
#######################################################
#                                                     #
#                        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   21 (  161),  selected   21 , name T0298TS022_5_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   21 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_5_2-D1.T0298_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:    21       316 - 336         4.54     4.54
  LCS_AVERAGE:     14.19

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       324 - 332         1.96     8.40
  LCS_AVERAGE:      5.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       324 - 330         0.54    10.38
  LCS_AVERAGE:      3.22

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:  148
LCS_GDT     V     316     V     316      3    4   21     3    3    3    3    4    4    4    5    5   15   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     R     317     R     317      3    4   21     3    3    3    3    4    4    4    5    6    8   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     K     318     K     318      3    5   21     3    3    3    3    4    5    7    8    9   15   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     G     319     G     319      4    7   21     2    4    4    5    6    7    7   11   12   15   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     A     320     A     320      4    7   21     4    4    6    6    7   10   12   14   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     A     321     A     321      4    7   21     4    4    6    6    8   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     L     322     L     322      4    7   21     4    4    6    6    7   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     N     323     N     323      4    7   21     4    4    6    6    8   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     A     324     A     324      7    9   21     6    6    7    7    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     V     325     V     325      7    9   21     6    6    7    7    9   11   13   15   16   17   17   17   20   21   21   21   21   21   21   21 
LCS_GDT     L     326     L     326      7    9   21     6    6    7    7    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     L     327     L     327      7    9   21     6    6    7    7    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     G     328     G     328      7    9   21     6    6    7    7    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     E     329     E     329      7    9   21     6    6    7    7    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     L     330     L     330      7    9   21     3    4    7    7    8   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     L     331     L     331      4    9   21     3    5    5    6    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     I     332     I     332      4    9   21     3    5    5    6    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     K     333     K     333      4    7   21     3    5    5    6    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     H     334     H     334      4    7   21     3    5    5    6    9   11   13   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     Y     335     Y     335      3    7   21     3    3    4    5    7    9   12   15   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_GDT     L     336     L     336      3    6   21     3    5    5    5    7   11   13   13   16   17   17   18   20   21   21   21   21   21   21   21 
LCS_AVERAGE  LCS_A:   7.48  (   3.22    5.02   14.19 )

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      6      6      7      7      9     11     13     15     16     17     17     18     20     21     21     21     21     21     21     21 
GDT PERCENT_CA   4.05   4.05   4.73   4.73   6.08   7.43   8.78  10.14  10.81  11.49  11.49  12.16  13.51  14.19  14.19  14.19  14.19  14.19  14.19  14.19
GDT RMS_LOCAL    0.26   0.26   0.54   0.54   1.79   2.13   2.76   2.96   3.10   3.33   3.33   4.05   4.39   4.54   4.54   4.54   4.54   4.54   4.54   4.54
GDT RMS_ALL_CA   9.95   9.95  10.38  10.38   8.43   8.21   5.23   6.07   5.81   5.44   5.44   4.62   4.56   4.54   4.54   4.54   4.54   4.54   4.54   4.54

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316         11.920
LGA    R     317      R     317         12.079
LGA    K     318      K     318         12.084
LGA    G     319      G     319         11.353
LGA    A     320      A     320          6.989
LGA    A     321      A     321          3.574
LGA    L     322      L     322          3.325
LGA    N     323      N     323          3.838
LGA    A     324      A     324          3.584
LGA    V     325      V     325          3.455
LGA    L     326      L     326          2.398
LGA    L     327      L     327          1.955
LGA    G     328      G     328          2.488
LGA    E     329      E     329          1.909
LGA    L     330      L     330          2.946
LGA    L     331      L     331          2.698
LGA    I     332      I     332          2.850
LGA    K     333      K     333          2.698
LGA    H     334      H     334          1.756
LGA    Y     335      Y     335          3.780
LGA    L     336      L     336          5.428

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  148    4.0     15    2.96     8.277     7.777     0.490

LGA_LOCAL      RMSD =  2.961  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.066  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  4.540  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.801726 * X  +  -0.402024 * Y  +  -0.442281 * Z  +  50.381516
  Y_new =   0.437076 * X  +  -0.899078 * Y  +   0.024951 * Z  + 110.280266
  Z_new =  -0.407676 * X  +  -0.173306 * Y  +   0.896529 * Z  +  21.978907 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.190953    2.950640  [ DEG:   -10.9408    169.0592 ]
  Theta =   0.419908    2.721685  [ DEG:    24.0589    155.9411 ]
  Phi   =   2.642466   -0.499126  [ DEG:   151.4022    -28.5978 ]
 
# 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: T0298TS022_5_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_5_2-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  148   4.0   15   2.96   7.777     4.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1qor_A
ATOM   2316  N   VAL   316      -9.493  58.072  -6.589  1.00  0.00
ATOM   2317  CA  VAL   316      -9.822  57.823  -5.218  1.00  0.00
ATOM   2318  C   VAL   316     -11.314  57.828  -5.137  1.00  0.00
ATOM   2319  O   VAL   316     -11.993  58.203  -6.091  1.00  0.00
ATOM   2320  CB  VAL   316      -9.237  58.905  -4.292  1.00  0.00
ATOM   2321  CG1 VAL   316      -7.718  58.895  -4.353  1.00  0.00
ATOM   2322  CG2 VAL   316      -9.726  60.283  -4.707  1.00  0.00
ATOM   2323  N   ARG   317     -11.870  57.383  -3.994  1.00  0.00
ATOM   2324  CA  ARG   317     -13.295  57.388  -3.842  1.00  0.00
ATOM   2325  C   ARG   317     -13.635  58.602  -3.040  1.00  0.00
ATOM   2326  O   ARG   317     -13.147  58.771  -1.923  1.00  0.00
ATOM   2327  CB  ARG   317     -13.761  56.123  -3.119  1.00  0.00
ATOM   2328  CG  ARG   317     -15.272  55.977  -3.034  1.00  0.00
ATOM   2329  CD  ARG   317     -15.664  54.679  -2.349  1.00  0.00
ATOM   2330  NE  ARG   317     -17.112  54.481  -2.338  1.00  0.00
ATOM   2331  CZ  ARG   317     -17.733  53.557  -1.613  1.00  0.00
ATOM   2332  NH1 ARG   317     -19.055  53.451  -1.667  1.00  0.00
ATOM   2333  NH2 ARG   317     -17.034  52.742  -0.835  1.00  0.00
ATOM   2334  N   LYS   318     -14.472  59.498  -3.601  1.00  0.00
ATOM   2335  CA  LYS   318     -14.817  60.692  -2.885  1.00  0.00
ATOM   2336  C   LYS   318     -16.217  61.082  -3.227  1.00  0.00
ATOM   2337  O   LYS   318     -16.904  60.393  -3.980  1.00  0.00
ATOM   2338  CB  LYS   318     -13.873  61.835  -3.261  1.00  0.00
ATOM   2339  CG  LYS   318     -13.965  62.262  -4.718  1.00  0.00
ATOM   2340  CD  LYS   318     -13.005  63.401  -5.021  1.00  0.00
ATOM   2341  CE  LYS   318     -13.058  63.792  -6.489  1.00  0.00
ATOM   2342  NZ  LYS   318     -12.179  64.956  -6.786  1.00  0.00
ATOM   2343  N   GLY   319     -16.681  62.204  -2.636  1.00  0.00
ATOM   2344  CA  GLY   319     -18.010  62.666  -2.898  1.00  0.00
ATOM   2345  C   GLY   319     -18.000  64.162  -2.963  1.00  0.00
ATOM   2346  O   GLY   319     -17.364  64.843  -2.158  1.00  0.00
ATOM   2347  N   ALA   320     -18.734  64.689  -3.958  1.00  0.00
ATOM   2348  CA  ALA   320     -18.928  66.083  -4.232  1.00  0.00
ATOM   2349  C   ALA   320     -19.719  66.699  -3.119  1.00  0.00
ATOM   2350  O   ALA   320     -19.514  67.854  -2.751  1.00  0.00
ATOM   2351  CB  ALA   320     -19.681  66.267  -5.541  1.00  0.00
ATOM   2352  N   ALA   321     -20.632  65.904  -2.534  1.00  0.00
ATOM   2353  CA  ALA   321     -21.621  66.338  -1.589  1.00  0.00
ATOM   2354  C   ALA   321     -20.988  67.007  -0.413  1.00  0.00
ATOM   2355  O   ALA   321     -21.551  67.956   0.133  1.00  0.00
ATOM   2356  CB  ALA   321     -22.425  65.151  -1.080  1.00  0.00
ATOM   2357  N   LEU   322     -19.806  66.546   0.022  1.00  0.00
ATOM   2358  CA  LEU   322     -19.223  67.155   1.178  1.00  0.00
ATOM   2359  C   LEU   322     -18.983  68.595   0.862  1.00  0.00
ATOM   2360  O   LEU   322     -19.006  69.429   1.768  1.00  0.00
ATOM   2361  CB  LEU   322     -17.900  66.475   1.533  1.00  0.00
ATOM   2362  CG  LEU   322     -17.994  65.037   2.048  1.00  0.00
ATOM   2363  CD1 LEU   322     -16.608  64.429   2.202  1.00  0.00
ATOM   2364  CD2 LEU   322     -18.684  64.995   3.404  1.00  0.00
ATOM   2365  N   ASN   323     -18.728  68.907  -0.431  1.00  0.00
ATOM   2366  CA  ASN   323     -18.560  70.265  -0.874  1.00  0.00
ATOM   2367  C   ASN   323     -19.756  70.966  -0.347  1.00  0.00
ATOM   2368  O   ASN   323     -20.831  70.370  -0.326  1.00  0.00
ATOM   2369  CB  ASN   323     -18.496  70.327  -2.401  1.00  0.00
ATOM   2370  CG  ASN   323     -17.207  69.750  -2.954  1.00  0.00
ATOM   2371  OD1 ASN   323     -16.193  69.694  -2.259  1.00  0.00
ATOM   2372  ND2 ASN   323     -17.243  69.320  -4.209  1.00  0.00
ATOM   2373  N   ALA   324     -19.578  72.238   0.073  1.00  0.00
ATOM   2374  CA  ALA   324     -20.547  72.976   0.836  1.00  0.00
ATOM   2375  C   ALA   324     -21.931  72.740   0.346  1.00  0.00
ATOM   2376  O   ALA   324     -22.266  72.974  -0.814  1.00  0.00
ATOM   2377  CB  ALA   324     -20.269  74.468   0.744  1.00  0.00
ATOM   2378  N   VAL   325     -22.761  72.227   1.271  1.00  0.00
ATOM   2379  CA  VAL   325     -24.124  71.919   0.985  1.00  0.00
ATOM   2380  C   VAL   325     -24.754  73.210   0.620  1.00  0.00
ATOM   2381  O   VAL   325     -25.537  73.293  -0.323  1.00  0.00
ATOM   2382  CB  VAL   325     -24.831  71.300   2.205  1.00  0.00
ATOM   2383  CG1 VAL   325     -26.324  71.166   1.946  1.00  0.00
ATOM   2384  CG2 VAL   325     -24.269  69.919   2.503  1.00  0.00
ATOM   2385  N   LEU   326     -24.400  74.265   1.370  1.00  0.00
ATOM   2386  CA  LEU   326     -24.946  75.559   1.103  1.00  0.00
ATOM   2387  C   LEU   326     -24.486  75.954  -0.260  1.00  0.00
ATOM   2388  O   LEU   326     -25.236  76.541  -1.038  1.00  0.00
ATOM   2389  CB  LEU   326     -24.457  76.571   2.141  1.00  0.00
ATOM   2390  CG  LEU   326     -24.997  76.399   3.562  1.00  0.00
ATOM   2391  CD1 LEU   326     -24.296  77.349   4.522  1.00  0.00
ATOM   2392  CD2 LEU   326     -26.489  76.690   3.610  1.00  0.00
ATOM   2393  N   LEU   327     -23.231  75.603  -0.591  1.00  0.00
ATOM   2394  CA  LEU   327     -22.668  75.903  -1.873  1.00  0.00
ATOM   2395  C   LEU   327     -23.530  75.236  -2.894  1.00  0.00
ATOM   2396  O   LEU   327     -23.860  75.814  -3.929  1.00  0.00
ATOM   2397  CB  LEU   327     -21.235  75.377  -1.964  1.00  0.00
ATOM   2398  CG  LEU   327     -20.498  75.640  -3.279  1.00  0.00
ATOM   2399  CD1 LEU   327     -20.364  77.135  -3.530  1.00  0.00
ATOM   2400  CD2 LEU   327     -19.102  75.038  -3.244  1.00  0.00
ATOM   2401  N   GLY   328     -23.943  73.998  -2.585  1.00  0.00
ATOM   2402  CA  GLY   328     -24.723  73.156  -3.443  1.00  0.00
ATOM   2403  C   GLY   328     -26.047  73.789  -3.714  1.00  0.00
ATOM   2404  O   GLY   328     -26.675  73.513  -4.733  1.00  0.00
ATOM   2405  N   GLU   329     -26.537  74.627  -2.784  1.00  0.00
ATOM   2406  CA  GLU   329     -27.860  75.138  -2.959  1.00  0.00
ATOM   2407  C   GLU   329     -27.996  75.875  -4.253  1.00  0.00
ATOM   2408  O   GLU   329     -28.933  75.611  -5.004  1.00  0.00
ATOM   2409  CB  GLU   329     -28.216  76.104  -1.828  1.00  0.00
ATOM   2410  CG  GLU   329     -29.626  76.662  -1.909  1.00  0.00
ATOM   2411  CD  GLU   329     -29.954  77.589  -0.754  1.00  0.00
ATOM   2412  OE1 GLU   329     -29.081  77.783   0.118  1.00  0.00
ATOM   2413  OE2 GLU   329     -31.084  78.119  -0.720  1.00  0.00
ATOM   2414  N   LEU   330     -27.087  76.808  -4.598  1.00  0.00
ATOM   2415  CA  LEU   330     -27.317  77.497  -5.841  1.00  0.00
ATOM   2416  C   LEU   330     -28.628  78.234  -5.756  1.00  0.00
ATOM   2417  O   LEU   330     -29.344  78.175  -4.757  1.00  0.00
ATOM   2418  CB  LEU   330     -27.374  76.502  -7.003  1.00  0.00
ATOM   2419  CG  LEU   330     -28.428  75.398  -6.899  1.00  0.00
ATOM   2420  CD1 LEU   330     -29.797  75.922  -7.303  1.00  0.00
ATOM   2421  CD2 LEU   330     -28.077  74.232  -7.809  1.00  0.00
ATOM   2422  N   LEU   331     -28.975  79.023  -6.790  1.00  0.00
ATOM   2423  CA  LEU   331     -30.227  79.711  -6.667  1.00  0.00
ATOM   2424  C   LEU   331     -31.117  79.259  -7.780  1.00  0.00
ATOM   2425  O   LEU   331     -32.016  79.990  -8.193  1.00  0.00
ATOM   2426  CB  LEU   331     -30.017  81.224  -6.757  1.00  0.00
ATOM   2427  CG  LEU   331     -29.163  81.857  -5.659  1.00  0.00
ATOM   2428  CD1 LEU   331     -28.888  83.321  -5.966  1.00  0.00
ATOM   2429  CD2 LEU   331     -29.870  81.779  -4.314  1.00  0.00
ATOM   2430  N   ILE   332     -30.898  78.031  -8.287  1.00  0.00
ATOM   2431  CA  ILE   332     -31.705  77.511  -9.354  1.00  0.00
ATOM   2432  C   ILE   332     -33.088  77.244  -8.853  1.00  0.00
ATOM   2433  O   ILE   332     -34.070  77.524  -9.538  1.00  0.00
ATOM   2434  CB  ILE   332     -31.128  76.196  -9.909  1.00  0.00
ATOM   2435  CG1 ILE   332     -29.796  76.454 -10.616  1.00  0.00
ATOM   2436  CG2 ILE   332     -32.092  75.571 -10.907  1.00  0.00
ATOM   2437  CD1 ILE   332     -29.033  75.194 -10.961  1.00  0.00
ATOM   2438  N   LYS   333     -33.199  76.693  -7.632  1.00  0.00
ATOM   2439  CA  LYS   333     -34.481  76.359  -7.085  1.00  0.00
ATOM   2440  C   LYS   333     -35.263  77.626  -6.995  1.00  0.00
ATOM   2441  O   LYS   333     -36.470  77.647  -7.226  1.00  0.00
ATOM   2442  CB  LYS   333     -34.325  75.736  -5.697  1.00  0.00
ATOM   2443  CG  LYS   333     -33.720  74.341  -5.707  1.00  0.00
ATOM   2444  CD  LYS   333     -33.597  73.782  -4.298  1.00  0.00
ATOM   2445  CE  LYS   333     -32.969  72.398  -4.307  1.00  0.00
ATOM   2446  NZ  LYS   333     -32.811  71.852  -2.930  1.00  0.00
ATOM   2447  N   HIS   334     -34.576  78.727  -6.653  1.00  0.00
ATOM   2448  CA  HIS   334     -35.200  80.011  -6.554  1.00  0.00
ATOM   2449  C   HIS   334     -35.673  80.380  -7.923  1.00  0.00
ATOM   2450  O   HIS   334     -36.696  81.046  -8.080  1.00  0.00
ATOM   2451  CB  HIS   334     -34.202  81.053  -6.044  1.00  0.00
ATOM   2452  CG  HIS   334     -33.831  80.881  -4.604  1.00  0.00
ATOM   2453  ND1 HIS   334     -32.754  81.520  -4.031  1.00  0.00
ATOM   2454  CD2 HIS   334     -34.362  80.122  -3.479  1.00  0.00
ATOM   2455  CE1 HIS   334     -32.676  81.170  -2.735  1.00  0.00
ATOM   2456  NE2 HIS   334     -33.637  80.332  -2.397  1.00  0.00
ATOM   2457  N   TYR   335     -34.939  79.929  -8.958  1.00  0.00
ATOM   2458  CA  TYR   335     -35.236  80.294 -10.311  1.00  0.00
ATOM   2459  C   TYR   335     -34.978  81.755 -10.454  1.00  0.00
ATOM   2460  O   TYR   335     -35.588  82.432 -11.279  1.00  0.00
ATOM   2461  CB  TYR   335     -36.699  79.991 -10.640  1.00  0.00
ATOM   2462  CG  TYR   335     -37.093  78.550 -10.407  1.00  0.00
ATOM   2463  CD1 TYR   335     -37.888  78.196  -9.324  1.00  0.00
ATOM   2464  CD2 TYR   335     -36.668  77.548 -11.271  1.00  0.00
ATOM   2465  CE1 TYR   335     -38.254  76.881  -9.105  1.00  0.00
ATOM   2466  CE2 TYR   335     -37.023  76.228 -11.066  1.00  0.00
ATOM   2467  CZ  TYR   335     -37.823  75.900  -9.972  1.00  0.00
ATOM   2468  OH  TYR   335     -38.185  74.591  -9.754  1.00  0.00
ATOM   2469  N   LEU   336     -34.037  82.276  -9.646  1.00  0.00
ATOM   2470  CA  LEU   336     -33.687  83.660  -9.741  1.00  0.00
ATOM   2471  C   LEU   336     -32.508  83.762 -10.701  1.00  0.00
ATOM   2472  O   LEU   336     -31.550  82.956 -10.553  1.00  0.00
ATOM   2473  CB  LEU   336     -33.295  84.209  -8.367  1.00  0.00
ATOM   2474  CG  LEU   336     -34.352  84.097  -7.266  1.00  0.00
ATOM   2475  CD1 LEU   336     -33.817  84.642  -5.951  1.00  0.00
ATOM   2476  CD2 LEU   336     -35.599  84.885  -7.635  1.00  0.00
TER
END
