
#######################################################
#                                                     #
#                        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 T0356AL380_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   27 , name T0356_D3.pdb
# PARAMETERS: T0356AL380_1-D3.T0356_D3.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:    16       448 - 463         4.33    15.50
  LONGEST_CONTINUOUS_SEGMENT:    16       449 - 464         4.90    15.74
  LCS_AVERAGE:     11.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       449 - 456         1.82    17.74
  LONGEST_CONTINUOUS_SEGMENT:     8       450 - 457         1.68    17.32
  LCS_AVERAGE:      5.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       450 - 456         0.98    17.77
  LCS_AVERAGE:      3.98

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:  120
LCS_GDT     A     441     A     441      4    4    7     3    3    4    4    4    4    5    6    6    6    6    6    7    7    8   10   10   12   12   13 
LCS_GDT     S     442     S     442      4    4    7     3    3    4    4    4    4    5    6    6    6    6    6    7    7    8   10   11   12   12   13 
LCS_GDT     P     443     P     443      4    4    9     3    3    4    4    4    4    5    6    6    6    6    8    9    9    9   10   11   12   12   13 
LCS_GDT     V     444     V     444      4    4    9     3    3    4    4    4    4    5    6    7    7    8    8    9    9    9   10   11   12   12   13 
LCS_GDT     S     445     S     445      3    6    9     3    3    4    4    5    5    6    6    7    7    8    8    9    9    9   10   11   12   12   13 
LCS_GDT     G     446     G     446      5    6    9     3    4    5    5    5    5    6    6    7    7    8    8    9    9    9   10   11   12   12   13 
LCS_GDT     L     447     L     447      5    6    9     3    4    5    5    5    5    6    6    7    7    8    8    9    9    9   10   13   16   16   16 
LCS_GDT     G     448     G     448      5    6   16     3    4    5    5    5    5    6    6    7    7    8   13   14   15   15   15   16   17   17   18 
LCS_GDT     S     449     S     449      5    8   16     3    4    5    5    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     K     450     K     450      7    8   16     3    6    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     M     451     M     451      7    8   16     3    6    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     G     452     G     452      7    8   16     3    6    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     L     453     L     453      7    8   16     3    6    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     D     454     D     454      7    8   16     3    6    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     A     455     A     455      7    8   16     3    6    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     T     456     T     456      7    8   16     3    4    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     N     457     N     457      4    8   16     3    5    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     K     458     K     458      4    6   16     3    4    4    4    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     W     459     W     459      4    6   16     3    4    4    6    9   10   12   12   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     P     460     P     460      3    5   16     3    3    6    7    9   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     G     461     G     461      3    5   16     3    3    3    4    5   12   12   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     E     462     E     462      4    6   16     3    4    5    5    5    7   10   13   13   13   14   14   14   15   15   15   16   17   17   18 
LCS_GDT     T     463     T     463      4    6   16     3    4    5    5    5    6    6    7    8   10   10   11   12   14   15   15   16   17   17   18 
LCS_GDT     Q     464     Q     464      4    6   16     3    4    5    5    5    5    6    7    8    8    9   10   12   12   13   14   15   17   17   18 
LCS_GDT     R     465     R     465      4    6   12     3    4    5    5    5    6    6    7    8    8    9   10   12   12   13   13   15   17   17   18 
LCS_GDT     E     466     E     466      4    6   12     3    3    5    5    5    6    6    7    8    8    9   10   12   12   13   13   13   14   15   15 
LCS_GDT     W     467     W     467      3    6   12     0    3    3    4    5    5    6    7    7    7    9   10   12   12   13   13   13   14   15   15 
LCS_AVERAGE  LCS_A:   6.85  (   3.98    5.25   11.33 )

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      6      6      7      9     12     12     13     13     13     14     14     14     15     15     15     16     17     17     18 
GDT PERCENT_CA   2.50   5.00   5.00   5.83   7.50  10.00  10.00  10.83  10.83  10.83  11.67  11.67  11.67  12.50  12.50  12.50  13.33  14.17  14.17  15.00
GDT RMS_LOCAL    0.03   0.54   0.54   0.98   1.73   2.27   2.26   2.64   2.52   2.52   2.94   2.94   2.94   3.74   3.72   3.72   4.33   5.30   5.30   6.16
GDT RMS_ALL_CA  25.87  18.00  18.00  17.77  16.27  15.86  15.99  15.74  15.97  15.97  15.87  15.87  15.87  15.55  15.84  15.84  15.50  15.39  15.39  15.20

#      Molecule1      Molecule2       DISTANCE
LGA    A     441      A     441         34.160
LGA    S     442      S     442         30.915
LGA    P     443      P     443         28.888
LGA    V     444      V     444         28.414
LGA    S     445      S     445         26.178
LGA    G     446      G     446         22.524
LGA    L     447      L     447         16.993
LGA    G     448      G     448          9.994
LGA    S     449      S     449          3.201
LGA    K     450      K     450          1.061
LGA    M     451      M     451          2.320
LGA    G     452      G     452          1.852
LGA    L     453      L     453          2.397
LGA    D     454      D     454          1.370
LGA    A     455      A     455          2.919
LGA    T     456      T     456          2.153
LGA    N     457      N     457          3.032
LGA    K     458      K     458          3.523
LGA    W     459      W     459          7.197
LGA    P     460      P     460          3.653
LGA    G     461      G     461          3.117
LGA    E     462      E     462          3.734
LGA    T     463      T     463          7.965
LGA    Q     464      Q     464         13.276
LGA    R     465      R     465         16.153
LGA    E     466      E     466         18.205
LGA    W     467      W     467         18.319

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  120    4.0     13    2.64     8.542     8.147     0.475

LGA_LOCAL      RMSD =  2.637  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.711  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 13.511  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.031424 * X  +   0.907899 * Y  +  -0.418010 * Z  +  -8.501786
  Y_new =  -0.906713 * X  +  -0.150085 * Y  +  -0.394140 * Z  +  65.240204
  Z_new =  -0.420576 * X  +   0.391400 * Y  +   0.818487 * Z  +  39.615482 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.446056   -2.695537  [ DEG:    25.5571   -154.4429 ]
  Theta =   0.434080    2.707512  [ DEG:    24.8710    155.1290 ]
  Phi   =  -1.536153    1.605440  [ DEG:   -88.0151     91.9849 ]
 
# 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: T0356AL380_1-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL380_1-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  120   4.0   13   2.64   8.147    13.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL380_1-D3
REMARK Aligment from pdb entry: 1xc3A
ATOM      1  N   ALA   441      32.304  67.918  51.471  1.00  0.00              
ATOM      2  CA  ALA   441      33.621  67.441  51.834  1.00  0.00              
ATOM      3  C   ALA   441      33.569  66.195  52.702  1.00  0.00              
ATOM      4  O   ALA   441      32.771  66.107  53.632  1.00  0.00              
ATOM      5  N   SER   442      34.427  65.236  52.369  1.00  0.00              
ATOM      6  CA  SER   442      34.452  63.927  53.031  1.00  0.00              
ATOM      7  C   SER   442      35.803  63.680  53.685  1.00  0.00              
ATOM      8  O   SER   442      36.834  64.104  53.164  1.00  0.00              
ATOM      9  N   PRO   443      35.784  62.993  54.826  1.00  0.00              
ATOM     10  CA  PRO   443      37.013  62.549  55.482  1.00  0.00              
ATOM     11  C   PRO   443      37.270  61.061  55.258  1.00  0.00              
ATOM     12  O   PRO   443      36.332  60.266  55.151  1.00  0.00              
ATOM     13  N   VAL   444      38.543  60.689  55.189  1.00  0.00              
ATOM     14  CA  VAL   444      38.937  59.293  55.094  1.00  0.00              
ATOM     15  C   VAL   444      40.015  58.958  56.097  1.00  0.00              
ATOM     16  O   VAL   444      40.946  59.749  56.321  1.00  0.00              
ATOM     17  N   SER   445      39.884  57.797  56.722  1.00  0.00              
ATOM     18  CA  SER   445      40.902  57.286  57.623  1.00  0.00              
ATOM     19  C   SER   445      41.324  55.913  57.115  1.00  0.00              
ATOM     20  O   SER   445      40.504  54.992  57.044  1.00  0.00              
ATOM     21  N   GLY   446      42.587  55.782  56.732  1.00  0.00              
ATOM     22  CA  GLY   446      43.151  54.470  56.462  1.00  0.00              
ATOM     23  C   GLY   446      44.023  54.106  57.648  1.00  0.00              
ATOM     24  O   GLY   446      45.124  54.655  57.832  1.00  0.00              
ATOM     25  N   LEU   447      43.488  53.207  58.468  1.00  0.00              
ATOM     26  CA  LEU   447      44.103  52.809  59.727  1.00  0.00              
ATOM     27  C   LEU   447      44.985  51.598  59.489  1.00  0.00              
ATOM     28  O   LEU   447      44.488  50.518  59.163  1.00  0.00              
ATOM     29  N   GLY   448      46.291  51.792  59.641  1.00  0.00              
ATOM     30  CA  GLY   448      47.275  50.734  59.469  1.00  0.00              
ATOM     31  C   GLY   448      47.912  50.386  60.787  1.00  0.00              
ATOM     32  O   GLY   448      47.789  51.126  61.772  1.00  0.00              
ATOM     33  N   SER   449      48.590  49.246  60.814  1.00  0.00              
ATOM     34  CA  SER   449      49.302  48.800  62.014  1.00  0.00              
ATOM     35  C   SER   449      50.502  49.677  62.337  1.00  0.00              
ATOM     36  O   SER   449      50.855  49.842  63.508  1.00  0.00              
ATOM     37  N   LYS   450      51.115  50.257  61.302  1.00  0.00              
ATOM     38  CA  LYS   450      52.300  51.114  61.476  1.00  0.00              
ATOM     39  C   LYS   450      51.986  52.620  61.387  1.00  0.00              
ATOM     40  O   LYS   450      52.546  53.419  62.141  1.00  0.00              
ATOM     41  N   MET   451      51.089  53.013  60.486  1.00  0.00              
ATOM     42  CA  MET   451      50.667  54.418  60.424  1.00  0.00              
ATOM     43  C   MET   451      49.182  54.570  60.121  1.00  0.00              
ATOM     44  O   MET   451      48.540  53.641  59.606  1.00  0.00              
ATOM     45  N   GLY   452      48.654  55.739  60.478  1.00  0.00              
ATOM     46  CA  GLY   452      47.360  56.202  60.026  1.00  0.00              
ATOM     47  C   GLY   452      47.579  57.240  58.930  1.00  0.00              
ATOM     48  O   GLY   452      48.492  58.074  59.022  1.00  0.00              
ATOM     49  N   LEU   453      46.743  57.183  57.903  1.00  0.00              
ATOM     50  CA  LEU   453      46.628  58.248  56.919  1.00  0.00              
ATOM     51  C   LEU   453      45.205  58.796  57.059  1.00  0.00              
ATOM     52  O   LEU   453      44.235  58.027  57.037  1.00  0.00              
ATOM     53  N   ASP   454      45.087  60.112  57.223  1.00  0.00              
ATOM     54  CA  ASP   454      43.788  60.781  57.162  1.00  0.00              
ATOM     55  C   ASP   454      43.799  61.729  55.989  1.00  0.00              
ATOM     56  O   ASP   454      44.838  62.327  55.676  1.00  0.00              
ATOM     57  N   ALA   455      42.643  61.874  55.352  1.00  0.00              
ATOM     58  CA  ALA   455      42.517  62.708  54.179  1.00  0.00              
ATOM     59  C   ALA   455      41.170  63.376  54.179  1.00  0.00              
ATOM     60  O   ALA   455      40.201  62.864  54.750  1.00  0.00              
ATOM     61  N   THR   456      41.135  64.535  53.532  1.00  0.00              
ATOM     62  CA  THR   456      39.903  65.218  53.207  1.00  0.00              
ATOM     63  C   THR   456      39.817  65.235  51.694  1.00  0.00              
ATOM     64  O   THR   456      40.798  65.522  51.021  1.00  0.00              
ATOM     65  N   ASN   457      38.647  64.909  51.161  1.00  0.00              
ATOM     66  CA  ASN   457      38.464  64.830  49.726  1.00  0.00              
ATOM     67  C   ASN   457      37.015  64.923  49.301  1.00  0.00              
ATOM     68  O   ASN   457      36.146  65.312  50.087  1.00  0.00              
ATOM     69  N   LYS   458      36.772  64.547  48.047  1.00  0.00              
ATOM     70  CA  LYS   458      35.463  64.681  47.399  1.00  0.00              
ATOM     71  C   LYS   458      34.945  63.321  46.939  1.00  0.00              
ATOM     72  O   LYS   458      35.706  62.354  46.857  1.00  0.00              
ATOM     73  N   TRP   459      33.657  63.269  46.604  1.00  0.00              
ATOM     74  CA  TRP   459      33.005  62.027  46.176  1.00  0.00              
ATOM     75  C   TRP   459      33.603  61.455  44.899  1.00  0.00              
ATOM     76  O   TRP   459      33.510  60.253  44.664  1.00  0.00              
ATOM     77  N   PRO   460      34.244  62.307  44.097  1.00  0.00              
ATOM     78  CA  PRO   460      34.884  61.864  42.863  1.00  0.00              
ATOM     79  C   PRO   460      36.318  61.353  43.074  1.00  0.00              
ATOM     80  O   PRO   460      37.028  61.078  42.114  1.00  0.00              
ATOM     81  N   GLY   461      36.740  61.238  44.334  1.00  0.00              
ATOM     82  CA  GLY   461      38.046  60.682  44.650  1.00  0.00              
ATOM     83  C   GLY   461      39.173  61.692  44.722  1.00  0.00              
ATOM     84  O   GLY   461      40.305  61.318  45.005  1.00  0.00              
ATOM     85  N   GLU   462      38.877  62.966  44.469  1.00  0.00              
ATOM     86  CA  GLU   462      39.876  64.030  44.635  1.00  0.00              
ATOM     87  C   GLU   462      40.351  64.106  46.089  1.00  0.00              
ATOM     88  O   GLU   462      39.544  64.179  47.000  1.00  0.00              
ATOM     89  N   THR   463      41.660  64.095  46.292  1.00  0.00              
ATOM     90  CA  THR   463      42.236  64.360  47.615  1.00  0.00              
ATOM     91  C   THR   463      42.585  65.854  47.726  1.00  0.00              
ATOM     92  O   THR   463      43.411  66.363  46.968  1.00  0.00              
ATOM     93  N   GLN   464      41.942  66.527  48.678  1.00  0.00              
ATOM     94  CA  GLN   464      42.134  67.960  48.934  1.00  0.00              
ATOM     95  C   GLN   464      43.334  68.207  49.859  1.00  0.00              
ATOM     96  O   GLN   464      44.133  69.124  49.649  1.00  0.00              
ATOM     97  N   ARG   465      43.456  67.374  50.886  1.00  0.00              
ATOM     98  CA  ARG   465      44.483  67.541  51.893  1.00  0.00              
ATOM     99  C   ARG   465      44.734  66.187  52.511  1.00  0.00              
ATOM    100  O   ARG   465      43.846  65.333  52.519  1.00  0.00              
ATOM    101  N   GLU   466      45.930  65.980  53.043  1.00  0.00              
ATOM    102  CA  GLU   466      46.179  64.748  53.789  1.00  0.00              
ATOM    103  C   GLU   466      47.220  64.903  54.880  1.00  0.00              
ATOM    104  O   GLU   466      48.024  65.844  54.879  1.00  0.00              
ATOM    105  N   TRP   467      47.179  63.966  55.816  1.00  0.00              
ATOM    106  CA  TRP   467      48.153  63.867  56.878  1.00  0.00              
ATOM    107  C   TRP   467      48.399  62.394  57.214  1.00  0.00              
ATOM    108  O   TRP   467      47.536  61.542  56.992  1.00  0.00              
END
