
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0356AL044_5-D1
# Molecule2: number of CA atoms  124 (  963),  selected   24 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_5-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:    14       318 - 335         4.49    13.11
  LONGEST_CONTINUOUS_SEGMENT:    14       324 - 344         4.91    16.63
  LCS_AVERAGE:     10.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       321 - 324         1.86    25.53
  LONGEST_CONTINUOUS_SEGMENT:     4       322 - 327         1.55    18.75
  LONGEST_CONTINUOUS_SEGMENT:     4       327 - 330         1.29    19.38
  LONGEST_CONTINUOUS_SEGMENT:     4       330 - 335         1.13    15.07
  LCS_AVERAGE:      2.79

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       316 - 318         0.63    29.13
  LONGEST_CONTINUOUS_SEGMENT:     3       317 - 319         0.39    27.83
  LONGEST_CONTINUOUS_SEGMENT:     3       319 - 321         0.97    11.66
  LONGEST_CONTINUOUS_SEGMENT:     3       320 - 322         0.99    21.15
  LONGEST_CONTINUOUS_SEGMENT:     3       321 - 323         0.88    26.57
  LONGEST_CONTINUOUS_SEGMENT:     3       322 - 324         0.74    24.14
  LONGEST_CONTINUOUS_SEGMENT:     3       327 - 329         0.27    20.34
  LONGEST_CONTINUOUS_SEGMENT:     3       328 - 330         0.97    19.66
  LONGEST_CONTINUOUS_SEGMENT:     3       329 - 331         0.74    17.41
  LONGEST_CONTINUOUS_SEGMENT:     3       330 - 333         0.99    16.52
  LONGEST_CONTINUOUS_SEGMENT:     3       331 - 335         0.94    13.83
  LONGEST_CONTINUOUS_SEGMENT:     3       336 - 338         0.12    25.89
  LONGEST_CONTINUOUS_SEGMENT:     3       342 - 344         0.18    29.18
  LCS_AVERAGE:      2.22

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     D     314     D     314      0    3    9     0    1    3    3    4    5    6    6    6    7    7    9   10   12   12   14   14   14   14   15 
LCS_GDT     A     315     A     315      0    3    9     0    0    3    3    4    5    6    6    6    7    7    9   10   12   13   14   14   15   15   17 
LCS_GDT     I     316     I     316      3    3   12     0    3    3    3    4    4    6    6    6    7    7    9   10   12   13   14   15   16   17   18 
LCS_GDT     Y     317     Y     317      3    3   13     3    3    3    3    3    5    6    6    6    7    8    9   10   12   13   14   15   16   17   18 
LCS_GDT     H     318     H     318      3    3   14     3    3    3    3    4    5    6    6    6   10   10   12   13   14   15   16   17   17   18   18 
LCS_GDT     S     319     S     319      3    3   14     3    3    5    6    7    7    8    8   10   11   12   12   13   14   15   16   17   17   18   18 
LCS_GDT     T     320     T     320      3    3   14     4    4    5    6    7    7    8    8   10   11   12   12   13   14   15   16   17   17   18   18 
LCS_GDT     Y     321     Y     321      3    4   14     4    4    5    6    7    7    8    8   10   11   12   12   13   15   15   17   17   17   18   18 
LCS_GDT     T     322     T     322      3    4   14     0    3    3    5    5    6    6    7   10   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     G     323     G     323      3    4   14     1    3    3    5    5    6    7    8    9   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     R     324     R     324      3    4   14     0    3    3    3    4    6    7    8   10   11   12   12   14   14   15   17   17   17   18   18 
LCS_GDT     D     327     D     327      3    4   14     3    3    3    5    5    6    8    8   10   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     E     328     E     328      3    4   14     3    3    3    5    5    6    6    8    9    9   11   12   14   15   15   17   17   17   18   18 
LCS_GDT     P     329     P     329      3    4   14     3    3    3    4    4    7    7    8    9   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     A     330     A     330      3    4   14     1    3    4    6    7    7    8    8   10   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     V     331     V     331      3    4   14     4    4    5    6    7    7    8    8   10   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     G     333     G     333      3    4   14     2    3    5    6    7    7    8    8   10   11   12   12   13   14   15   17   17   17   18   18 
LCS_GDT     A     335     A     335      3    4   14     4    4    5    6    7    7    8    8   10   11   12   12   14   15   15   17   17   17   18   18 
LCS_GDT     L     336     L     336      3    3   14     3    3    3    3    3    3    6    6    6    7   10   12   14   15   15   17   17   17   18   18 
LCS_GDT     N     337     N     337      3    3   14     3    3    3    3    4    4    6    6    7    8   10   12   14   15   15   17   17   17   18   18 
LCS_GDT     E     338     E     338      3    3   14     3    3    3    3    3    4    6    6    7    8   11   12   14   15   15   17   17   17   18   18 
LCS_GDT     P     342     P     342      3    3   14     3    3    3    3    3    4    6    6    6    6    9   12   14   15   15   17   17   17   18   18 
LCS_GDT     I     343     I     343      3    3   14     3    3    3    4    4    5    6    7    8    9   11   12   14   15   15   17   17   17   17   18 
LCS_GDT     L     344     L     344      3    3   14     3    3    3    4    4    5    6    7    8    9   11   12   14   15   15   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   5.29  (   2.22    2.79   10.85 )

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      4      5      6      7      7      8      8     10     11     12     12     14     15     15     17     17     17     18     18 
GDT PERCENT_CA   3.23   3.23   4.03   4.84   5.65   5.65   6.45   6.45   8.06   8.87   9.68   9.68  11.29  12.10  12.10  13.71  13.71  13.71  14.52  14.52
GDT RMS_LOCAL    0.38   0.38   0.89   1.18   1.41   1.41   2.13   2.13   3.38   3.55   3.79   3.79   4.75   5.17   5.04   5.63   5.63   5.63   6.63   6.59
GDT RMS_ALL_CA  13.23  13.23  13.03  12.73  12.65  12.65  12.60  12.60  13.02  13.02  13.23  13.23  16.41  15.44  16.32  15.59  15.59  15.59   9.93  10.15

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         23.896
LGA    A     315      A     315         17.346
LGA    I     316      I     316         11.309
LGA    Y     317      Y     317         11.826
LGA    H     318      H     318          7.404
LGA    S     319      S     319          1.351
LGA    T     320      T     320          1.655
LGA    Y     321      Y     321          1.004
LGA    T     322      T     322          6.760
LGA    G     323      G     323          9.611
LGA    R     324      R     324          9.000
LGA    D     327      D     327          3.981
LGA    E     328      E     328          6.140
LGA    P     329      P     329          4.265
LGA    A     330      A     330          1.828
LGA    V     331      V     331          2.707
LGA    G     333      G     333          2.567
LGA    A     335      A     335          1.328
LGA    L     336      L     336         14.094
LGA    N     337      N     337         18.105
LGA    E     338      E     338         14.462
LGA    P     342      P     342         17.938
LGA    I     343      I     343         22.458
LGA    L     344      L     344         26.628

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  124    4.0      8    2.13     7.056     6.052     0.358

LGA_LOCAL      RMSD =  2.133  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.551  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  9.277  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.416673 * X  +  -0.793014 * Y  +  -0.444424 * Z  + 135.758728
  Y_new =  -0.011520 * X  +  -0.484240 * Y  +   0.874859 * Z  + -17.401897
  Z_new =  -0.908984 * X  +   0.369650 * Y  +   0.192634 * Z  +  93.259857 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.090390   -2.051202  [ DEG:    62.4748   -117.5252 ]
  Theta =   1.140839    2.000754  [ DEG:    65.3653    114.6347 ]
  Phi   =  -3.113953    0.027640  [ DEG:  -178.4164      1.5836 ]
 
# 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: T0356AL044_5-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_5-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  124   4.0    8   2.13   6.052     9.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_5-D1
REMARK Aligment from pdb entry: 1yw4_A
ATOM     29  N   ASP   314      70.064  69.724  74.031  1.00  0.00              
ATOM     30  CA  ASP   314      69.277  69.586  75.251  1.00  0.00              
ATOM     31  C   ASP   314      70.084  68.895  76.347  1.00  0.00              
ATOM     32  O   ASP   314      70.644  67.818  76.137  1.00  0.00              
ATOM     33  N   ALA   315      70.681  66.632  79.258  1.00  0.00              
ATOM     34  CA  ALA   315      70.021  65.476  79.851  1.00  0.00              
ATOM     35  C   ALA   315      70.164  65.398  81.364  1.00  0.00              
ATOM     36  O   ALA   315      69.466  64.626  82.019  1.00  0.00              
ATOM     37  N   ILE   316      69.371  67.776  83.301  1.00  0.00              
ATOM     38  CA  ILE   316      68.134  68.385  83.777  1.00  0.00              
ATOM     39  C   ILE   316      66.949  67.470  83.490  1.00  0.00              
ATOM     40  O   ILE   316      65.994  67.415  84.264  1.00  0.00              
ATOM     41  N   TYR   317      67.010  66.757  82.372  1.00  0.00              
ATOM     42  CA  TYR   317      65.944  65.830  82.024  1.00  0.00              
ATOM     43  C   TYR   317      65.880  64.771  83.113  1.00  0.00              
ATOM     44  O   TYR   317      64.808  64.270  83.453  1.00  0.00              
ATOM     45  N   HIS   318      67.040  64.440  83.670  1.00  0.00              
ATOM     46  CA  HIS   318      67.114  63.442  84.726  1.00  0.00              
ATOM     47  C   HIS   318      66.415  63.969  85.973  1.00  0.00              
ATOM     48  O   HIS   318      65.567  63.291  86.556  1.00  0.00              
ATOM     49  N   SER   319      66.768  65.190  86.370  1.00  0.00              
ATOM     50  CA  SER   319      66.175  65.820  87.550  1.00  0.00              
ATOM     51  C   SER   319      64.661  65.900  87.399  1.00  0.00              
ATOM     52  O   SER   319      63.913  65.686  88.354  1.00  0.00              
ATOM     53  N   THR   320      64.220  66.240  86.195  1.00  0.00              
ATOM     54  CA  THR   320      62.798  66.342  85.910  1.00  0.00              
ATOM     55  C   THR   320      62.154  64.966  86.040  1.00  0.00              
ATOM     56  O   THR   320      61.098  64.818  86.664  1.00  0.00              
ATOM     57  N   TYR   321      62.803  63.961  85.459  1.00  0.00              
ATOM     58  CA  TYR   321      62.298  62.592  85.506  1.00  0.00              
ATOM     59  C   TYR   321      62.093  62.165  86.954  1.00  0.00              
ATOM     60  O   TYR   321      60.986  61.802  87.351  1.00  0.00              
ATOM     61  N   THR   322      63.163  62.199  87.739  1.00  0.00              
ATOM     62  CA  THR   322      63.067  61.828  89.143  1.00  0.00              
ATOM     63  C   THR   322      62.494  63.007  89.921  1.00  0.00              
ATOM     64  O   THR   322      63.075  63.469  90.901  1.00  0.00              
ATOM     65  N   GLY   323      61.348  63.491  89.460  1.00  0.00              
ATOM     66  CA  GLY   323      60.665  64.614  90.084  1.00  0.00              
ATOM     67  C   GLY   323      59.165  64.442  89.890  1.00  0.00              
ATOM     68  O   GLY   323      58.355  65.011  90.626  1.00  0.00              
ATOM     69  N   ARG   324      58.805  63.656  88.882  1.00  0.00              
ATOM     70  CA  ARG   324      57.407  63.414  88.593  1.00  0.00              
ATOM     71  C   ARG   324      57.071  63.615  87.128  1.00  0.00              
ATOM     72  O   ARG   324      56.098  63.051  86.634  1.00  0.00              
ATOM     73  N   ASP   327      57.866  64.424  86.429  1.00  0.00              
ATOM     74  CA  ASP   327      57.621  64.672  85.013  1.00  0.00              
ATOM     75  C   ASP   327      57.593  63.324  84.303  1.00  0.00              
ATOM     76  O   ASP   327      58.498  62.508  84.478  1.00  0.00              
ATOM     77  N   GLU   328      56.557  63.097  83.501  1.00  0.00              
ATOM     78  CA  GLU   328      56.394  61.835  82.795  1.00  0.00              
ATOM     79  C   GLU   328      56.637  61.955  81.296  1.00  0.00              
ATOM     80  O   GLU   328      56.618  60.954  80.580  1.00  0.00              
ATOM     81  N   PRO   329      56.865  63.177  80.823  1.00  0.00              
ATOM     82  CA  PRO   329      57.103  63.419  79.405  1.00  0.00              
ATOM     83  C   PRO   329      57.629  64.827  79.168  1.00  0.00              
ATOM     84  O   PRO   329      57.359  65.740  79.952  1.00  0.00              
ATOM     85  N   ALA   330      58.380  64.999  78.084  1.00  0.00              
ATOM     86  CA  ALA   330      58.938  66.303  77.747  1.00  0.00              
ATOM     87  C   ALA   330      58.691  66.657  76.283  1.00  0.00              
ATOM     88  O   ALA   330      58.937  65.851  75.385  1.00  0.00              
ATOM     89  N   VAL   331      58.169  67.855  76.051  1.00  0.00              
ATOM     90  CA  VAL   331      57.928  68.332  74.696  1.00  0.00              
ATOM     91  C   VAL   331      59.097  69.264  74.370  1.00  0.00              
ATOM     92  O   VAL   331      59.373  70.201  75.118  1.00  0.00              
ATOM     93  N   GLY   333      59.790  68.990  73.271  1.00  0.00              
ATOM     94  CA  GLY   333      60.924  69.808  72.849  1.00  0.00              
ATOM     95  C   GLY   333      60.450  70.759  71.753  1.00  0.00              
ATOM     96  O   GLY   333      60.031  70.318  70.679  1.00  0.00              
ATOM     97  N   ALA   335      60.504  72.060  72.031  1.00  0.00              
ATOM     98  CA  ALA   335      60.083  73.069  71.061  1.00  0.00              
ATOM     99  C   ALA   335      61.083  73.154  69.915  1.00  0.00              
ATOM    100  O   ALA   335      62.291  73.185  70.138  1.00  0.00              
ATOM    101  N   LEU   336      57.107  82.570  75.238  1.00  0.00              
ATOM    102  CA  LEU   336      56.931  82.100  76.607  1.00  0.00              
ATOM    103  C   LEU   336      58.062  82.569  77.512  1.00  0.00              
ATOM    104  O   LEU   336      59.146  82.920  77.052  1.00  0.00              
ATOM    105  N   ASN   337      57.804  82.570  78.810  1.00  0.00              
ATOM    106  CA  ASN   337      58.804  83.016  79.753  1.00  0.00              
ATOM    107  C   ASN   337      60.015  82.081  79.733  1.00  0.00              
ATOM    108  O   ASN   337      61.156  82.541  79.770  1.00  0.00              
ATOM    109  N   GLU   338      59.776  80.772  79.656  1.00  0.00              
ATOM    110  CA  GLU   338      60.887  79.820  79.645  1.00  0.00              
ATOM    111  C   GLU   338      61.756  79.951  78.386  1.00  0.00              
ATOM    112  O   GLU   338      62.953  79.661  78.416  1.00  0.00              
ATOM    113  N   PRO   342      61.162  80.372  77.274  1.00  0.00              
ATOM    114  CA  PRO   342      61.949  80.552  76.063  1.00  0.00              
ATOM    115  C   PRO   342      62.837  81.783  76.273  1.00  0.00              
ATOM    116  O   PRO   342      64.038  81.746  76.000  1.00  0.00              
ATOM    117  N   ILE   343      62.237  82.867  76.766  1.00  0.00              
ATOM    118  CA  ILE   343      62.973  84.108  77.010  1.00  0.00              
ATOM    119  C   ILE   343      64.213  83.889  77.868  1.00  0.00              
ATOM    120  O   ILE   343      65.310  84.317  77.500  1.00  0.00              
ATOM    121  N   LEU   344      64.058  83.224  79.011  1.00  0.00              
ATOM    122  CA  LEU   344      65.211  83.007  79.886  1.00  0.00              
ATOM    123  C   LEU   344      66.231  82.058  79.265  1.00  0.00              
ATOM    124  O   LEU   344      67.443  82.276  79.362  1.00  0.00              
END
