
#######################################################
#                                                     #
#                        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   38 (  152),  selected   28 , name T0292AL170_1_2-D2
# Molecule2: number of CA atoms  173 ( 1393),  selected   28 , name T0292_D2.pdb
# PARAMETERS: T0292AL170_1_2-D2.T0292_D2.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:    28       137 - 164         4.84     4.84
  LCS_AVERAGE:     16.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       137 - 160         1.96     6.09
  LCS_AVERAGE:     12.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20       137 - 156         0.96     6.09
  LCS_AVERAGE:      8.86

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:  173
LCS_GDT     H     137     H     137     20   24   28     0    3    4   15   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     R     138     R     138     20   24   28     5   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     D     139     D     139     20   24   28     4   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     L     140     L     140     20   24   28    10   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     K     141     K     141     20   24   28    11   16   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     P     142     P     142     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     A     143     A     143     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     N     144     N     144     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     V     145     V     145     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     F     146     F     146     20   24   28    10   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     L     147     L     147     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     D     148     D     148     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     G     149     G     149     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     K     150     K     150     20   24   28    10   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     Q     151     Q     151     20   24   28     4   14   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     N     152     N     152     20   24   28    10   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     V     153     V     153     20   24   28    10   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     K     154     K     154     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     L     155     L     155     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     G     156     G     156     20   24   28    11   17   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     D     157     D     157      4   24   28     3    4    7   15   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     F     158     F     158      4   24   28     4   16   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     G     159     G     159      4   24   28     4    5   19   21   22   23   23   23   23   23   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     L     160     L     160      4   24   28     4    4    4    7    8   12   12   12   16   20   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     A     161     A     161      4   10   28     4    4    5    7    8   17   19   19   21   21   25   25   26   26   26   26   27   27   27   27 
LCS_GDT     R     162     R     162      3   10   28     3    3    3    3    7   12   12   19   21   21   23   24   26   26   26   26   27   27   27   27 
LCS_GDT     I     163     I     163      3    3   28     3    3    3    3    3    5    7   14   17   19   19   19   23   25   25   26   27   27   27   27 
LCS_GDT     L     164     L     164      3    3   28     3    3    3    3    3    4    7    7   13   14   15   17   18   18   18   19   20   23   23   24 
LCS_AVERAGE  LCS_A:  12.49  (   8.86   12.43   16.18 )

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     11     17     19     21     22     23     23     23     23     23     25     25     26     26     26     26     27     27     27     27 
GDT PERCENT_CA   6.36   9.83  10.98  12.14  12.72  13.29  13.29  13.29  13.29  13.29  14.45  14.45  15.03  15.03  15.03  15.03  15.61  15.61  15.61  15.61
GDT RMS_LOCAL    0.33   0.65   0.73   0.97   1.08   1.24   1.24   1.24   1.24   1.24   2.52   2.52   3.03   3.03   3.03   3.03   3.83   3.83   3.83   3.83
GDT RMS_ALL_CA   5.85   6.08   6.16   6.20   6.24   6.37   6.37   6.37   6.37   6.37   5.73   5.73   5.36   5.36   5.36   5.36   4.98   4.98   4.98   4.98

#      Molecule1      Molecule2       DISTANCE
LGA    H     137      H     137          2.402
LGA    R     138      R     138          0.791
LGA    D     139      D     139          1.113
LGA    L     140      L     140          0.605
LGA    K     141      K     141          0.870
LGA    P     142      P     142          0.565
LGA    A     143      A     143          0.581
LGA    N     144      N     144          0.654
LGA    V     145      V     145          0.634
LGA    F     146      F     146          1.007
LGA    L     147      L     147          0.522
LGA    D     148      D     148          0.776
LGA    G     149      G     149          0.936
LGA    K     150      K     150          0.618
LGA    Q     151      Q     151          1.935
LGA    N     152      N     152          1.159
LGA    V     153      V     153          0.337
LGA    K     154      K     154          1.073
LGA    L     155      L     155          0.940
LGA    G     156      G     156          0.822
LGA    D     157      D     157          2.905
LGA    F     158      F     158          1.551
LGA    G     159      G     159          1.784
LGA    L     160      L     160          8.020
LGA    A     161      A     161          9.260
LGA    R     162      R     162         11.474
LGA    I     163      I     163         17.542
LGA    L     164      L     164         22.586

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   38  173    4.0     23    1.24    12.572    12.827     1.717

LGA_LOCAL      RMSD =  1.239  Number of atoms =   23  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.367  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  4.843  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.820499 * X  +   0.306196 * Y  +  -0.482728 * Z  +  47.491508
  Y_new =   0.336143 * X  +   0.941457 * Y  +   0.025823 * Z  + -37.735226
  Z_new =   0.462374 * X  +  -0.141078 * Y  +  -0.875390 * Z  +  83.350365 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.981806    0.159786  [ DEG:  -170.8449      9.1551 ]
  Theta =  -0.480671   -2.660922  [ DEG:   -27.5404   -152.4596 ]
  Phi   =   2.752768   -0.388825  [ DEG:   157.7220    -22.2780 ]
 
# 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: T0292AL170_1_2-D2                             
REMARK     2: T0292_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0292AL170_1_2-D2.T0292_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   38  173   4.0   23   1.24  12.827     4.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0292AL170_1_2-D2
REMARK PARENT number 2
PARENT 1QPC_A
REMARK Aligment from pdb entry: 1QPC_A
ATOM    769  N   HIS   137      14.992  12.855  11.871  1.00  0.00              
ATOM    770  CA  HIS   137      13.530  12.772  11.900  1.00  0.00              
ATOM    771  C   HIS   137      12.886  13.880  11.045  1.00  0.00              
ATOM    772  O   HIS   137      11.989  13.636  10.263  1.00  0.00              
ATOM    773  N   ARG   138      13.342  15.116  11.266  1.00  0.00              
ATOM    774  CA  ARG   138      12.906  16.303  10.523  1.00  0.00              
ATOM    775  C   ARG   138      11.543  16.856  10.828  1.00  0.00              
ATOM    776  O   ARG   138      11.178  17.904  10.285  1.00  0.00              
ATOM    777  N   ASP   139      10.786  16.183  11.687  1.00  0.00              
ATOM    778  CA  ASP   139       9.425  16.655  12.026  1.00  0.00              
ATOM    779  C   ASP   139       9.241  16.478  13.537  1.00  0.00              
ATOM    780  O   ASP   139       8.153  16.139  14.010  1.00  0.00              
ATOM    781  N   LEU   140      10.258  16.824  14.314  1.00  0.00              
ATOM    782  CA  LEU   140      10.193  16.653  15.744  1.00  0.00              
ATOM    783  C   LEU   140       9.444  17.848  16.341  1.00  0.00              
ATOM    784  O   LEU   140       9.887  18.976  16.243  1.00  0.00              
ATOM    785  N   LYS   141       8.317  17.567  16.962  1.00  0.00              
ATOM    786  CA  LYS   141       7.446  18.556  17.602  1.00  0.00              
ATOM    787  C   LYS   141       6.514  17.780  18.508  1.00  0.00              
ATOM    788  O   LYS   141       6.322  16.589  18.303  1.00  0.00              
ATOM    789  N   PRO   142       5.827  18.466  19.414  1.00  0.00              
ATOM    790  CA  PRO   142       4.940  17.738  20.334  1.00  0.00              
ATOM    791  C   PRO   142       3.779  17.004  19.647  1.00  0.00              
ATOM    792  O   PRO   142       3.292  15.986  20.232  1.00  0.00              
ATOM    793  N   ALA   143       3.340  17.477  18.489  1.00  0.00              
ATOM    794  CA  ALA   143       2.280  16.781  17.763  1.00  0.00              
ATOM    795  C   ALA   143       2.732  15.382  17.343  1.00  0.00              
ATOM    796  O   ALA   143       1.886  14.523  17.104  1.00  0.00              
ATOM    797  N   ASN   144       4.044  15.182  17.262  1.00  0.00              
ATOM    798  CA  ASN   144       4.595  13.907  16.774  1.00  0.00              
ATOM    799  C   ASN   144       5.225  13.065  17.839  1.00  0.00              
ATOM    800  O   ASN   144       6.053  12.197  17.568  1.00  0.00              
ATOM    801  N   VAL   145       4.844  13.342  19.065  1.00  0.00              
ATOM    802  CA  VAL   145       5.216  12.483  20.201  1.00  0.00              
ATOM    803  C   VAL   145       3.887  11.881  20.678  1.00  0.00              
ATOM    804  O   VAL   145       2.897  12.567  20.789  1.00  0.00              
ATOM    805  N   PHE   146       3.861  10.567  20.830  1.00  0.00              
ATOM    806  CA  PHE   146       2.629   9.905  21.327  1.00  0.00              
ATOM    807  C   PHE   146       2.817   9.495  22.784  1.00  0.00              
ATOM    808  O   PHE   146       3.935   9.220  23.269  1.00  0.00              
ATOM    809  N   LEU   147       1.701   9.475  23.548  1.00  0.00              
ATOM    810  CA  LEU   147       1.748   9.185  24.968  1.00  0.00              
ATOM    811  C   LEU   147       0.963   7.896  25.280  1.00  0.00              
ATOM    812  O   LEU   147      -0.157   7.753  24.803  1.00  0.00              
ATOM    813  N   ASP   148       1.579   7.002  26.048  1.00  0.00              
ATOM    814  CA  ASP   148       0.937   5.711  26.388  1.00  0.00              
ATOM    815  C   ASP   148      -0.013   5.841  27.555  1.00  0.00              
ATOM    816  O   ASP   148      -0.085   6.866  28.226  1.00  0.00              
ATOM    817  N   GLY   149      -0.719   4.742  27.818  1.00  0.00              
ATOM    818  CA  GLY   149      -1.592   4.740  28.958  1.00  0.00              
ATOM    819  C   GLY   149      -0.863   4.909  30.291  1.00  0.00              
ATOM    820  O   GLY   149      -1.482   5.261  31.268  1.00  0.00              
ATOM    821  N   LYS   150       0.449   4.599  30.359  1.00  0.00              
ATOM    822  CA  LYS   150       1.218   4.736  31.578  1.00  0.00              
ATOM    823  C   LYS   150       2.021   6.031  31.630  1.00  0.00              
ATOM    824  O   LYS   150       2.908   6.209  32.436  1.00  0.00              
ATOM    825  N   GLN   151       1.723   6.897  30.681  1.00  0.00              
ATOM    826  CA  GLN   151       2.322   8.226  30.595  1.00  0.00              
ATOM    827  C   GLN   151       3.779   8.177  30.170  1.00  0.00              
ATOM    828  O   GLN   151       4.631   8.896  30.709  1.00  0.00              
ATOM    829  N   ASN   152       4.092   7.175  29.361  1.00  0.00              
ATOM    830  CA  ASN   152       5.434   7.156  28.759  1.00  0.00              
ATOM    831  C   ASN   152       5.286   7.738  27.329  1.00  0.00              
ATOM    832  O   ASN   152       4.229   7.748  26.701  1.00  0.00              
ATOM    833  N   VAL   153       6.385   8.248  26.789  1.00  0.00              
ATOM    834  CA  VAL   153       6.295   8.917  25.490  1.00  0.00              
ATOM    835  C   VAL   153       7.140   8.218  24.454  1.00  0.00              
ATOM    836  O   VAL   153       8.184   7.662  24.807  1.00  0.00              
ATOM    837  N   LYS   154       6.689   8.260  23.208  1.00  0.00              
ATOM    838  CA  LYS   154       7.418   7.623  22.103  1.00  0.00              
ATOM    839  C   LYS   154       7.425   8.544  20.894  1.00  0.00              
ATOM    840  O   LYS   154       6.468   9.269  20.597  1.00  0.00              
ATOM    841  N   LEU   155       8.526   8.488  20.139  1.00  0.00              
ATOM    842  CA  LEU   155       8.617   9.276  18.908  1.00  0.00              
ATOM    843  C   LEU   155       7.723   8.622  17.839  1.00  0.00              
ATOM    844  O   LEU   155       7.749   7.404  17.636  1.00  0.00              
ATOM    845  N   GLY   156       7.000   9.447  17.109  1.00  0.00              
ATOM    846  CA  GLY   156       6.128   8.975  16.062  1.00  0.00              
ATOM    847  C   GLY   156       6.298   9.804  14.771  1.00  0.00              
ATOM    848  O   GLY   156       7.081  10.760  14.746  1.00  0.00              
ATOM    849  N   ASP   157       5.545   9.422  13.750  1.00  0.00              
ATOM    850  CA  ASP   157       5.483  10.086  12.457  1.00  0.00              
ATOM    851  C   ASP   157       6.831  10.159  11.773  1.00  0.00              
ATOM    852  O   ASP   157       7.511  11.195  11.739  1.00  0.00              
ATOM    853  N   PHE   158       7.157   9.062  11.102  1.00  0.00              
ATOM    854  CA  PHE   158       8.444   8.942  10.435  1.00  0.00              
ATOM    855  C   PHE   158       8.410   9.256   8.941  1.00  0.00              
ATOM    856  O   PHE   158       9.351   8.926   8.190  1.00  0.00              
ATOM    857  N   GLY   159       7.393   9.994   8.519  1.00  0.00              
ATOM    858  CA  GLY   159       7.230  10.308   7.110  1.00  0.00              
ATOM    859  C   GLY   159       8.387  11.093   6.497  1.00  0.00              
ATOM    860  O   GLY   159       8.680  10.932   5.304  1.00  0.00              
ATOM    861  N   LEU   160       8.975  11.996   7.279  1.00  0.00              
ATOM    862  CA  LEU   160      10.099  12.794   6.774  1.00  0.00              
ATOM    863  C   LEU   160      11.421  12.254   7.217  1.00  0.00              
ATOM    864  O   LEU   160      12.461  12.804   6.861  1.00  0.00              
ATOM    865  N   ALA   161      11.434  11.172   8.000  1.00  0.00              
ATOM    866  CA  ALA   161      12.709  10.625   8.518  1.00  0.00              
ATOM    867  C   ALA   161      13.576  10.040   7.430  1.00  0.00              
ATOM    868  O   ALA   161      13.056   9.569   6.446  1.00  0.00              
ATOM    869  N   ARG   162      14.891  10.134   7.590  1.00  0.00              
ATOM    870  CA  ARG   162      15.820   9.664   6.555  1.00  0.00              
ATOM    871  C   ARG   162      17.095   9.116   7.125  1.00  0.00              
ATOM    872  O   ARG   162      17.566   9.576   8.168  1.00  0.00              
ATOM    873  N   ILE   163      17.652   8.117   6.409  1.00  0.00              
ATOM    874  CA  ILE   163      18.936   7.534   6.760  1.00  0.00              
ATOM    875  C   ILE   163      19.942   8.491   6.143  1.00  0.00              
ATOM    876  O   ILE   163      19.896   8.782   4.940  1.00  0.00              
ATOM    877  N   LEU   164      20.871   8.915   6.979  1.00  0.00              
ATOM    878  CA  LEU   164      21.892   9.884   6.643  1.00  0.00              
ATOM    879  C   LEU   164      23.232   9.133   6.362  1.00  0.00              
ATOM    880  O   LEU   164      23.865   8.566   7.233  1.00  0.00              
ATOM    881  N   ASN   165      23.563   9.050   5.079  1.00  0.00              
ATOM    882  CA  ASN   165      24.774   8.367   4.571  1.00  0.00              
ATOM    883  C   ASN   165      26.033   9.192   4.907  1.00  0.00              
ATOM    884  O   ASN   165      26.980   8.686   5.517  1.00  0.00              
ATOM    885  N   HIS   166      25.973  10.482   4.609  1.00  0.00              
ATOM    886  CA  HIS   166      26.993  11.468   4.906  1.00  0.00              
ATOM    887  C   HIS   166      26.305  12.423   5.903  1.00  0.00              
ATOM    888  O   HIS   166      25.067  12.486   5.969  1.00  0.00              
ATOM    889  N   ASP   167      27.071  13.134   6.707  1.00  0.00              
ATOM    890  CA  ASP   167      26.511  14.039   7.730  1.00  0.00              
ATOM    891  C   ASP   167      25.176  14.773   7.420  1.00  0.00              
ATOM    892  O   ASP   167      24.294  14.819   8.310  1.00  0.00              
ATOM    893  N   THR   168      24.911  15.076   6.142  1.00  0.00              
ATOM    894  CA  THR   168      23.718  15.870   5.780  1.00  0.00              
ATOM    895  C   THR   168      22.700  15.438   4.674  1.00  0.00              
ATOM    896  O   THR   168      23.072  14.807   3.664  1.00  0.00              
ATOM    897  N   PHE   170      19.867  16.915   2.063  1.00  0.00              
ATOM    898  CA  PHE   170      19.445  18.150   1.431  1.00  0.00              
ATOM    899  C   PHE   170      18.084  17.923   0.763  1.00  0.00              
ATOM    900  O   PHE   170      17.925  17.049  -0.076  1.00  0.00              
ATOM    901  N   ALA   171      17.063  18.635   1.226  1.00  0.00              
ATOM    902  CA  ALA   171      15.704  18.512   0.700  1.00  0.00              
ATOM    903  C   ALA   171      15.545  19.024  -0.755  1.00  0.00              
ATOM    904  O   ALA   171      16.529  19.241  -1.449  1.00  0.00              
ATOM    905  N   LYS   172      14.297  19.275  -1.172  1.00  0.00              
ATOM    906  CA  LYS   172      13.930  19.788  -2.514  1.00  0.00              
ATOM    907  C   LYS   172      13.777  21.333  -2.427  1.00  0.00              
ATOM    908  O   LYS   172      13.099  21.802  -1.521  1.00  0.00              
ATOM    909  N   ALA   173      14.383  22.129  -3.330  1.00  0.00              
ATOM    910  CA  ALA   173      14.274  23.605  -3.240  1.00  0.00              
ATOM    911  C   ALA   173      12.863  24.088  -2.908  1.00  0.00              
ATOM    912  O   ALA   173      12.679  25.019  -2.097  1.00  0.00              
ATOM    913  N   PHE   174      11.873  23.411  -3.491  1.00  0.00              
ATOM    914  CA  PHE   174      10.480  23.749  -3.252  1.00  0.00              
ATOM    915  C   PHE   174       9.894  23.229  -1.947  1.00  0.00              
ATOM    916  O   PHE   174       8.889  23.778  -1.487  1.00  0.00              
ATOM    917  N   VAL   175      10.471  22.172  -1.363  1.00  0.00              
ATOM    918  CA  VAL   175       9.971  21.595  -0.093  1.00  0.00              
ATOM    919  C   VAL   175       9.896  22.658   1.001  1.00  0.00              
ATOM    920  O   VAL   175      10.821  23.452   1.160  1.00  0.00              
TER
END
