
#######################################################
#                                                     #
#                        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 T0298TS268_5_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   21 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_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:    18       319 - 336         4.88     5.66
  LCS_AVERAGE:     11.68

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       316 - 320         0.74    19.51
  LONGEST_CONTINUOUS_SEGMENT:     5       331 - 335         1.40    18.30
  LCS_AVERAGE:      2.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       316 - 320         0.74    19.51
  LCS_AVERAGE:      2.70

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      5    5   13     3    4    5    6    6    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     R     317     R     317      5    5   13     3    4    5    5    5    5    6    6    6    8    9   12   15   18   20   21   21   21   21   21 
LCS_GDT     K     318     K     318      5    5   13     3    4    5    5    5    5    6    6    6    8    8    9   16   18   20   21   21   21   21   21 
LCS_GDT     G     319     G     319      5    5   18     2    4    5    5    5    5    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     A     320     A     320      5    5   18     3    4    5    6    6    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     A     321     A     321      3    3   18     3    3    5    6    6    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     L     322     L     322      4    4   18     3    3    5    6    6    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     N     323     N     323      4    4   18     3    3    4    4    4    5    7    9   10   13   13   14   16   17   20   21   21   21   21   21 
LCS_GDT     A     324     A     324      4    4   18     3    3    4    4    4    7    8    9   11   13   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     V     325     V     325      4    4   18     3    3    4    5    5    6    8   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     L     326     L     326      3    4   18     3    3    3    5    5    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     L     327     L     327      3    4   18     3    3    3    4    5    7    8    9   11   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     G     328     G     328      3    4   18     3    3    3    4    5    5    7   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     E     329     E     329      4    4   18     3    3    4    4    5    7    8    9   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     L     330     L     330      4    4   18     3    3    4    4    5    6    7   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     L     331     L     331      4    5   18     3    3    4    4    5    5    6    8    9   12   13   14   17   18   20   21   21   21   21   21 
LCS_GDT     I     332     I     332      4    5   18     3    4    4    4    5    7    8    9   11   13   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     K     333     K     333      4    5   18     3    4    4    4    5    5    6    9   11   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     H     334     H     334      4    5   18     3    4    4    5    5    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     Y     335     Y     335      4    5   18     3    4    4    6    6    7    9   12   13   14   16   17   17   18   20   21   21   21   21   21 
LCS_GDT     L     336     L     336      3    3   18     0    3    5    6    6    7    9   12   13   14   15   17   17   18   20   21   21   21   21   21 
LCS_AVERAGE  LCS_A:   5.78  (   2.70    2.96   11.68 )

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      5      6      6      7      9     12     13     14     16     17     17     18     20     21     21     21     21     21 
GDT PERCENT_CA   2.03   2.70   3.38   4.05   4.05   4.73   6.08   8.11   8.78   9.46  10.81  11.49  11.49  12.16  13.51  14.19  14.19  14.19  14.19  14.19
GDT RMS_LOCAL    0.05   0.61   0.74   1.40   1.40   1.81   2.65   3.32   3.57   3.76   4.33   4.42   4.42   4.67   5.08   5.33   5.33   5.33   5.33   5.33
GDT RMS_ALL_CA  12.66  14.18  19.51   6.65   6.65   6.52   6.02   5.68   5.61   5.58   5.42   5.44   5.44   5.37   5.35   5.33   5.33   5.33   5.33   5.33

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          3.689
LGA    R     317      R     317          8.964
LGA    K     318      K     318          8.601
LGA    G     319      G     319          3.863
LGA    A     320      A     320          3.742
LGA    A     321      A     321          2.210
LGA    L     322      L     322          2.359
LGA    N     323      N     323          8.871
LGA    A     324      A     324          7.750
LGA    V     325      V     325          3.597
LGA    L     326      L     326          3.775
LGA    L     327      L     327          5.583
LGA    G     328      G     328          3.945
LGA    E     329      E     329          5.078
LGA    L     330      L     330          3.984
LGA    L     331      L     331          7.927
LGA    I     332      I     332          7.621
LGA    K     333      K     333          5.504
LGA    H     334      H     334          2.708
LGA    Y     335      Y     335          3.506
LGA    L     336      L     336          3.795

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  148    4.0     12    3.32     7.264     6.080     0.351

LGA_LOCAL      RMSD =  3.320  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.550  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  5.326  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.201588 * X  +   0.744216 * Y  +   0.636792 * Z  + -40.532635
  Y_new =  -0.267087 * X  +  -0.667268 * Y  +   0.695282 * Z  + 130.624161
  Z_new =   0.942352 * X  +  -0.029919 * Y  +   0.333284 * Z  +  29.120922 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.089530    3.052063  [ DEG:    -5.1297    174.8703 ]
  Theta =  -1.229590   -1.912003  [ DEG:   -70.4503   -109.5497 ]
  Phi   =  -2.217339    0.924254  [ DEG:  -127.0442     52.9558 ]
 
# 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: T0298TS268_5_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_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   12   3.32   6.080     5.33
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4b_A
ATOM   2298  N   VAL   316      -9.732  66.547   3.029  1.00  0.00
ATOM   2299  CA  VAL   316     -10.631  65.627   3.672  1.00  0.00
ATOM   2300  C   VAL   316     -10.714  65.890   5.145  1.00  0.00
ATOM   2301  O   VAL   316     -11.803  65.893   5.716  1.00  0.00
ATOM   2302  CB  VAL   316     -10.175  64.168   3.486  1.00  0.00
ATOM   2303  CG1 VAL   316     -11.022  63.233   4.335  1.00  0.00
ATOM   2304  CG2 VAL   316     -10.309  63.749   2.029  1.00  0.00
ATOM   2305  N   ARG   317      -9.570  66.123   5.816  1.00  0.00
ATOM   2306  CA  ARG   317      -9.620  66.325   7.233  1.00  0.00
ATOM   2307  C   ARG   317      -9.581  67.794   7.478  1.00  0.00
ATOM   2308  O   ARG   317      -8.993  68.554   6.713  1.00  0.00
ATOM   2309  CB  ARG   317      -8.427  65.650   7.914  1.00  0.00
ATOM   2310  CG  ARG   317      -8.430  64.134   7.809  1.00  0.00
ATOM   2311  CD  ARG   317      -7.243  63.527   8.540  1.00  0.00
ATOM   2312  NE  ARG   317      -7.152  62.085   8.333  1.00  0.00
ATOM   2313  CZ  ARG   317      -6.215  61.311   8.872  1.00  0.00
ATOM   2314  NH1 ARG   317      -6.210  60.007   8.627  1.00  0.00
ATOM   2315  NH2 ARG   317      -5.286  61.842   9.655  1.00  0.00
ATOM   2316  N   LYS   318     -10.297  68.264   8.505  1.00  0.00
ATOM   2317  CA  LYS   318     -10.329  69.655   8.863  1.00  0.00
ATOM   2318  C   LYS   318     -10.765  70.482   7.694  1.00  0.00
ATOM   2319  O   LYS   318     -10.640  71.707   7.701  1.00  0.00
ATOM   2320  CB  LYS   318      -8.942  70.128   9.301  1.00  0.00
ATOM   2321  CG  LYS   318      -8.421  69.445  10.556  1.00  0.00
ATOM   2322  CD  LYS   318      -7.046  69.968  10.939  1.00  0.00
ATOM   2323  CE  LYS   318      -6.473  69.201  12.119  1.00  0.00
ATOM   2324  NZ  LYS   318      -5.105  69.669  12.475  1.00  0.00
ATOM   2325  N   GLY   319     -11.342  69.822   6.679  1.00  0.00
ATOM   2326  CA  GLY   319     -11.872  70.441   5.508  1.00  0.00
ATOM   2327  C   GLY   319     -12.925  69.479   5.080  1.00  0.00
ATOM   2328  O   GLY   319     -12.811  68.284   5.348  1.00  0.00
ATOM   2329  N   ALA   320     -13.982  69.943   4.398  1.00  0.00
ATOM   2330  CA  ALA   320     -14.964  68.953   4.083  1.00  0.00
ATOM   2331  C   ALA   320     -15.591  69.274   2.774  1.00  0.00
ATOM   2332  O   ALA   320     -15.530  70.404   2.292  1.00  0.00
ATOM   2333  CB  ALA   320     -16.044  68.919   5.154  1.00  0.00
ATOM   2334  N   ALA   321     -16.194  68.243   2.156  1.00  0.00
ATOM   2335  CA  ALA   321     -16.903  68.411   0.928  1.00  0.00
ATOM   2336  C   ALA   321     -18.236  67.778   1.153  1.00  0.00
ATOM   2337  O   ALA   321     -18.364  66.854   1.956  1.00  0.00
ATOM   2338  CB  ALA   321     -16.158  67.731  -0.211  1.00  0.00
ATOM   2339  N   LEU   322     -19.283  68.276   0.467  1.00  0.00
ATOM   2340  CA  LEU   322     -20.578  67.700   0.672  1.00  0.00
ATOM   2341  C   LEU   322     -20.819  66.732  -0.439  1.00  0.00
ATOM   2342  O   LEU   322     -20.688  67.068  -1.614  1.00  0.00
ATOM   2343  CB  LEU   322     -21.655  68.787   0.662  1.00  0.00
ATOM   2344  CG  LEU   322     -21.538  69.868   1.738  1.00  0.00
ATOM   2345  CD1 LEU   322     -22.622  70.920   1.565  1.00  0.00
ATOM   2346  CD2 LEU   322     -21.681  69.262   3.127  1.00  0.00
ATOM   2347  N   ASN   323     -21.174  65.484  -0.078  1.00  0.00
ATOM   2348  CA  ASN   323     -21.397  64.463  -1.059  1.00  0.00
ATOM   2349  C   ASN   323     -22.567  64.853  -1.906  1.00  0.00
ATOM   2350  O   ASN   323     -22.518  64.760  -3.132  1.00  0.00
ATOM   2351  CB  ASN   323     -21.689  63.122  -0.381  1.00  0.00
ATOM   2352  CG  ASN   323     -20.454  62.506   0.245  1.00  0.00
ATOM   2353  OD1 ASN   323     -19.328  62.853  -0.108  1.00  0.00
ATOM   2354  ND2 ASN   323     -20.664  61.587   1.182  1.00  0.00
ATOM   2355  N   ALA   324     -23.646  65.336  -1.262  1.00  0.00
ATOM   2356  CA  ALA   324     -24.853  65.679  -1.957  1.00  0.00
ATOM   2357  C   ALA   324     -24.629  66.914  -2.761  1.00  0.00
ATOM   2358  O   ALA   324     -23.637  67.622  -2.592  1.00  0.00
ATOM   2359  CB  ALA   324     -25.981  65.929  -0.968  1.00  0.00
ATOM   2360  N   VAL   325     -25.563  67.165  -3.696  1.00  0.00
ATOM   2361  CA  VAL   325     -25.515  68.296  -4.569  1.00  0.00
ATOM   2362  C   VAL   325     -25.814  69.522  -3.775  1.00  0.00
ATOM   2363  O   VAL   325     -26.536  69.476  -2.780  1.00  0.00
ATOM   2364  CB  VAL   325     -26.546  68.174  -5.707  1.00  0.00
ATOM   2365  CG1 VAL   325     -26.614  69.469  -6.503  1.00  0.00
ATOM   2366  CG2 VAL   325     -26.164  67.048  -6.653  1.00  0.00
ATOM   2367  N   LEU   326     -25.228  70.658  -4.200  1.00  0.00
ATOM   2368  CA  LEU   326     -25.499  71.894  -3.532  1.00  0.00
ATOM   2369  C   LEU   326     -26.928  72.187  -3.798  1.00  0.00
ATOM   2370  O   LEU   326     -27.430  71.938  -4.894  1.00  0.00
ATOM   2371  CB  LEU   326     -24.603  73.006  -4.079  1.00  0.00
ATOM   2372  CG  LEU   326     -23.102  72.852  -3.829  1.00  0.00
ATOM   2373  CD1 LEU   326     -22.324  73.960  -4.522  1.00  0.00
ATOM   2374  CD2 LEU   326     -22.795  72.914  -2.341  1.00  0.00
ATOM   2375  N   LEU   327     -27.638  72.710  -2.787  1.00  0.00
ATOM   2376  CA  LEU   327     -29.023  72.942  -3.026  1.00  0.00
ATOM   2377  C   LEU   327     -29.149  74.346  -3.497  1.00  0.00
ATOM   2378  O   LEU   327     -29.206  75.268  -2.683  1.00  0.00
ATOM   2379  CB  LEU   327     -29.830  72.738  -1.742  1.00  0.00
ATOM   2380  CG  LEU   327     -29.772  71.342  -1.121  1.00  0.00
ATOM   2381  CD1 LEU   327     -30.559  71.299   0.180  1.00  0.00
ATOM   2382  CD2 LEU   327     -30.363  70.307  -2.067  1.00  0.00
ATOM   2383  N   GLY   328     -29.174  74.520  -4.835  1.00  0.00
ATOM   2384  CA  GLY   328     -29.350  75.799  -5.465  1.00  0.00
ATOM   2385  C   GLY   328     -28.426  76.772  -4.815  1.00  0.00
ATOM   2386  O   GLY   328     -27.206  76.640  -4.864  1.00  0.00
ATOM   2387  N   GLU   329     -29.031  77.796  -4.190  1.00  0.00
ATOM   2388  CA  GLU   329     -28.313  78.784  -3.450  1.00  0.00
ATOM   2389  C   GLU   329     -29.035  78.866  -2.150  1.00  0.00
ATOM   2390  O   GLU   329     -30.132  78.327  -2.014  1.00  0.00
ATOM   2391  CB  GLU   329     -28.330  80.124  -4.188  1.00  0.00
ATOM   2392  CG  GLU   329     -27.625  80.100  -5.535  1.00  0.00
ATOM   2393  CD  GLU   329     -27.645  81.449  -6.226  1.00  0.00
ATOM   2394  OE1 GLU   329     -28.169  82.414  -5.631  1.00  0.00
ATOM   2395  OE2 GLU   329     -27.135  81.541  -7.363  1.00  0.00
ATOM   2396  N   LEU   330     -28.448  79.532  -1.143  1.00  0.00
ATOM   2397  CA  LEU   330     -29.136  79.564   0.110  1.00  0.00
ATOM   2398  C   LEU   330     -30.171  80.638   0.022  1.00  0.00
ATOM   2399  O   LEU   330     -30.321  81.441   0.941  1.00  0.00
ATOM   2400  CB  LEU   330     -28.162  79.867   1.249  1.00  0.00
ATOM   2401  CG  LEU   330     -26.998  78.890   1.425  1.00  0.00
ATOM   2402  CD1 LEU   330     -26.087  79.335   2.558  1.00  0.00
ATOM   2403  CD2 LEU   330     -27.513  77.495   1.750  1.00  0.00
ATOM   2404  N   LEU   331     -30.926  80.673  -1.092  1.00  0.00
ATOM   2405  CA  LEU   331     -31.978  81.636  -1.223  1.00  0.00
ATOM   2406  C   LEU   331     -32.976  80.981  -2.111  1.00  0.00
ATOM   2407  O   LEU   331     -32.613  80.419  -3.144  1.00  0.00
ATOM   2408  CB  LEU   331     -31.446  82.931  -1.839  1.00  0.00
ATOM   2409  CG  LEU   331     -32.475  84.034  -2.094  1.00  0.00
ATOM   2410  CD1 LEU   331     -33.030  84.565  -0.781  1.00  0.00
ATOM   2411  CD2 LEU   331     -31.844  85.194  -2.848  1.00  0.00
ATOM   2412  N   ILE   332     -34.268  81.017  -1.741  1.00  0.00
ATOM   2413  CA  ILE   332     -35.190  80.395  -2.634  1.00  0.00
ATOM   2414  C   ILE   332     -35.785  81.489  -3.449  1.00  0.00
ATOM   2415  O   ILE   332     -36.771  82.118  -3.069  1.00  0.00
ATOM   2416  CB  ILE   332     -36.295  79.641  -1.870  1.00  0.00
ATOM   2417  CG1 ILE   332     -35.680  78.596  -0.937  1.00  0.00
ATOM   2418  CG2 ILE   332     -37.225  78.932  -2.842  1.00  0.00
ATOM   2419  CD1 ILE   332     -36.680  77.952  -0.001  1.00  0.00
ATOM   2420  N   LYS   333     -35.144  81.721  -4.608  1.00  0.00
ATOM   2421  CA  LYS   333     -35.497  82.699  -5.590  1.00  0.00
ATOM   2422  C   LYS   333     -35.429  81.938  -6.867  1.00  0.00
ATOM   2423  O   LYS   333     -36.219  81.027  -7.108  1.00  0.00
ATOM   2424  CB  LYS   333     -34.510  83.867  -5.564  1.00  0.00
ATOM   2425  CG  LYS   333     -34.856  84.995  -6.523  1.00  0.00
ATOM   2426  CD  LYS   333     -33.872  86.147  -6.398  1.00  0.00
ATOM   2427  CE  LYS   333     -34.209  87.268  -7.367  1.00  0.00
ATOM   2428  NZ  LYS   333     -33.250  88.401  -7.262  1.00  0.00
ATOM   2429  N   HIS   334     -34.471  82.311  -7.733  1.00  0.00
ATOM   2430  CA  HIS   334     -34.279  81.617  -8.965  1.00  0.00
ATOM   2431  C   HIS   334     -33.690  80.278  -8.652  1.00  0.00
ATOM   2432  O   HIS   334     -32.879  80.142  -7.737  1.00  0.00
ATOM   2433  CB  HIS   334     -33.331  82.398  -9.878  1.00  0.00
ATOM   2434  CG  HIS   334     -33.267  81.868 -11.276  1.00  0.00
ATOM   2435  ND1 HIS   334     -32.528  80.757 -11.619  1.00  0.00
ATOM   2436  CD2 HIS   334     -33.844  82.248 -12.558  1.00  0.00
ATOM   2437  CE1 HIS   334     -32.665  80.528 -12.937  1.00  0.00
ATOM   2438  NE2 HIS   334     -33.454  81.419 -13.507  1.00  0.00
ATOM   2439  N   TYR   335     -34.113  79.248  -9.407  1.00  0.00
ATOM   2440  CA  TYR   335     -33.609  77.918  -9.218  1.00  0.00
ATOM   2441  C   TYR   335     -32.792  77.575 -10.416  1.00  0.00
ATOM   2442  O   TYR   335     -33.274  77.633 -11.546  1.00  0.00
ATOM   2443  CB  TYR   335     -34.762  76.924  -9.068  1.00  0.00
ATOM   2444  CG  TYR   335     -34.315  75.493  -8.866  1.00  0.00
ATOM   2445  CD1 TYR   335     -33.834  75.065  -7.636  1.00  0.00
ATOM   2446  CD2 TYR   335     -34.376  74.576  -9.908  1.00  0.00
ATOM   2447  CE1 TYR   335     -33.423  73.761  -7.442  1.00  0.00
ATOM   2448  CE2 TYR   335     -33.970  73.266  -9.733  1.00  0.00
ATOM   2449  CZ  TYR   335     -33.491  72.863  -8.487  1.00  0.00
ATOM   2450  OH  TYR   335     -33.083  71.564  -8.296  1.00  0.00
ATOM   2451  N   LEU   336     -31.515  77.216 -10.189  1.00  0.00
ATOM   2452  CA  LEU   336     -30.643  76.900 -11.281  1.00  0.00
ATOM   2453  C   LEU   336     -31.147  75.595 -11.877  1.00  0.00
ATOM   2454  O   LEU   336     -31.483  75.591 -13.090  1.00  0.00
ATOM   2455  CB  LEU   336     -29.204  76.741 -10.788  1.00  0.00
ATOM   2456  CG  LEU   336     -28.583  77.959 -10.102  1.00  0.00
ATOM   2457  CD1 LEU   336     -27.195  77.630  -9.574  1.00  0.00
ATOM   2458  CD2 LEU   336     -28.457  79.118 -11.079  1.00  0.00
TER
END
