
ATOM    158  CA  ARG    40      53.011  24.998  49.848  1.00  0.00              
ATOM    159  C   ARG    40      54.431  25.078  49.284  1.00  0.00              
ATOM    160  O   ARG    40      54.648  24.703  48.117  1.00  0.00              
ATOM    161  N   LEU    41      55.432  25.531  50.052  1.00  0.00              
ATOM    162  CA  LEU    41      56.804  25.522  49.570  1.00  0.00              
ATOM    163  C   LEU    41      57.320  24.124  49.247  1.00  0.00              
ATOM    164  O   LEU    41      57.980  23.928  48.225  1.00  0.00              
ATOM    165  N   HIS    42      57.058  23.145  50.117  1.00  0.00              
ATOM    166  CA  HIS    42      57.479  21.768  49.866  1.00  0.00              
ATOM    167  C   HIS    42      56.730  21.213  48.653  1.00  0.00              
ATOM    168  O   HIS    42      57.346  20.548  47.833  1.00  0.00              
ATOM    169  N   TYR    43      55.456  21.528  48.447  1.00  0.00              
ATOM    170  CA  TYR    43      54.712  21.095  47.280  1.00  0.00              
ATOM    171  C   TYR    43      55.380  21.616  45.998  1.00  0.00              
ATOM    172  O   TYR    43      55.574  20.877  45.023  1.00  0.00              
ATOM    173  N   LEU    44      55.725  22.903  45.959  1.00  0.00              
ATOM    174  CA  LEU    44      56.365  23.486  44.785  1.00  0.00              
ATOM    175  C   LEU    44      57.758  22.903  44.580  1.00  0.00              
ATOM    176  O   LEU    44      58.179  22.664  43.444  1.00  0.00              
ATOM    177  N   ALA    45      58.475  22.576  45.653  1.00  0.00              
ATOM    178  CA  ALA    45      59.793  21.960  45.546  1.00  0.00              
ATOM    179  C   ALA    45      59.645  20.590  44.911  1.00  0.00              
ATOM    180  O   ALA    45      60.384  20.230  44.002  1.00  0.00              
ATOM    181  N   ASP    46      58.646  19.829  45.318  1.00  0.00              
ATOM    182  CA  ASP    46      58.394  18.479  44.814  1.00  0.00              
ATOM    183  C   ASP    46      57.953  18.549  43.357  1.00  0.00              
ATOM    184  O   ASP    46      58.591  17.965  42.477  1.00  0.00              
ATOM    185  N   ARG    47      56.960  19.374  43.039  1.00  0.00              
ATOM    186  CA  ARG    47      56.455  19.375  41.697  1.00  0.00              
ATOM    187  C   ARG    47      57.337  20.066  40.697  1.00  0.00              
ATOM    188  O   ARG    47      57.225  19.747  39.516  1.00  0.00              
ATOM    189  N   ALA    48      58.215  20.998  41.072  1.00  0.00              
ATOM    190  CA  ALA    48      59.028  21.679  40.093  1.00  0.00              
ATOM    191  C   ALA    48      60.460  21.172  40.114  1.00  0.00              
ATOM    192  O   ALA    48      61.331  21.726  39.443  1.00  0.00              
ATOM    193  N   GLY    49      60.749  20.104  40.855  1.00  0.00              
ATOM    194  CA  GLY    49      62.070  19.519  40.863  1.00  0.00              
ATOM    195  C   GLY    49      63.109  20.308  41.647  1.00  0.00              
ATOM    196  O   GLY    49      64.291  20.351  41.303  1.00  0.00              
ATOM    197  N   ILE    50      62.708  20.867  42.775  1.00  0.00              
ATOM    198  CA  ILE    50      63.560  21.668  43.637  1.00  0.00              
ATOM    199  C   ILE    50      63.687  21.052  45.004  1.00  0.00              
ATOM    200  O   ILE    50      63.690  21.793  45.999  1.00  0.00              
END
