
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected   24 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_4-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         4.54    13.11
  LONGEST_CONTINUOUS_SEGMENT:    14       324 - 344         4.89    16.91
  LCS_AVERAGE:     10.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       321 - 324         1.97    25.56
  LONGEST_CONTINUOUS_SEGMENT:     4       322 - 327         1.70    19.20
  LONGEST_CONTINUOUS_SEGMENT:     4       327 - 330         1.14    19.92
  LONGEST_CONTINUOUS_SEGMENT:     4       330 - 335         1.22    15.00
  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         0.56    28.72
  LONGEST_CONTINUOUS_SEGMENT:     3       317 - 319         0.38    27.54
  LONGEST_CONTINUOUS_SEGMENT:     3       321 - 323         0.79    26.37
  LONGEST_CONTINUOUS_SEGMENT:     3       327 - 329         0.10    20.57
  LONGEST_CONTINUOUS_SEGMENT:     3       328 - 330         0.97    20.32
  LONGEST_CONTINUOUS_SEGMENT:     3       329 - 331         0.62    17.71
  LONGEST_CONTINUOUS_SEGMENT:     3       336 - 338         0.07    25.70
  LONGEST_CONTINUOUS_SEGMENT:     3       342 - 344         0.15    28.80
  LCS_AVERAGE:      1.81

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    0    3    3    3    4    6    6    6    7    7    8   10   12   12   14   14   14   15   16 
LCS_GDT     A     315     A     315      0    3    9     0    1    3    3    3    4    6    6    7    7    8    8   10   12   13   14   15   15   18   19 
LCS_GDT     I     316     I     316      3    3   12     0    3    3    3    3    3    6    6    7    7    8    8   10   12   14   15   16   16   18   19 
LCS_GDT     Y     317     Y     317      3    3   13     3    3    3    3    3    4    6    6    7    7    9    9   10   12   14   15   16   16   18   19 
LCS_GDT     H     318     H     318      3    3   14     3    3    3    3    3    4    6    6    7    8    9   12   13   14   14   16   16   17   18   19 
LCS_GDT     S     319     S     319      3    3   14     3    3    4    6    7    7    8    9   10   11   12   12   13   14   14   16   16   17   18   19 
LCS_GDT     T     320     T     320      0    3   14     0    4    4    6    7    7    8    9   10   11   12   12   13   14   14   16   16   17   18   19 
LCS_GDT     Y     321     Y     321      3    4   14     3    4    4    6    7    7    8    9   10   11   12   12   13   15   15   17   17   17   18   19 
LCS_GDT     T     322     T     322      3    4   14     0    3    3    5    5    5    6    8   10   11   12   12   13   15   15   17   17   17   18   19 
LCS_GDT     G     323     G     323      3    4   14     1    3    3    5    5    6    7    9    9   10   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     R     324     R     324      0    4   14     0    0    3    3    4    5    7    9    9   11   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     D     327     D     327      3    4   14     3    3    3    5    5    6    8    9   10   11   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     E     328     E     328      3    4   14     3    3    3    5    5    5    6    9    9    9   10   12   14   15   15   17   17   17   18   19 
LCS_GDT     P     329     P     329      3    4   14     3    3    3    4    4    5    8    9   10   11   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     A     330     A     330      3    4   14     0    3    3    4    7    7    8    9   10   11   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     V     331     V     331      3    4   14     3    4    4    6    7    7    8    9   10   11   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     G     333     G     333      0    4   14     2    2    4    6    7    7    8    9   10   11   12   12   13   14   15   17   17   17   18   19 
LCS_GDT     A     335     A     335      0    4   14     3    4    4    6    7    7    8    9   10   11   12   12   14   15   15   17   17   17   18   19 
LCS_GDT     L     336     L     336      3    3   14     3    3    3    3    4    4    6    6    6    8   10   12   14   15   15   17   17   17   18   19 
LCS_GDT     N     337     N     337      3    3   14     3    3    3    3    4    4    6    6    6    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   10   12   14   15   15   17   17   17   18   19 
LCS_GDT     P     342     P     342      3    3   14     3    3    3    3    3    4    6    6    6    6   10   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   10   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   10   12   14   15   15   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   5.15  (   1.81    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      3      4      4      6      7      7      8      9     10     11     12     12     14     15     15     17     17     17     18     19 
GDT PERCENT_CA   2.42   3.23   3.23   4.84   5.65   5.65   6.45   7.26   8.06   8.87   9.68   9.68  11.29  12.10  12.10  13.71  13.71  13.71  14.52  15.32
GDT RMS_LOCAL    0.07   0.45   0.45   1.31   1.60   1.60   2.19   2.61   3.11   3.55   3.80   3.80   4.78   5.09   5.09   5.61   5.61   5.61   6.69   7.07
GDT RMS_ALL_CA  25.70  13.17  13.17  12.59  12.52  12.52  12.48  12.53  12.79  12.96  13.19  13.19  16.68  16.35  16.35  15.87  15.87  15.87   9.72  10.44

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         20.979
LGA    A     315      A     315         15.182
LGA    I     316      I     316         10.168
LGA    Y     317      Y     317         11.111
LGA    H     318      H     318          6.841
LGA    S     319      S     319          1.542
LGA    T     320      T     320          1.993
LGA    Y     321      Y     321          1.506
LGA    T     322      T     322          6.383
LGA    G     323      G     323          9.196
LGA    R     324      R     324          8.371
LGA    D     327      D     327          3.575
LGA    E     328      E     328          6.510
LGA    P     329      P     329          3.881
LGA    A     330      A     330          2.583
LGA    V     331      V     331          2.137
LGA    G     333      G     333          3.869
LGA    A     335      A     335          1.688
LGA    L     336      L     336         15.579
LGA    N     337      N     337         19.845
LGA    E     338      E     338         16.368
LGA    P     342      P     342         20.222
LGA    I     343      I     343         25.103
LGA    L     344      L     344         28.814

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  124    4.0      9    2.61     7.258     6.035     0.333

LGA_LOCAL      RMSD =  2.606  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.944  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  9.210  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.856920 * X  +  -0.434627 * Y  +  -0.277105 * Z  + 195.257889
  Y_new =   0.261657 * X  +   0.096392 * Y  +  -0.960336 * Z  +  99.064674
  Z_new =   0.444099 * X  +  -0.895437 * Y  +   0.031123 * Z  + 133.196899 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.536053    1.605540  [ DEG:   -88.0093     91.9907 ]
  Theta =  -0.460168   -2.681425  [ DEG:   -26.3657   -153.6343 ]
  Phi   =   2.845239   -0.296354  [ DEG:   163.0202    -16.9798 ]
 
# 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_4-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_4-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    9   2.61   6.035     9.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_4-D1
REMARK Aligment from pdb entry: 1yw6_A
ATOM     41  N   ASP   314      70.417  71.911  76.368  1.00  0.00              
ATOM     42  CA  ASP   314      69.898  71.760  77.709  1.00  0.00              
ATOM     43  C   ASP   314      70.802  70.904  78.577  1.00  0.00              
ATOM     44  O   ASP   314      71.222  69.810  78.184  1.00  0.00              
ATOM     45  N   ALA   315      71.751  68.338  80.891  1.00  0.00              
ATOM     46  CA  ALA   315      71.076  67.084  81.180  1.00  0.00              
ATOM     47  C   ALA   315      70.809  66.820  82.645  1.00  0.00              
ATOM     48  O   ALA   315      69.999  65.956  82.976  1.00  0.00              
ATOM     49  N   ILE   316      69.466  68.901  84.630  1.00  0.00              
ATOM     50  CA  ILE   316      68.129  69.459  84.718  1.00  0.00              
ATOM     51  C   ILE   316      67.088  68.479  84.166  1.00  0.00              
ATOM     52  O   ILE   316      66.157  68.107  84.861  1.00  0.00              
ATOM     53  N   TYR   317      67.249  68.066  82.917  1.00  0.00              
ATOM     54  CA  TYR   317      66.315  67.136  82.320  1.00  0.00              
ATOM     55  C   TYR   317      66.175  65.891  83.169  1.00  0.00              
ATOM     56  O   TYR   317      65.086  65.340  83.297  1.00  0.00              
ATOM     57  N   HIS   318      67.288  65.440  83.736  1.00  0.00              
ATOM     58  CA  HIS   318      67.297  64.236  84.570  1.00  0.00              
ATOM     59  C   HIS   318      66.434  64.389  85.811  1.00  0.00              
ATOM     60  O   HIS   318      65.645  63.499  86.143  1.00  0.00              
ATOM     61  N   SER   319      66.597  65.518  86.495  1.00  0.00              
ATOM     62  CA  SER   319      65.829  65.821  87.695  1.00  0.00              
ATOM     63  C   SER   319      64.334  65.845  87.337  1.00  0.00              
ATOM     64  O   SER   319      63.512  65.284  88.053  1.00  0.00              
ATOM     65  N   THR   320      64.003  66.487  86.215  1.00  0.00              
ATOM     66  CA  THR   320      62.634  66.590  85.736  1.00  0.00              
ATOM     67  C   THR   320      62.040  65.200  85.612  1.00  0.00              
ATOM     68  O   THR   320      60.893  64.964  85.993  1.00  0.00              
ATOM     69  N   TYR   321      62.827  64.274  85.083  1.00  0.00              
ATOM     70  CA  TYR   321      62.350  62.912  84.952  1.00  0.00              
ATOM     71  C   TYR   321      62.123  62.323  86.328  1.00  0.00              
ATOM     72  O   TYR   321      61.158  61.583  86.531  1.00  0.00              
ATOM     73  N   THR   322      63.006  62.674  87.267  1.00  0.00              
ATOM     74  CA  THR   322      62.956  62.196  88.649  1.00  0.00              
ATOM     75  C   THR   322      61.936  62.915  89.528  1.00  0.00              
ATOM     76  O   THR   322      61.752  62.560  90.694  1.00  0.00              
ATOM     77  N   GLY   323      61.288  63.932  88.969  1.00  0.00              
ATOM     78  CA  GLY   323      60.264  64.681  89.688  1.00  0.00              
ATOM     79  C   GLY   323      58.915  64.076  89.313  1.00  0.00              
ATOM     80  O   GLY   323      57.874  64.434  89.868  1.00  0.00              
ATOM     81  N   ARG   324      58.941  63.148  88.362  1.00  0.00              
ATOM     82  CA  ARG   324      57.705  62.507  87.957  1.00  0.00              
ATOM     83  C   ARG   324      57.177  62.865  86.581  1.00  0.00              
ATOM     84  O   ARG   324      56.168  62.312  86.143  1.00  0.00              
ATOM     85  N   ASP   327      57.825  63.801  85.898  1.00  0.00              
ATOM     86  CA  ASP   327      57.369  64.133  84.565  1.00  0.00              
ATOM     87  C   ASP   327      57.644  62.884  83.731  1.00  0.00              
ATOM     88  O   ASP   327      58.748  62.329  83.747  1.00  0.00              
ATOM     89  N   GLU   328      56.614  62.426  83.038  1.00  0.00              
ATOM     90  CA  GLU   328      56.698  61.236  82.224  1.00  0.00              
ATOM     91  C   GLU   328      57.090  61.618  80.799  1.00  0.00              
ATOM     92  O   GLU   328      57.302  60.759  79.944  1.00  0.00              
ATOM     93  N   PRO   329      57.199  62.917  80.548  1.00  0.00              
ATOM     94  CA  PRO   329      57.555  63.399  79.220  1.00  0.00              
ATOM     95  C   PRO   329      58.078  64.833  79.243  1.00  0.00              
ATOM     96  O   PRO   329      57.679  65.643  80.085  1.00  0.00              
ATOM     97  N   ALA   330      58.967  65.137  78.300  1.00  0.00              
ATOM     98  CA  ALA   330      59.558  66.468  78.185  1.00  0.00              
ATOM     99  C   ALA   330      59.311  67.041  76.799  1.00  0.00              
ATOM    100  O   ALA   330      59.689  66.438  75.801  1.00  0.00              
ATOM    101  N   VAL   331      58.691  68.209  76.729  1.00  0.00              
ATOM    102  CA  VAL   331      58.424  68.803  75.432  1.00  0.00              
ATOM    103  C   VAL   331      59.313  70.018  75.191  1.00  0.00              
ATOM    104  O   VAL   331      59.408  70.904  76.040  1.00  0.00              
ATOM    105  N   GLY   333      59.981  70.052  74.036  1.00  0.00              
ATOM    106  CA  GLY   333      60.870  71.167  73.714  1.00  0.00              
ATOM    107  C   GLY   333      60.345  72.068  72.605  1.00  0.00              
ATOM    108  O   GLY   333      60.108  71.630  71.483  1.00  0.00              
ATOM    109  N   ALA   335      60.151  73.335  72.938  1.00  0.00              
ATOM    110  CA  ALA   335      59.694  74.303  71.971  1.00  0.00              
ATOM    111  C   ALA   335      60.866  74.546  71.050  1.00  0.00              
ATOM    112  O   ALA   335      62.014  74.364  71.452  1.00  0.00              
ATOM    113  N   LEU   336      56.176  83.054  77.112  1.00  0.00              
ATOM    114  CA  LEU   336      55.995  82.418  78.407  1.00  0.00              
ATOM    115  C   LEU   336      56.971  82.981  79.427  1.00  0.00              
ATOM    116  O   LEU   336      58.051  83.494  79.094  1.00  0.00              
ATOM    117  N   ASN   337      56.571  82.864  80.687  1.00  0.00              
ATOM    118  CA  ASN   337      57.363  83.327  81.800  1.00  0.00              
ATOM    119  C   ASN   337      58.642  82.490  81.861  1.00  0.00              
ATOM    120  O   ASN   337      59.717  83.019  82.138  1.00  0.00              
ATOM    121  N   GLU   338      58.542  81.186  81.610  1.00  0.00              
ATOM    122  CA  GLU   338      59.749  80.373  81.631  1.00  0.00              
ATOM    123  C   GLU   338      60.709  80.821  80.523  1.00  0.00              
ATOM    124  O   GLU   338      61.887  81.042  80.783  1.00  0.00              
ATOM    125  N   PRO   342      60.217  80.974  79.298  1.00  0.00              
ATOM    126  CA  PRO   342      61.088  81.412  78.209  1.00  0.00              
ATOM    127  C   PRO   342      61.834  82.701  78.569  1.00  0.00              
ATOM    128  O   PRO   342      63.025  82.847  78.269  1.00  0.00              
ATOM    129  N   ILE   343      61.131  83.635  79.205  1.00  0.00              
ATOM    130  CA  ILE   343      61.723  84.922  79.587  1.00  0.00              
ATOM    131  C   ILE   343      62.970  84.822  80.452  1.00  0.00              
ATOM    132  O   ILE   343      63.912  85.594  80.292  1.00  0.00              
ATOM    133  N   LEU   344      62.954  83.882  81.385  1.00  0.00              
ATOM    134  CA  LEU   344      64.076  83.688  82.271  1.00  0.00              
ATOM    135  C   LEU   344      65.138  82.861  81.584  1.00  0.00              
ATOM    136  O   LEU   344      66.320  83.134  81.732  1.00  0.00              
END
