
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0356AL333_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected   30 , name T0356_D1.pdb
# PARAMETERS: T0356AL333_1-D1.T0356_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:    20        38 - 57          4.50    14.76
  LCS_AVERAGE:     13.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        45 - 53          1.94    14.72
  LCS_AVERAGE:      4.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        48 - 53          0.72    13.41
  LONGEST_CONTINUOUS_SEGMENT:     6        49 - 54          0.69    12.73
  LCS_AVERAGE:      3.28

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:  124
LCS_GDT     L      13     L      13      3    3   10     0    3    3    4    5    8    8   12   12   12   13   13   14   16   18   19   21   21   21   23 
LCS_GDT     T      14     T      14      3    3   10     0    3    3    3    5    8    8   12   12   12   13   13   14   15   18   19   21   21   21   23 
LCS_GDT     L      15     L      15      4    4   10     3    3    5    5    5    5    6    7    9   10   11   13   14   16   18   19   21   21   22   23 
LCS_GDT     L      16     L      16      4    4   10     3    3    4    4    4    5    5    7    9   10   13   14   15   16   18   19   21   21   22   23 
LCS_GDT     E      17     E      17      4    4   10     3    3    4    4    4    5    5    7    9   10   11   13   15   16   18   19   21   21   22   23 
LCS_GDT     Q      18     Q      18      4    5   10     3    4    4    5    5    5    5    7    9    9    9   11   12   13   15   17   18   20   22   23 
LCS_GDT     Q      19     Q      19      4    5   10     3    4    4    5    5    5    5    6    9    9    9   10   12   12   13   14   16   18   19   20 
LCS_GDT     G      20     G      20      4    5   10     3    4    4    5    5    5    5    6    9    9    9   10   12   12   13   14   15   16   17   18 
LCS_GDT     E      21     E      21      4    5   10     3    4    4    5    5    5    5    6    7    9    9   10   10   11   13   14   15   16   17   18 
LCS_GDT     L      22     L      22      3    5   10     3    3    3    5    5    5    5    6    9    9    9   10   12   12   13   15   16   18   22   23 
LCS_GDT     I      38     I      38      3    3   20     0    3    3    3    3    4    4    6    7   12   12   13   16   20   20   20   20   20   20   20 
LCS_GDT     A      39     A      39      3    3   20     1    3    3    3    3    4    5    9    9   12   16   19   19   20   20   20   20   20   22   23 
LCS_GDT     D      40     D      40      3    3   20     0    3    3    3    3    4    5    7   11   13   17   19   19   20   20   20   20   20   20   23 
LCS_GDT     R      41     R      41      3    3   20     0    3    3    3    3    4    5    7   11   13   17   19   19   20   20   20   20   20   22   23 
LCS_GDT     T      42     T      42      3    3   20     1    3    4    5    7   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     L      43     L      43      3    7   20     3    4    5    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     R      44     R      44      3    7   20     3    4    5    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     A      45     A      45      3    9   20     3    3    4    6    8   11   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     G      46     G      46      4    9   20     3    3    5    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     G      47     G      47      4    9   20     3    3    5    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     P      48     P      48      6    9   20     3    4    6    7    8   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     A      49     A      49      6    9   20     5    5    6    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     L      50     L      50      6    9   20     5    5    6    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     L      51     L      51      6    9   20     5    5    6    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     F      52     F      52      6    9   20     5    5    6    7    9   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     E      53     E      53      6    9   20     5    5    6    7    9   12   13   13   14   15   16   19   19   20   20   20   21   21   22   23 
LCS_GDT     N      54     N      54      6    7   20     3    5    6    7    8   12   13   13   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     P      55     P      55      4    5   20     3    4    4    5    6    6    8   12   14   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     K      56     K      56      4    5   20     3    4    4    5    6    8    9   12   13   15   17   19   19   20   20   20   21   21   22   23 
LCS_GDT     G      57     G      57      3    5   20     0    3    3    6    8    8    9   12   12   15   17   19   19   20   20   20   21   21   22   23 
LCS_AVERAGE  LCS_A:   7.14  (   3.28    4.70   13.44 )

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      6      7      9     12     13     13     14     15     17     19     19     20     20     20     21     21     22     23 
GDT PERCENT_CA   4.03   4.03   4.84   5.65   7.26   9.68  10.48  10.48  11.29  12.10  13.71  15.32  15.32  16.13  16.13  16.13  16.94  16.94  17.74  18.55
GDT RMS_LOCAL    0.37   0.37   0.69   1.05   1.90   2.35   2.49   2.49   2.79   3.27   3.98   4.24   4.24   4.50   4.50   4.50   5.95   5.95   6.88   6.61
GDT RMS_ALL_CA  12.92  12.92  12.73  13.20  14.20  14.09  14.23  14.23  14.02  14.16  14.87  14.75  14.75  14.76  14.76  14.76  10.15  10.15   9.34   9.92

#      Molecule1      Molecule2       DISTANCE
LGA    L      13      L      13         19.111
LGA    T      14      T      14         21.254
LGA    L      15      L      15         22.491
LGA    L      16      L      16         18.030
LGA    E      17      E      17         19.725
LGA    Q      18      Q      18         26.358
LGA    Q      19      Q      19         28.572
LGA    G      20      G      20         28.828
LGA    E      21      E      21         25.607
LGA    L      22      L      22         18.232
LGA    I      38      I      38         11.876
LGA    A      39      A      39          9.475
LGA    D      40      D      40          9.113
LGA    R      41      R      41          8.547
LGA    T      42      T      42          3.077
LGA    L      43      L      43          2.170
LGA    R      44      R      44          2.169
LGA    A      45      A      45          3.357
LGA    G      46      G      46          2.187
LGA    G      47      G      47          2.080
LGA    P      48      P      48          3.048
LGA    A      49      A      49          2.756
LGA    L      50      L      50          0.837
LGA    L      51      L      51          2.413
LGA    F      52      F      52          1.632
LGA    E      53      E      53          2.142
LGA    N      54      N      54          3.220
LGA    P      55      P      55          5.939
LGA    K      56      K      56          8.922
LGA    G      57      G      57         11.258

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30  124    4.0     13    2.49     9.073     8.607     0.503

LGA_LOCAL      RMSD =  2.485  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.231  Number of atoms =   30 
Std_ALL_ATOMS  RMSD =  9.092  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.573864 * X  +   0.770061 * Y  +  -0.278721 * Z  + -89.999054
  Y_new =  -0.814309 * X  +   0.572731 * Y  +  -0.094235 * Z  + 110.522141
  Z_new =   0.087066 * X  +   0.281043 * Y  +   0.955738 * Z  + -22.201311 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.285998   -2.855595  [ DEG:    16.3864   -163.6136 ]
  Theta =  -0.087176   -3.054417  [ DEG:    -4.9948   -175.0052 ]
  Phi   =  -0.956906    2.184687  [ DEG:   -54.8267    125.1733 ]
 
# 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: T0356AL333_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_1-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30  124   4.0   13   2.49   8.607     9.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_1-D1
REMARK Aligment from pdb entry: 1lwh_A
ATOM      9  N   LEU    13      54.025  66.892  91.492  1.00  0.00              
ATOM     10  CA  LEU    13      55.366  66.904  92.081  1.00  0.00              
ATOM     11  C   LEU    13      56.259  65.907  91.350  1.00  0.00              
ATOM     12  O   LEU    13      55.863  64.758  91.140  1.00  0.00              
ATOM     13  N   THR    14      57.454  66.356  90.964  1.00  0.00              
ATOM     14  CA  THR    14      58.442  65.517  90.277  1.00  0.00              
ATOM     15  C   THR    14      59.771  65.634  91.014  1.00  0.00              
ATOM     16  O   THR    14      60.341  66.720  91.090  1.00  0.00              
ATOM     17  N   LEU    15      60.271  64.527  91.552  1.00  0.00              
ATOM     18  CA  LEU    15      61.537  64.566  92.284  1.00  0.00              
ATOM     19  C   LEU    15      62.723  64.644  91.347  1.00  0.00              
ATOM     20  O   LEU    15      62.753  63.990  90.311  1.00  0.00              
ATOM     21  N   LEU    16      63.701  65.461  91.712  1.00  0.00              
ATOM     22  CA  LEU    16      64.894  65.607  90.895  1.00  0.00              
ATOM     23  C   LEU    16      66.141  65.281  91.707  1.00  0.00              
ATOM     24  O   LEU    16      67.193  65.009  91.141  1.00  0.00              
ATOM     25  N   GLU    17      66.024  65.305  93.030  1.00  0.00              
ATOM     26  CA  GLU    17      67.159  65.027  93.896  1.00  0.00              
ATOM     27  C   GLU    17      66.714  64.629  95.289  1.00  0.00              
ATOM     28  O   GLU    17      66.177  65.448  96.029  1.00  0.00              
ATOM     29  N   GLN    18      66.943  63.369  95.639  1.00  0.00              
ATOM     30  CA  GLN    18      66.570  62.845  96.950  1.00  0.00              
ATOM     31  C   GLN    18      67.816  62.425  97.737  1.00  0.00              
ATOM     32  O   GLN    18      68.095  61.233  97.881  1.00  0.00              
ATOM     33  N   GLN    19      68.562  63.396  98.245  1.00  0.00              
ATOM     34  CA  GLN    19      69.765  63.099  99.024  1.00  0.00              
ATOM     35  C   GLN    19      69.421  63.207 100.500  1.00  0.00              
ATOM     36  O   GLN    19      68.504  63.925 100.881  1.00  0.00              
ATOM     37  N   GLY    20      70.176  62.517 101.340  1.00  0.00              
ATOM     38  CA  GLY    20      69.949  62.559 102.783  1.00  0.00              
ATOM     39  C   GLY    20      69.891  63.996 103.314  1.00  0.00              
ATOM     40  O   GLY    20      68.914  64.392 103.940  1.00  0.00              
ATOM     41  N   GLU    21      70.930  64.778 103.047  1.00  0.00              
ATOM     42  CA  GLU    21      70.981  66.153 103.533  1.00  0.00              
ATOM     43  C   GLU    21      70.091  67.152 102.778  1.00  0.00              
ATOM     44  O   GLU    21      69.667  68.160 103.352  1.00  0.00              
ATOM     45  N   LEU    22      69.815  66.892 101.499  1.00  0.00              
ATOM     46  CA  LEU    22      68.979  67.805 100.725  1.00  0.00              
ATOM     47  C   LEU    22      68.047  67.188  99.681  1.00  0.00              
ATOM     48  O   LEU    22      68.243  66.082  99.190  1.00  0.00              
ATOM     49  N   ILE    38      67.027  67.959  99.336  1.00  0.00              
ATOM     50  CA  ILE    38      65.990  67.524  98.425  1.00  0.00              
ATOM     51  C   ILE    38      65.698  68.625  97.418  1.00  0.00              
ATOM     52  O   ILE    38      65.869  69.819  97.702  1.00  0.00              
ATOM     53  N   ALA    39      65.260  68.203  96.237  1.00  0.00              
ATOM     54  CA  ALA    39      64.921  69.110  95.152  1.00  0.00              
ATOM     55  C   ALA    39      63.809  68.445  94.358  1.00  0.00              
ATOM     56  O   ALA    39      63.888  67.249  94.074  1.00  0.00              
ATOM     57  N   ASP    40      62.763  69.209  94.038  1.00  0.00              
ATOM     58  CA  ASP    40      61.639  68.700  93.238  1.00  0.00              
ATOM     59  C   ASP    40      61.065  69.793  92.348  1.00  0.00              
ATOM     60  O   ASP    40      61.436  70.958  92.454  1.00  0.00              
ATOM     61  N   ARG    41      60.154  69.403  91.470  1.00  0.00              
ATOM     62  CA  ARG    41      59.547  70.329  90.530  1.00  0.00              
ATOM     63  C   ARG    41      58.014  70.298  90.560  1.00  0.00              
ATOM     64  O   ARG    41      57.391  69.237  90.483  1.00  0.00              
ATOM     65  N   THR    42      57.420  71.479  90.687  1.00  0.00              
ATOM     66  CA  THR    42      55.972  71.621  90.724  1.00  0.00              
ATOM     67  C   THR    42      55.554  72.068  89.347  1.00  0.00              
ATOM     68  O   THR    42      56.222  72.901  88.732  1.00  0.00              
ATOM     69  N   LEU    43      54.443  71.539  88.862  1.00  0.00              
ATOM     70  CA  LEU    43      54.001  71.924  87.544  1.00  0.00              
ATOM     71  C   LEU    43      52.581  71.468  87.260  1.00  0.00              
ATOM     72  O   LEU    43      52.055  70.581  87.929  1.00  0.00              
ATOM     73  N   ARG    44      51.961  72.125  86.285  1.00  0.00              
ATOM     74  CA  ARG    44      50.627  71.787  85.804  1.00  0.00              
ATOM     75  C   ARG    44      50.686  72.181  84.332  1.00  0.00              
ATOM     76  O   ARG    44      51.786  72.318  83.788  1.00  0.00              
ATOM     77  N   ALA    45      49.555  72.365  83.668  1.00  0.00              
ATOM     78  CA  ALA    45      49.628  72.707  82.251  1.00  0.00              
ATOM     79  C   ALA    45      50.301  74.031  81.856  1.00  0.00              
ATOM     80  O   ALA    45      50.933  74.113  80.802  1.00  0.00              
ATOM     81  N   GLY    46      50.192  75.062  82.686  1.00  0.00              
ATOM     82  CA  GLY    46      50.780  76.338  82.330  1.00  0.00              
ATOM     83  C   GLY    46      51.867  76.900  83.266  1.00  0.00              
ATOM     84  O   GLY    46      52.167  78.103  83.216  1.00  0.00              
ATOM     85  N   GLY    47      52.465  76.045  84.103  1.00  0.00              
ATOM     86  CA  GLY    47      53.541  76.470  85.018  1.00  0.00              
ATOM     87  C   GLY    47      54.493  75.335  85.358  1.00  0.00              
ATOM     88  O   GLY    47      54.252  74.172  85.030  1.00  0.00              
ATOM     89  N   PRO    48      55.564  75.702  86.056  1.00  0.00              
ATOM     90  CA  PRO    48      56.579  74.771  86.526  1.00  0.00              
ATOM     91  C   PRO    48      57.535  75.570  87.393  1.00  0.00              
ATOM     92  O   PRO    48      58.004  76.624  86.979  1.00  0.00              
ATOM     93  N   ALA    49      57.808  75.081  88.597  1.00  0.00              
ATOM     94  CA  ALA    49      58.704  75.765  89.518  1.00  0.00              
ATOM     95  C   ALA    49      59.579  74.690  90.141  1.00  0.00              
ATOM     96  O   ALA    49      59.107  73.580  90.412  1.00  0.00              
ATOM     97  N   LEU    50      60.853  75.013  90.344  1.00  0.00              
ATOM     98  CA  LEU    50      61.788  74.080  90.952  1.00  0.00              
ATOM     99  C   LEU    50      62.067  74.564  92.368  1.00  0.00              
ATOM    100  O   LEU    50      62.387  75.738  92.588  1.00  0.00              
ATOM    101  N   LEU    51      61.922  73.644  93.319  1.00  0.00              
ATOM    102  CA  LEU    51      62.095  73.920  94.739  1.00  0.00              
ATOM    103  C   LEU    51      63.302  73.202  95.311  1.00  0.00              
ATOM    104  O   LEU    51      63.495  72.004  95.083  1.00  0.00              
ATOM    105  N   PHE    52      64.081  73.931  96.101  1.00  0.00              
ATOM    106  CA  PHE    52      65.298  73.378  96.694  1.00  0.00              
ATOM    107  C   PHE    52      65.327  73.498  98.219  1.00  0.00              
ATOM    108  O   PHE    52      65.331  74.612  98.764  1.00  0.00              
ATOM    109  N   GLU    53      65.384  72.349  98.893  1.00  0.00              
ATOM    110  CA  GLU    53      65.403  72.303 100.358  1.00  0.00              
ATOM    111  C   GLU    53      66.700  71.738 100.912  1.00  0.00              
ATOM    112  O   GLU    53      67.052  70.594 100.614  1.00  0.00              
ATOM    113  N   ASN    54      67.395  72.536 101.729  1.00  0.00              
ATOM    114  CA  ASN    54      68.645  72.101 102.348  1.00  0.00              
ATOM    115  C   ASN    54      68.489  71.980 103.860  1.00  0.00              
ATOM    116  O   ASN    54      68.584  72.964 104.605  1.00  0.00              
ATOM    117  N   PRO    55      68.258  70.753 104.303  1.00  0.00              
ATOM    118  CA  PRO    55      68.073  70.482 105.714  1.00  0.00              
ATOM    119  C   PRO    55      69.349  70.472 106.547  1.00  0.00              
ATOM    120  O   PRO    55      69.282  70.256 107.759  1.00  0.00              
ATOM    121  N   LYS    56      70.499  70.711 105.917  1.00  0.00              
ATOM    122  CA  LYS    56      71.774  70.706 106.643  1.00  0.00              
ATOM    123  C   LYS    56      72.478  72.054 106.661  1.00  0.00              
ATOM    124  O   LYS    56      71.985  73.033 106.107  1.00  0.00              
ATOM    125  N   GLY    57      73.645  72.091 107.297  1.00  0.00              
ATOM    126  CA  GLY    57      74.395  73.330 107.396  1.00  0.00              
ATOM    127  C   GLY    57      75.686  73.427 106.598  1.00  0.00              
ATOM    128  O   GLY    57      76.760  73.144 107.122  1.00  0.00              
END
