
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   24 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_3-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         4.58    13.05
  LONGEST_CONTINUOUS_SEGMENT:    14       324 - 344         4.90    17.18
  LCS_AVERAGE:     10.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       327 - 330         1.32    19.96
  LONGEST_CONTINUOUS_SEGMENT:     4       330 - 335         1.13    15.16
  LCS_AVERAGE:      2.65

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         0.48    29.10
  LONGEST_CONTINUOUS_SEGMENT:     3       317 - 319         0.55    26.87
  LONGEST_CONTINUOUS_SEGMENT:     3       318 - 320         0.96    21.53
  LONGEST_CONTINUOUS_SEGMENT:     3       319 - 321         0.99    13.97
  LONGEST_CONTINUOUS_SEGMENT:     3       320 - 322         0.97    18.70
  LONGEST_CONTINUOUS_SEGMENT:     3       321 - 323         0.84    27.13
  LONGEST_CONTINUOUS_SEGMENT:     3       327 - 329         0.24    21.23
  LONGEST_CONTINUOUS_SEGMENT:     3       329 - 331         0.65    17.55
  LONGEST_CONTINUOUS_SEGMENT:     3       331 - 335         0.88    13.71
  LONGEST_CONTINUOUS_SEGMENT:     3       336 - 338         0.08    26.55
  LONGEST_CONTINUOUS_SEGMENT:     3       342 - 344         0.14    29.25
  LCS_AVERAGE:      2.12

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    2    2    3    3    6    6    6    6    7    8    9   10   11   12   13   14   14   14 
LCS_GDT     A     315     A     315      0    3    9     0    1    2    3    3    3    6    6    7    7    8    9   10   11   14   15   16   17   18   19 
LCS_GDT     I     316     I     316      3    3   12     0    3    3    3    3    3    6    6    7    7    8    9   10   11   14   15   16   17   17   18 
LCS_GDT     Y     317     Y     317      3    3   13     1    3    3    3    3    4    6    6    7    7    8    9   10   12   14   15   16   17   18   19 
LCS_GDT     H     318     H     318      3    3   14     1    3    4    4    4    4    6    9   10   10   10   11   13   14   14   16   17   17   18   19 
LCS_GDT     S     319     S     319      3    3   14     3    4    6    6    7    7    8    9   10   11   12   12   13   14   14   16   17   17   18   19 
LCS_GDT     T     320     T     320      3    3   14     2    4    6    6    7    7    8    9   10   11   12   12   13   14   14   16   17   17   18   19 
LCS_GDT     Y     321     Y     321      3    3   14     1    3    6    6    7    7    8    9   10   11   12   12   13   14   15   16   17   17   18   19 
LCS_GDT     T     322     T     322      3    3   14     0    3    3    3    4    5    5    7    9   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     G     323     G     323      3    3   14     1    3    3    3    6    6    7    8    9   10   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     R     324     R     324      0    3   14     0    1    3    3    6    6    7    8    9   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     D     327     D     327      3    4   14     3    3    3    4    4    5    8    9   10   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     E     328     E     328      3    4   14     3    3    5    5    5    5    7    8    9   10   11   12   14   15   15   16   17   17   18   19 
LCS_GDT     P     329     P     329      3    4   14     3    3    5    5    5    5    7    9   10   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     A     330     A     330      3    4   14     1    3    4    5    7    7    8    9   10   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     V     331     V     331      3    4   14     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     G     333     G     333      3    4   14     0    1    6    6    7    7    8    9   10   11   12   12   13   14   15   16   17   17   18   19 
LCS_GDT     A     335     A     335      3    4   14     3    4    6    6    7    7    8    9   10   11   12   12   14   15   15   16   17   17   18   19 
LCS_GDT     L     336     L     336      3    3   14     3    3    3    3    3    3    6    6    6    7    9   12   14   15   15   16   17   17   18   19 
LCS_GDT     N     337     N     337      3    3   14     3    3    3    3    3    4    6    6    6    8   10   11   14   15   15   16   17   17   18   19 
LCS_GDT     E     338     E     338      3    3   14     3    3    3    3    3    4    6    6    6    8   11   12   14   15   15   16   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   16   17   17   18   19 
LCS_GDT     I     343     I     343      3    3   14     3    3    3    4    4    5    6    7    9   10   11   12   14   15   15   16   17   17   18   19 
LCS_GDT     L     344     L     344      3    3   14     3    3    3    4    4    5    6    6    9   10   11   12   14   15   15   16   17   17   17   17 
LCS_AVERAGE  LCS_A:   5.21  (   2.12    2.65   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      6      6      7      7      8      9     10     11     12     12     14     15     15     16     17     17     18     19 
GDT PERCENT_CA   2.42   3.23   4.84   4.84   5.65   5.65   6.45   7.26   8.06   8.87   9.68   9.68  11.29  12.10  12.10  12.90  13.71  13.71  14.52  15.32
GDT RMS_LOCAL    0.08   0.56   1.21   1.21   1.59   1.59   2.29   2.69   3.01   3.72   3.93   3.93   4.70   5.08   5.08   5.47   5.68   5.68   6.76   6.95
GDT RMS_ALL_CA  26.55  12.84  12.55  12.55  12.42  12.42  12.40  12.45  12.46  12.94  13.19  13.19  16.89  16.45  16.45  15.95  15.91  15.91   9.90  10.18

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314         20.748
LGA    A     315      A     315         13.220
LGA    I     316      I     316         10.638
LGA    Y     317      Y     317         10.603
LGA    H     318      H     318          5.171
LGA    S     319      S     319          2.576
LGA    T     320      T     320          2.497
LGA    Y     321      Y     321          1.754
LGA    T     322      T     322          7.337
LGA    G     323      G     323          8.864
LGA    R     324      R     324          8.200
LGA    D     327      D     327          3.391
LGA    E     328      E     328          6.025
LGA    P     329      P     329          3.711
LGA    A     330      A     330          2.508
LGA    V     331      V     331          2.907
LGA    G     333      G     333          3.846
LGA    A     335      A     335          1.824
LGA    L     336      L     336         15.712
LGA    N     337      N     337         19.608
LGA    E     338      E     338         15.751
LGA    P     342      P     342         19.480
LGA    I     343      I     343         24.438
LGA    L     344      L     344         28.084

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  124    4.0      9    2.69     7.056     6.107     0.322

LGA_LOCAL      RMSD =  2.692  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.604  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  9.321  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.454846 * X  +   0.886576 * Y  +  -0.084251 * Z  +  23.865076
  Y_new =   0.694522 * X  +  -0.293909 * Y  +   0.656701 * Z  +  76.057449
  Z_new =   0.557454 * X  +  -0.357212 * Y  +  -0.749430 * Z  +  98.857506 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.696804    0.444789  [ DEG:  -154.5155     25.4845 ]
  Theta =  -0.591315   -2.550277  [ DEG:   -33.8799   -146.1201 ]
  Phi   =   0.990981   -2.150611  [ DEG:    56.7790   -123.2210 ]
 
# 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_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_3-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   2.69   6.107     9.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_3-D1
REMARK Aligment from pdb entry: 2bco_A
ATOM     29  N   ASP   314      68.928  74.061  78.303  1.00  0.00              
ATOM     30  CA  ASP   314      68.447  72.694  78.412  1.00  0.00              
ATOM     31  C   ASP   314      69.560  71.845  79.001  1.00  0.00              
ATOM     32  O   ASP   314      70.076  70.944  78.352  1.00  0.00              
ATOM     33  N   ALA   315      71.836  69.523  82.048  1.00  0.00              
ATOM     34  CA  ALA   315      71.847  68.206  82.654  1.00  0.00              
ATOM     35  C   ALA   315      71.017  68.260  83.939  1.00  0.00              
ATOM     36  O   ALA   315      70.230  67.365  84.219  1.00  0.00              
ATOM     37  N   ILE   316      68.579  70.393  84.728  1.00  0.00              
ATOM     38  CA  ILE   316      67.163  70.572  84.412  1.00  0.00              
ATOM     39  C   ILE   316      66.506  69.255  84.021  1.00  0.00              
ATOM     40  O   ILE   316      65.409  68.955  84.483  1.00  0.00              
ATOM     41  N   TYR   317      67.174  68.485  83.164  1.00  0.00              
ATOM     42  CA  TYR   317      66.664  67.193  82.709  1.00  0.00              
ATOM     43  C   TYR   317      66.594  66.211  83.871  1.00  0.00              
ATOM     44  O   TYR   317      65.624  65.471  84.002  1.00  0.00              
ATOM     45  N   HIS   318      67.622  66.200  84.714  1.00  0.00              
ATOM     46  CA  HIS   318      67.610  65.323  85.880  1.00  0.00              
ATOM     47  C   HIS   318      66.405  65.680  86.750  1.00  0.00              
ATOM     48  O   HIS   318      65.800  64.804  87.368  1.00  0.00              
ATOM     49  N   SER   319      66.078  66.972  86.803  1.00  0.00              
ATOM     50  CA  SER   319      64.947  67.443  87.601  1.00  0.00              
ATOM     51  C   SER   319      63.662  66.867  87.045  1.00  0.00              
ATOM     52  O   SER   319      62.835  66.361  87.800  1.00  0.00              
ATOM     53  N   THR   320      63.503  66.947  85.723  1.00  0.00              
ATOM     54  CA  THR   320      62.318  66.418  85.055  1.00  0.00              
ATOM     55  C   THR   320      62.129  64.949  85.417  1.00  0.00              
ATOM     56  O   THR   320      61.030  64.528  85.775  1.00  0.00              
ATOM     57  N   TYR   321      63.210  64.176  85.308  1.00  0.00              
ATOM     58  CA  TYR   321      63.164  62.751  85.588  1.00  0.00              
ATOM     59  C   TYR   321      62.840  62.472  87.050  1.00  0.00              
ATOM     60  O   TYR   321      61.998  61.631  87.358  1.00  0.00              
ATOM     61  N   THR   322      63.494  63.188  87.953  1.00  0.00              
ATOM     62  CA  THR   322      63.234  62.986  89.371  1.00  0.00              
ATOM     63  C   THR   322      61.800  63.360  89.720  1.00  0.00              
ATOM     64  O   THR   322      61.194  62.732  90.587  1.00  0.00              
ATOM     65  N   GLY   323      61.261  64.372  89.037  1.00  0.00              
ATOM     66  CA  GLY   323      59.896  64.838  89.283  1.00  0.00              
ATOM     67  C   GLY   323      58.866  63.913  88.677  1.00  0.00              
ATOM     68  O   GLY   323      57.683  64.039  88.963  1.00  0.00              
ATOM     69  N   ARG   324      59.318  62.989  87.837  1.00  0.00              
ATOM     70  CA  ARG   324      58.428  62.035  87.189  1.00  0.00              
ATOM     71  C   ARG   324      57.539  62.677  86.129  1.00  0.00              
ATOM     72  O   ARG   324      56.437  62.194  85.862  1.00  0.00              
ATOM     73  N   ASP   327      58.023  63.764  85.529  1.00  0.00              
ATOM     74  CA  ASP   327      57.280  64.442  84.471  1.00  0.00              
ATOM     75  C   ASP   327      57.380  63.491  83.283  1.00  0.00              
ATOM     76  O   ASP   327      58.469  63.182  82.800  1.00  0.00              
ATOM     77  N   GLU   328      56.233  63.008  82.833  1.00  0.00              
ATOM     78  CA  GLU   328      56.175  62.034  81.756  1.00  0.00              
ATOM     79  C   GLU   328      56.803  62.407  80.425  1.00  0.00              
ATOM     80  O   GLU   328      57.327  61.539  79.732  1.00  0.00              
ATOM     81  N   PRO   329      56.760  63.684  80.060  1.00  0.00              
ATOM     82  CA  PRO   329      57.335  64.093  78.792  1.00  0.00              
ATOM     83  C   PRO   329      57.732  65.561  78.755  1.00  0.00              
ATOM     84  O   PRO   329      57.180  66.385  79.494  1.00  0.00              
ATOM     85  N   ALA   330      58.709  65.871  77.903  1.00  0.00              
ATOM     86  CA  ALA   330      59.159  67.244  77.723  1.00  0.00              
ATOM     87  C   ALA   330      59.169  67.568  76.234  1.00  0.00              
ATOM     88  O   ALA   330      59.728  66.826  75.433  1.00  0.00              
ATOM     89  N   VAL   331      58.524  68.666  75.871  1.00  0.00              
ATOM     90  CA  VAL   331      58.459  69.100  74.481  1.00  0.00              
ATOM     91  C   VAL   331      59.533  70.194  74.310  1.00  0.00              
ATOM     92  O   VAL   331      59.541  71.188  75.038  1.00  0.00              
ATOM     93  N   GLY   333      60.449  69.990  73.372  1.00  0.00              
ATOM     94  CA  GLY   333      61.503  70.959  73.111  1.00  0.00              
ATOM     95  C   GLY   333      61.007  71.901  72.013  1.00  0.00              
ATOM     96  O   GLY   333      60.891  71.494  70.864  1.00  0.00              
ATOM     97  N   ALA   335      60.701  73.147  72.356  1.00  0.00              
ATOM     98  CA  ALA   335      60.218  74.090  71.347  1.00  0.00              
ATOM     99  C   ALA   335      61.261  74.328  70.258  1.00  0.00              
ATOM    100  O   ALA   335      62.459  74.265  70.522  1.00  0.00              
ATOM    101  N   LEU   336      55.775  83.344  76.029  1.00  0.00              
ATOM    102  CA  LEU   336      55.443  82.954  77.394  1.00  0.00              
ATOM    103  C   LEU   336      56.400  83.514  78.427  1.00  0.00              
ATOM    104  O   LEU   336      57.460  84.037  78.101  1.00  0.00              
ATOM    105  N   ASN   337      56.003  83.386  79.683  1.00  0.00              
ATOM    106  CA  ASN   337      56.788  83.873  80.802  1.00  0.00              
ATOM    107  C   ASN   337      58.089  83.069  80.908  1.00  0.00              
ATOM    108  O   ASN   337      59.155  83.623  81.193  1.00  0.00              
ATOM    109  N   GLU   338      57.985  81.761  80.673  1.00  0.00              
ATOM    110  CA  GLU   338      59.126  80.856  80.712  1.00  0.00              
ATOM    111  C   GLU   338      60.128  81.210  79.609  1.00  0.00              
ATOM    112  O   GLU   338      61.334  81.293  79.847  1.00  0.00              
ATOM    113  N   PRO   342      59.618  81.407  78.396  1.00  0.00              
ATOM    114  CA  PRO   342      60.466  81.765  77.265  1.00  0.00              
ATOM    115  C   PRO   342      61.192  83.080  77.541  1.00  0.00              
ATOM    116  O   PRO   342      62.359  83.228  77.195  1.00  0.00              
ATOM    117  N   ILE   343      60.504  84.033  78.164  1.00  0.00              
ATOM    118  CA  ILE   343      61.113  85.327  78.457  1.00  0.00              
ATOM    119  C   ILE   343      62.364  85.216  79.336  1.00  0.00              
ATOM    120  O   ILE   343      63.345  85.929  79.123  1.00  0.00              
ATOM    121  N   LEU   344      62.314  84.343  80.335  1.00  0.00              
ATOM    122  CA  LEU   344      63.446  84.150  81.229  1.00  0.00              
ATOM    123  C   LEU   344      64.588  83.449  80.511  1.00  0.00              
ATOM    124  O   LEU   344      65.743  83.788  80.709  1.00  0.00              
END
