
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0299AL586_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   27 , name T0299_D1.pdb
# PARAMETERS: T0299AL586_1-D1.T0299_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:    15         2 - 43          4.98    13.81
  LCS_AVERAGE:     12.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         6 - 10          0.56    15.57
  LONGEST_CONTINUOUS_SEGMENT:     5         8 - 12          1.96    14.04
  LONGEST_CONTINUOUS_SEGMENT:     5         9 - 13          1.90    16.06
  LONGEST_CONTINUOUS_SEGMENT:     5        21 - 31          1.71    17.26
  LONGEST_CONTINUOUS_SEGMENT:     5       169 - 175         1.56    21.68
  LONGEST_CONTINUOUS_SEGMENT:     5       171 - 178         1.54    21.37
  LCS_AVERAGE:      4.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         6 - 10          0.56    15.57
  LCS_AVERAGE:      3.46

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:   91
LCS_GDT     T       2     T       2      0    3   15     0    0    2    3    3    3    4    5    6    9   10   13   14   14   15   16   17   17   17   18 
LCS_GDT     L       6     L       6      5    5   15     3    5    5    5    5    7    7   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     L       7     L       7      5    5   15     4    5    5    5    5    7    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     V       8     V       8      5    5   15     4    5    5    6    7    7    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     R       9     R       9      5    5   15     4    5    5    6    7    7    9   10   11   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     G      10     G      10      5    5   15     4    5    5    5    5    5    7    9   11   13   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     I      11     I      11      3    5   15     3    3    4    6    7    7    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     N      12     N      12      3    5   15     0    3    4    6    7    7    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     V      13     V      13      3    5   15     0    3    3    4    5    7    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     M      21     M      21      3    5   15     2    3    4    6    7    7    9   10   11   11   13   13   14   14   15   16   17   17   17   18 
LCS_GDT     L      24     L      24      3    5   15     2    3    4    6    7    7    9   10   11   11   13   13   14   14   15   16   17   17   17   18 
LCS_GDT     L      28     L      28      3    5   15     1    3    4    6    7    7    9   10   11   11   13   13   14   14   15   16   17   17   17   18 
LCS_GDT     T      29     T      29      3    5   15     0    3    3    4    5    6    6    6    9   11   13   13   14   14   15   16   17   17   17   18 
LCS_GDT     L      31     L      31      3    5   15     2    3    3    4    6    7    9   10   11   11   13   13   14   14   15   16   17   17   17   18 
LCS_GDT     G      43     G      43      0    0   15     0    1    1    1    3    3    3    5    6    7    9    9    9   10   10   11   11   14   15   16 
LCS_GDT     T      48     T      48      0    0    3     0    2    3    4    4    6    6    6    6    8    8   11   13   14   15   16   17   17   17   18 
LCS_GDT     F      74     F      74      4    4    7     3    4    5    5    5    5    7   10   13   14   15   15   16   16   16   17   17   17   17   17 
LCS_GDT     S      75     S      75      4    4    7     3    4    5    5    5    5    6    6   10   11   13   15   16   16   16   17   17   17   17   17 
LCS_GDT     L      77     L      77      4    4    7     3    4    5    5    5    5    6    6    6    7    9    9    9   10   10   11   11   14   14   14 
LCS_GDT     S      78     S      78      4    4    7     2    4    5    5    5    5    6    6    6    7    9    9    9   10   10   11   11   14   14   14 
LCS_GDT     K     169     K     169      4    5    7     1    3    4    4    5    5    9   12   13   14   15   15   16   16   16   17   17   17   17   17 
LCS_GDT     F     171     F     171      4    5    7     3    4    4    4    5    5    6   12   13   14   15   15   16   16   16   17   17   17   17   17 
LCS_GDT     D     172     D     172      4    5    7     3    4    4    4    5    5    9   12   13   14   15   15   16   16   16   17   17   17   17   17 
LCS_GDT     I     174     I     174      4    5    7     3    4    4    4    5    5    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     G     175     G     175      4    5    7     3    4    4    4    5    5    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     L     178     L     178      0    5    7     0    0    1    3    5    5    9   12   13   14   15   15   16   16   16   17   17   17   17   18 
LCS_GDT     K     180     K     180      0    3    7     0    0    1    2    3    5    5    6    6    8    8    8    9    9   14   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   6.88  (   3.46    4.76   12.41 )

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      5      6      7      7      9     12     13     14     15     15     16     16     16     17     17     17     17     18 
GDT PERCENT_CA   4.40   5.49   5.49   6.59   7.69   7.69   9.89  13.19  14.29  15.38  16.48  16.48  17.58  17.58  17.58  18.68  18.68  18.68  18.68  19.78
GDT RMS_LOCAL    0.47   0.56   0.56   1.39   1.62   1.62   2.39   3.23   3.33   3.54   3.69   3.69   3.97   3.97   3.97   4.67   4.67   4.67   4.67   7.01
GDT RMS_ALL_CA  15.47  15.57  15.57  15.07  15.00  15.00  14.84  14.33  14.12  14.33  14.42  14.42  14.32  14.32  14.32  14.19  14.19  14.19  14.19  12.34

#      Molecule1      Molecule2       DISTANCE
LGA    T       2      T       2         17.320
LGA    L       6      L       6          3.681
LGA    L       7      L       7          3.260
LGA    V       8      V       8          3.743
LGA    R       9      R       9          5.304
LGA    G      10      G      10          5.591
LGA    I      11      I      11          2.638
LGA    N      12      N      12          3.442
LGA    V      13      V      13          1.174
LGA    M      21      M      21         17.460
LGA    L      24      L      24         21.675
LGA    L      28      L      28         27.788
LGA    T      29      T      29         27.357
LGA    L      31      L      31         31.903
LGA    G      43      G      43         14.533
LGA    T      48      T      48         15.967
LGA    F      74      F      74          4.461
LGA    S      75      S      75          7.183
LGA    L      77      L      77         19.527
LGA    S      78      S      78         25.939
LGA    K     169      K     169          3.449
LGA    F     171      F     171          3.904
LGA    D     172      D     172          3.665
LGA    I     174      I     174          0.858
LGA    G     175      G     175          3.751
LGA    L     178      L     178          3.749
LGA    K     180      K     180         12.298

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   91    4.0     12    3.23    10.989     9.533     0.361

LGA_LOCAL      RMSD =  3.225  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.329  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 11.759  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.195572 * X  +   0.572084 * Y  +  -0.796537 * Z  +  11.500877
  Y_new =  -0.439340 * X  +  -0.777267 * Y  +  -0.450374 * Z  +  83.174286
  Z_new =  -0.876774 * X  +   0.261870 * Y  +   0.403351 * Z  + -18.832745 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.575838   -2.565755  [ DEG:    32.9931   -147.0069 ]
  Theta =   1.069112    2.072481  [ DEG:    61.2556    118.7444 ]
  Phi   =  -1.989609    1.151983  [ DEG:  -113.9962     66.0038 ]
 
# 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: T0299AL586_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL586_1-D1.T0299_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   91   4.0   12   3.23   9.533    11.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL586_1-D1
REMARK Aligment from pdb entry: 1k66_A
ATOM      1  N   THR     2       0.439  59.427  -3.701  1.00  0.00              
ATOM      2  CA  THR     2      -0.537  58.842  -4.611  1.00  0.00              
ATOM      3  C   THR     2      -1.132  57.592  -3.974  1.00  0.00              
ATOM      4  O   THR     2      -0.478  56.928  -3.172  1.00  0.00              
ATOM      5  N   LEU     6      -6.741  51.161   0.954  1.00  0.00              
ATOM      6  CA  LEU     6      -6.880  50.109  -0.054  1.00  0.00              
ATOM      7  C   LEU     6      -5.589  49.298  -0.200  1.00  0.00              
ATOM      8  O   LEU     6      -4.688  49.669  -0.951  1.00  0.00              
ATOM      9  N   LEU     7      -5.491  48.167   0.512  1.00  0.00              
ATOM     10  CA  LEU     7      -4.284  47.340   0.434  1.00  0.00              
ATOM     11  C   LEU     7      -4.004  46.703  -0.922  1.00  0.00              
ATOM     12  O   LEU     7      -4.916  46.372  -1.680  1.00  0.00              
ATOM     13  N   VAL     8      -2.719  46.536  -1.208  1.00  0.00              
ATOM     14  CA  VAL     8      -2.271  45.884  -2.424  1.00  0.00              
ATOM     15  C   VAL     8      -1.595  44.607  -1.950  1.00  0.00              
ATOM     16  O   VAL     8      -0.643  44.662  -1.170  1.00  0.00              
ATOM     17  N   ARG     9      -2.105  43.464  -2.388  1.00  0.00              
ATOM     18  CA  ARG     9      -1.504  42.190  -2.023  1.00  0.00              
ATOM     19  C   ARG     9      -0.598  41.777  -3.177  1.00  0.00              
ATOM     20  O   ARG     9      -1.057  41.632  -4.311  1.00  0.00              
ATOM     21  N   GLY    10       0.688  41.604  -2.889  1.00  0.00              
ATOM     22  CA  GLY    10       1.648  41.207  -3.913  1.00  0.00              
ATOM     23  C   GLY    10       2.118  39.783  -3.636  1.00  0.00              
ATOM     24  O   GLY    10       2.714  39.519  -2.596  1.00  0.00              
ATOM     25  N   ILE    11       1.833  38.865  -4.554  1.00  0.00              
ATOM     26  CA  ILE    11       2.258  37.478  -4.386  1.00  0.00              
ATOM     27  C   ILE    11       3.472  37.311  -5.286  1.00  0.00              
ATOM     28  O   ILE    11       3.359  37.114  -6.497  1.00  0.00              
ATOM     29  N   ASN    12       4.642  37.396  -4.663  1.00  0.00              
ATOM     30  CA  ASN    12       5.912  37.329  -5.374  1.00  0.00              
ATOM     31  C   ASN    12       6.953  36.581  -4.550  1.00  0.00              
ATOM     32  O   ASN    12       7.228  36.961  -3.416  1.00  0.00              
ATOM     33  N   VAL    13       7.544  35.539  -5.123  1.00  0.00              
ATOM     34  CA  VAL    13       8.542  34.771  -4.385  1.00  0.00              
ATOM     35  C   VAL    13       9.978  35.256  -4.581  1.00  0.00              
ATOM     36  O   VAL    13      10.857  34.890  -3.805  1.00  0.00              
ATOM     37  N   MET    21      10.558  41.633  -5.796  1.00  0.00              
ATOM     38  CA  MET    21       9.704  42.350  -4.861  1.00  0.00              
ATOM     39  C   MET    21      10.358  43.633  -4.366  1.00  0.00              
ATOM     40  O   MET    21       9.711  44.677  -4.295  1.00  0.00              
ATOM     41  N   LEU    24      10.446  46.307  -7.053  1.00  0.00              
ATOM     42  CA  LEU    24       9.079  46.804  -7.204  1.00  0.00              
ATOM     43  C   LEU    24       8.694  47.729  -6.051  1.00  0.00              
ATOM     44  O   LEU    24       8.183  48.831  -6.260  1.00  0.00              
ATOM     45  N   LEU    28      10.307  51.146  -6.188  1.00  0.00              
ATOM     46  CA  LEU    28       9.713  51.979  -7.226  1.00  0.00              
ATOM     47  C   LEU    28       8.413  52.608  -6.729  1.00  0.00              
ATOM     48  O   LEU    28       8.127  53.764  -7.043  1.00  0.00              
ATOM     49  N   THR    29       7.618  51.857  -5.966  1.00  0.00              
ATOM     50  CA  THR    29       6.373  52.410  -5.433  1.00  0.00              
ATOM     51  C   THR    29       6.690  53.492  -4.408  1.00  0.00              
ATOM     52  O   THR    29       5.991  54.502  -4.313  1.00  0.00              
ATOM     53  N   LEU    31       7.443  56.850  -5.850  1.00  0.00              
ATOM     54  CA  LEU    31       6.268  57.568  -6.343  1.00  0.00              
ATOM     55  C   LEU    31       5.380  58.045  -5.200  1.00  0.00              
ATOM     56  O   LEU    31       4.354  58.689  -5.424  1.00  0.00              
ATOM     57  N   GLY    43       3.610  56.158  -3.052  1.00  0.00              
ATOM     58  CA  GLY    43       2.400  55.361  -2.874  1.00  0.00              
ATOM     59  C   GLY    43       2.116  55.135  -1.390  1.00  0.00              
ATOM     60  O   GLY    43       3.000  54.711  -0.644  1.00  0.00              
ATOM     61  N   THR    48      -0.683  53.250  -0.340  1.00  0.00              
ATOM     62  CA  THR    48      -1.417  52.004  -0.149  1.00  0.00              
ATOM     63  C   THR    48      -0.522  51.035   0.617  1.00  0.00              
ATOM     64  O   THR    48       0.656  50.885   0.293  1.00  0.00              
ATOM     65  N   PHE    74       1.292  47.779   1.458  1.00  0.00              
ATOM     66  CA  PHE    74       1.670  46.631   0.648  1.00  0.00              
ATOM     67  C   PHE    74       1.869  45.386   1.509  1.00  0.00              
ATOM     68  O   PHE    74       2.632  45.404   2.471  1.00  0.00              
ATOM     69  N   SER    75       1.165  44.314   1.163  1.00  0.00              
ATOM     70  CA  SER    75       1.281  43.050   1.876  1.00  0.00              
ATOM     71  C   SER    75       1.882  42.051   0.907  1.00  0.00              
ATOM     72  O   SER    75       1.459  41.972  -0.242  1.00  0.00              
ATOM     73  N   LEU    77       3.072  38.011  -0.055  1.00  0.00              
ATOM     74  CA  LEU    77       2.976  36.573   0.162  1.00  0.00              
ATOM     75  C   LEU    77       4.004  35.981  -0.800  1.00  0.00              
ATOM     76  O   LEU    77       4.158  36.463  -1.928  1.00  0.00              
ATOM     77  N   SER    78       4.714  34.953  -0.350  1.00  0.00              
ATOM     78  CA  SER    78       5.736  34.307  -1.165  1.00  0.00              
ATOM     79  C   SER    78       5.232  33.024  -1.809  1.00  0.00              
ATOM     80  O   SER    78       5.574  32.732  -2.951  1.00  0.00              
ATOM    281  N   LYS   169       5.763  49.963 -13.913  1.00  0.00              
ATOM    282  CA  LYS   169       5.285  50.170 -12.556  1.00  0.00              
ATOM    283  C   LYS   169       4.628  51.533 -12.374  1.00  0.00              
ATOM    284  O   LYS   169       3.602  51.642 -11.712  1.00  0.00              
ATOM    285  N   PHE   171       1.211  51.268 -13.840  1.00  0.00              
ATOM    286  CA  PHE   171       0.382  50.405 -13.002  1.00  0.00              
ATOM    287  C   PHE   171      -0.152  51.228 -11.834  1.00  0.00              
ATOM    288  O   PHE   171      -1.327  51.147 -11.477  1.00  0.00              
ATOM    289  N   ASP   172       0.724  52.029 -11.233  1.00  0.00              
ATOM    290  CA  ASP   172       0.327  52.864 -10.104  1.00  0.00              
ATOM    291  C   ASP   172      -0.763  53.871 -10.472  1.00  0.00              
ATOM    292  O   ASP   172      -1.783  53.977  -9.791  1.00  0.00              
ATOM    293  N   ILE   174      -4.224  51.708 -11.524  1.00  0.00              
ATOM    294  CA  ILE   174      -4.916  51.023 -10.437  1.00  0.00              
ATOM    295  C   ILE   174      -5.105  51.776  -9.139  1.00  0.00              
ATOM    296  O   ILE   174      -6.145  51.650  -8.493  1.00  0.00              
ATOM    297  N   GLY   175      -4.113  52.563  -8.751  1.00  0.00              
ATOM    298  CA  GLY   175      -4.213  53.253  -7.480  1.00  0.00              
ATOM    299  C   GLY   175      -4.767  54.665  -7.524  1.00  0.00              
ATOM    300  O   GLY   175      -5.068  55.237  -6.478  1.00  0.00              
ATOM    301  N   LEU   178     -12.114  50.974  -7.580  1.00  0.00              
ATOM    302  CA  LEU   178     -12.043  49.581  -7.152  1.00  0.00              
ATOM    303  C   LEU   178     -13.266  49.195  -6.333  1.00  0.00              
ATOM    304  O   LEU   178     -13.864  50.037  -5.674  1.00  0.00              
ATOM    305  N   LYS   180     -13.041  47.049  -1.628  1.00  0.00              
ATOM    306  CA  LYS   180     -12.083  46.035  -1.206  1.00  0.00              
ATOM    307  C   LYS   180     -12.261  44.715  -1.948  1.00  0.00              
ATOM    308  O   LYS   180     -11.403  43.840  -1.878  1.00  0.00              
END
