
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   21 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_1_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:    16       316 - 331         4.92     9.20
  LCS_AVERAGE:     10.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       316 - 322         1.31    15.43
  LCS_AVERAGE:      3.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       316 - 320         0.47    15.08
  LCS_AVERAGE:      2.38

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    7   16     4    5    7    7    8    8    9   10   11   12   13   14   14   14   15   16   16   17   18   19 
LCS_GDT     R     317     R     317      5    7   16     4    5    7    7    8    8    9   10   11   12   13   14   14   14   16   16   18   19   19   19 
LCS_GDT     K     318     K     318      5    7   16     4    5    7    7    8    8    9   10   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     G     319     G     319      5    7   16     3    5    7    7    8    8    9   10   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     A     320     A     320      5    7   16     4    5    7    7    8    8    9   10   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     A     321     A     321      4    7   16     3    4    5    5    7    7    8    9   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     L     322     L     322      3    7   16     3    3    6    6    8    8    9   10   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     N     323     N     323      3    4   16     3    3    4    6    6    7    8    9   10   10   12   13   13   15   16   17   18   19   19   19 
LCS_GDT     A     324     A     324      3    4   16     3    3    3    6    6    7    8    9   10   11   12   13   13   15   16   17   18   19   19   19 
LCS_GDT     V     325     V     325      3    4   16     3    4    7    7    8    8    9   10   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     L     326     L     326      3    4   16     3    3    3    3    8    8    9   10   11   11   13   14   14   15   15   17   18   19   19   19 
LCS_GDT     L     327     L     327      3    4   16     1    4    7    7    8    8    9   10   11   11   13   14   14   14   16   17   18   19   19   19 
LCS_GDT     G     328     G     328      3    4   16     0    3    3    4    5    6    9   10   11   12   13   14   14   14   16   17   18   19   19   19 
LCS_GDT     E     329     E     329      3    4   16     3    4    5    5    6    7    8    9   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     L     330     L     330      3    4   16     3    4    5    5    6    7    8    9   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     L     331     L     331      3    4   16     3    3    3    5    6    7    8    9   11   12   13   14   14   15   16   17   18   19   19   19 
LCS_GDT     I     332     I     332      3    4   14     3    3    4    6    6    7    8    8    9   10   12   13   13   15   16   17   18   19   19   19 
LCS_GDT     K     333     K     333      3    4   14     3    3    4    4    6    7    8    8    9   10   12   13   13   15   16   17   18   19   19   19 
LCS_GDT     H     334     H     334      3    4   14     3    3    4    6    6    7    8    8    9   10   12   13   13   14   16   17   18   19   19   19 
LCS_GDT     Y     335     Y     335      3    4   14     3    3    4    6    6    7    8    8    9   10   12   13   13   15   16   17   18   19   19   19 
LCS_GDT     L     336     L     336      3    3   13     0    3    3    3    3    4    5    6    9   10   10   10   12   13   13   14   15   16   19   19 
LCS_AVERAGE  LCS_A:   5.39  (   2.38    3.35   10.46 )

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      4      5      7      7      8      8      9     10     11     12     13     14     14     15     16     17     18     19     19     19 
GDT PERCENT_CA   2.70   3.38   4.73   4.73   5.41   5.41   6.08   6.76   7.43   8.11   8.78   9.46   9.46  10.14  10.81  11.49  12.16  12.84  12.84  12.84
GDT RMS_LOCAL    0.20   0.47   1.04   1.04   1.35   1.35   1.77   2.38   2.63   3.59   3.85   4.10   4.10   5.63   5.48   5.79   5.97   6.25   6.25   6.25
GDT RMS_ALL_CA  15.27  15.08  12.24  12.24  11.96  11.96  12.09  11.69  11.76   9.06   9.23   9.29   9.29   7.16   7.73   7.33   7.35   7.25   7.25   7.25

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          2.681
LGA    R     317      R     317          2.420
LGA    K     318      K     318          2.399
LGA    G     319      G     319          2.275
LGA    A     320      A     320          1.455
LGA    A     321      A     321          4.379
LGA    L     322      L     322          3.268
LGA    N     323      N     323          7.007
LGA    A     324      A     324          7.966
LGA    V     325      V     325          2.612
LGA    L     326      L     326          3.548
LGA    L     327      L     327          2.148
LGA    G     328      G     328          3.422
LGA    E     329      E     329          8.929
LGA    L     330      L     330         10.711
LGA    L     331      L     331          9.500
LGA    I     332      I     332         14.000
LGA    K     333      K     333         20.272
LGA    H     334      H     334         22.581
LGA    Y     335      Y     335         20.786
LGA    L     336      L     336         22.818

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  148    4.0     10    2.38     6.588     5.895     0.403

LGA_LOCAL      RMSD =  2.380  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.038  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  7.091  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.872652 * X  +   0.354800 * Y  +   0.335551 * Z  + -36.592213
  Y_new =  -0.091024 * X  +  -0.793259 * Y  +   0.602042 * Z  + 137.407684
  Z_new =   0.479784 * X  +   0.494830 * Y  +   0.724535 * Z  +   1.975948 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.599199   -2.542393  [ DEG:    34.3316   -145.6684 ]
  Theta =  -0.500408   -2.641184  [ DEG:   -28.6713   -151.3287 ]
  Phi   =  -3.037661    0.103932  [ DEG:  -174.0452      5.9549 ]
 
# 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_1_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_1_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   10   2.38   5.895     7.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4b_A
ATOM   2298  N   VAL   316     -12.225  66.770   1.252  1.00  0.00
ATOM   2299  CA  VAL   316     -13.465  66.320   0.695  1.00  0.00
ATOM   2300  C   VAL   316     -14.618  66.496   1.637  1.00  0.00
ATOM   2301  O   VAL   316     -15.646  67.058   1.261  1.00  0.00
ATOM   2302  CB  VAL   316     -13.411  64.824   0.334  1.00  0.00
ATOM   2303  CG1 VAL   316     -14.788  64.326  -0.077  1.00  0.00
ATOM   2304  CG2 VAL   316     -12.450  64.589  -0.820  1.00  0.00
ATOM   2305  N   ARG   317     -14.474  66.032   2.894  1.00  0.00
ATOM   2306  CA  ARG   317     -15.629  66.001   3.750  1.00  0.00
ATOM   2307  C   ARG   317     -16.186  67.367   4.018  1.00  0.00
ATOM   2308  O   ARG   317     -17.265  67.710   3.537  1.00  0.00
ATOM   2309  CB  ARG   317     -15.275  65.381   5.104  1.00  0.00
ATOM   2310  CG  ARG   317     -16.443  65.298   6.072  1.00  0.00
ATOM   2311  CD  ARG   317     -17.482  64.294   5.601  1.00  0.00
ATOM   2312  NE  ARG   317     -16.966  62.928   5.609  1.00  0.00
ATOM   2313  CZ  ARG   317     -17.634  61.874   5.151  1.00  0.00
ATOM   2314  NH1 ARG   317     -17.085  60.668   5.200  1.00  0.00
ATOM   2315  NH2 ARG   317     -18.850  62.028   4.644  1.00  0.00
ATOM   2316  N   LYS   318     -15.443  68.191   4.780  1.00  0.00
ATOM   2317  CA  LYS   318     -15.846  69.525   5.135  1.00  0.00
ATOM   2318  C   LYS   318     -15.684  70.436   3.964  1.00  0.00
ATOM   2319  O   LYS   318     -16.530  71.283   3.683  1.00  0.00
ATOM   2320  CB  LYS   318     -14.991  70.054   6.289  1.00  0.00
ATOM   2321  CG  LYS   318     -15.398  71.434   6.780  1.00  0.00
ATOM   2322  CD  LYS   318     -14.628  71.823   8.032  1.00  0.00
ATOM   2323  CE  LYS   318     -15.038  73.201   8.525  1.00  0.00
ATOM   2324  NZ  LYS   318     -14.328  73.576   9.779  1.00  0.00
ATOM   2325  N   GLY   319     -14.569  70.241   3.243  1.00  0.00
ATOM   2326  CA  GLY   319     -14.135  71.102   2.186  1.00  0.00
ATOM   2327  C   GLY   319     -15.112  71.136   1.066  1.00  0.00
ATOM   2328  O   GLY   319     -15.260  72.172   0.421  1.00  0.00
ATOM   2329  N   ALA   320     -15.758  70.003   0.743  1.00  0.00
ATOM   2330  CA  ALA   320     -16.700  70.079  -0.332  1.00  0.00
ATOM   2331  C   ALA   320     -17.762  71.035   0.100  1.00  0.00
ATOM   2332  O   ALA   320     -18.161  71.925  -0.652  1.00  0.00
ATOM   2333  CB  ALA   320     -17.298  68.709  -0.610  1.00  0.00
ATOM   2334  N   ALA   321     -18.227  70.884   1.353  1.00  0.00
ATOM   2335  CA  ALA   321     -19.240  71.757   1.858  1.00  0.00
ATOM   2336  C   ALA   321     -19.769  71.120   3.095  1.00  0.00
ATOM   2337  O   ALA   321     -19.211  70.143   3.593  1.00  0.00
ATOM   2338  CB  ALA   321     -20.349  71.932   0.833  1.00  0.00
ATOM   2339  N   LEU   322     -20.868  71.674   3.640  1.00  0.00
ATOM   2340  CA  LEU   322     -21.451  71.066   4.795  1.00  0.00
ATOM   2341  C   LEU   322     -21.867  69.710   4.341  1.00  0.00
ATOM   2342  O   LEU   322     -22.110  69.505   3.155  1.00  0.00
ATOM   2343  CB  LEU   322     -22.650  71.882   5.283  1.00  0.00
ATOM   2344  CG  LEU   322     -22.345  73.282   5.818  1.00  0.00
ATOM   2345  CD1 LEU   322     -23.631  74.026   6.143  1.00  0.00
ATOM   2346  CD2 LEU   322     -21.507  73.203   7.085  1.00  0.00
ATOM   2347  N   ASN   323     -21.925  68.735   5.266  1.00  0.00
ATOM   2348  CA  ASN   323     -22.251  67.409   4.844  1.00  0.00
ATOM   2349  C   ASN   323     -23.616  67.434   4.245  1.00  0.00
ATOM   2350  O   ASN   323     -24.621  67.483   4.951  1.00  0.00
ATOM   2351  CB  ASN   323     -22.231  66.447   6.035  1.00  0.00
ATOM   2352  CG  ASN   323     -22.449  65.005   5.623  1.00  0.00
ATOM   2353  OD1 ASN   323     -22.302  64.655   4.452  1.00  0.00
ATOM   2354  ND2 ASN   323     -22.800  64.163   6.588  1.00  0.00
ATOM   2355  N   ALA   324     -23.657  67.412   2.898  1.00  0.00
ATOM   2356  CA  ALA   324     -24.869  67.389   2.135  1.00  0.00
ATOM   2357  C   ALA   324     -24.517  67.959   0.804  1.00  0.00
ATOM   2358  O   ALA   324     -23.550  68.709   0.684  1.00  0.00
ATOM   2359  CB  ALA   324     -25.941  68.224   2.817  1.00  0.00
ATOM   2360  N   VAL   325     -25.285  67.617  -0.245  1.00  0.00
ATOM   2361  CA  VAL   325     -24.971  68.222  -1.499  1.00  0.00
ATOM   2362  C   VAL   325     -26.141  69.044  -1.929  1.00  0.00
ATOM   2363  O   VAL   325     -27.170  68.527  -2.361  1.00  0.00
ATOM   2364  CB  VAL   325     -24.676  67.164  -2.578  1.00  0.00
ATOM   2365  CG1 VAL   325     -24.354  67.832  -3.906  1.00  0.00
ATOM   2366  CG2 VAL   325     -23.488  66.305  -2.172  1.00  0.00
ATOM   2367  N   LEU   326     -26.009  70.374  -1.784  1.00  0.00
ATOM   2368  CA  LEU   326     -27.039  71.252  -2.239  1.00  0.00
ATOM   2369  C   LEU   326     -26.373  72.573  -2.413  1.00  0.00
ATOM   2370  O   LEU   326     -25.993  73.213  -1.432  1.00  0.00
ATOM   2371  CB  LEU   326     -28.168  71.333  -1.209  1.00  0.00
ATOM   2372  CG  LEU   326     -29.336  72.259  -1.555  1.00  0.00
ATOM   2373  CD1 LEU   326     -30.032  71.794  -2.826  1.00  0.00
ATOM   2374  CD2 LEU   326     -30.361  72.274  -0.431  1.00  0.00
ATOM   2375  N   LEU   327     -26.189  73.019  -3.667  1.00  0.00
ATOM   2376  CA  LEU   327     -25.554  74.290  -3.822  1.00  0.00
ATOM   2377  C   LEU   327     -25.942  74.850  -5.148  1.00  0.00
ATOM   2378  O   LEU   327     -26.163  74.113  -6.108  1.00  0.00
ATOM   2379  CB  LEU   327     -24.033  74.141  -3.755  1.00  0.00
ATOM   2380  CG  LEU   327     -23.217  75.423  -3.938  1.00  0.00
ATOM   2381  CD1 LEU   327     -23.430  76.366  -2.764  1.00  0.00
ATOM   2382  CD2 LEU   327     -21.732  75.107  -4.032  1.00  0.00
ATOM   2383  N   GLY   328     -26.062  76.189  -5.218  1.00  0.00
ATOM   2384  CA  GLY   328     -26.379  76.819  -6.462  1.00  0.00
ATOM   2385  C   GLY   328     -25.443  77.974  -6.600  1.00  0.00
ATOM   2386  O   GLY   328     -25.348  78.822  -5.715  1.00  0.00
ATOM   2387  N   GLU   329     -24.723  78.028  -7.735  1.00  0.00
ATOM   2388  CA  GLU   329     -23.790  79.090  -7.964  1.00  0.00
ATOM   2389  C   GLU   329     -23.244  78.883  -9.330  1.00  0.00
ATOM   2390  O   GLU   329     -23.787  78.115 -10.122  1.00  0.00
ATOM   2391  CB  GLU   329     -22.667  79.050  -6.926  1.00  0.00
ATOM   2392  CG  GLU   329     -21.895  77.740  -6.896  1.00  0.00
ATOM   2393  CD  GLU   329     -20.856  77.701  -5.794  1.00  0.00
ATOM   2394  OE1 GLU   329     -20.783  78.672  -5.011  1.00  0.00
ATOM   2395  OE2 GLU   329     -20.114  76.700  -5.712  1.00  0.00
ATOM   2396  N   LEU   330     -22.150  79.596  -9.647  1.00  0.00
ATOM   2397  CA  LEU   330     -21.520  79.413 -10.914  1.00  0.00
ATOM   2398  C   LEU   330     -21.065  77.988 -10.856  1.00  0.00
ATOM   2399  O   LEU   330     -20.833  77.460  -9.770  1.00  0.00
ATOM   2400  CB  LEU   330     -20.353  80.389 -11.078  1.00  0.00
ATOM   2401  CG  LEU   330     -20.716  81.873 -11.150  1.00  0.00
ATOM   2402  CD1 LEU   330     -19.460  82.732 -11.181  1.00  0.00
ATOM   2403  CD2 LEU   330     -21.525  82.169 -12.403  1.00  0.00
ATOM   2404  N   LEU   331     -20.969  77.309 -12.015  1.00  0.00
ATOM   2405  CA  LEU   331     -20.626  75.917 -12.013  1.00  0.00
ATOM   2406  C   LEU   331     -19.332  75.751 -11.291  1.00  0.00
ATOM   2407  O   LEU   331     -18.460  76.616 -11.336  1.00  0.00
ATOM   2408  CB  LEU   331     -20.482  75.398 -13.445  1.00  0.00
ATOM   2409  CG  LEU   331     -21.757  75.379 -14.290  1.00  0.00
ATOM   2410  CD1 LEU   331     -21.448  74.968 -15.721  1.00  0.00
ATOM   2411  CD2 LEU   331     -22.766  74.394 -13.720  1.00  0.00
ATOM   2412  N   ILE   332     -19.204  74.616 -10.578  1.00  0.00
ATOM   2413  CA  ILE   332     -18.048  74.347  -9.779  1.00  0.00
ATOM   2414  C   ILE   332     -16.863  74.267 -10.681  1.00  0.00
ATOM   2415  O   ILE   332     -16.881  73.574 -11.696  1.00  0.00
ATOM   2416  CB  ILE   332     -18.188  73.019  -9.013  1.00  0.00
ATOM   2417  CG1 ILE   332     -19.328  73.107  -7.995  1.00  0.00
ATOM   2418  CG2 ILE   332     -16.902  72.694  -8.269  1.00  0.00
ATOM   2419  CD1 ILE   332     -19.674  71.782  -7.350  1.00  0.00
ATOM   2420  N   LYS   333     -15.793  75.004 -10.325  1.00  0.00
ATOM   2421  CA  LYS   333     -14.610  74.996 -11.129  1.00  0.00
ATOM   2422  C   LYS   333     -14.071  73.609 -11.118  1.00  0.00
ATOM   2423  O   LYS   333     -13.679  73.079 -12.156  1.00  0.00
ATOM   2424  CB  LYS   333     -13.571  75.966 -10.562  1.00  0.00
ATOM   2425  CG  LYS   333     -13.937  77.432 -10.722  1.00  0.00
ATOM   2426  CD  LYS   333     -12.863  78.337 -10.141  1.00  0.00
ATOM   2427  CE  LYS   333     -13.241  79.802 -10.279  1.00  0.00
ATOM   2428  NZ  LYS   333     -12.212  80.699  -9.684  1.00  0.00
ATOM   2429  N   HIS   334     -14.052  72.972  -9.934  1.00  0.00
ATOM   2430  CA  HIS   334     -13.518  71.650  -9.877  1.00  0.00
ATOM   2431  C   HIS   334     -14.444  70.764 -10.632  1.00  0.00
ATOM   2432  O   HIS   334     -15.663  70.925 -10.576  1.00  0.00
ATOM   2433  CB  HIS   334     -13.408  71.178  -8.425  1.00  0.00
ATOM   2434  CG  HIS   334     -12.381  71.917  -7.626  1.00  0.00
ATOM   2435  ND1 HIS   334     -11.028  71.701  -7.772  1.00  0.00
ATOM   2436  CD2 HIS   334     -12.408  72.943  -6.593  1.00  0.00
ATOM   2437  CE1 HIS   334     -10.361  72.506  -6.926  1.00  0.00
ATOM   2438  NE2 HIS   334     -11.183  73.254  -6.215  1.00  0.00
ATOM   2439  N   TYR   335     -13.876  69.808 -11.382  1.00  0.00
ATOM   2440  CA  TYR   335     -14.706  68.916 -12.124  1.00  0.00
ATOM   2441  C   TYR   335     -14.433  67.549 -11.599  1.00  0.00
ATOM   2442  O   TYR   335     -13.282  67.128 -11.494  1.00  0.00
ATOM   2443  CB  TYR   335     -14.374  68.991 -13.616  1.00  0.00
ATOM   2444  CG  TYR   335     -15.179  68.040 -14.472  1.00  0.00
ATOM   2445  CD1 TYR   335     -16.514  68.297 -14.756  1.00  0.00
ATOM   2446  CD2 TYR   335     -14.602  66.889 -14.993  1.00  0.00
ATOM   2447  CE1 TYR   335     -17.259  67.434 -15.537  1.00  0.00
ATOM   2448  CE2 TYR   335     -15.331  66.014 -15.775  1.00  0.00
ATOM   2449  CZ  TYR   335     -16.670  66.296 -16.045  1.00  0.00
ATOM   2450  OH  TYR   335     -17.409  65.434 -16.824  1.00  0.00
ATOM   2451  N   LEU   336     -15.504  66.824 -11.233  1.00  0.00
ATOM   2452  CA  LEU   336     -15.312  65.502 -10.727  1.00  0.00
ATOM   2453  C   LEU   336     -14.919  64.676 -11.933  1.00  0.00
ATOM   2454  O   LEU   336     -13.798  64.099 -11.925  1.00  0.00
ATOM   2455  CB  LEU   336     -16.602  64.979 -10.092  1.00  0.00
ATOM   2456  CG  LEU   336     -17.159  65.792  -8.922  1.00  0.00
ATOM   2457  CD1 LEU   336     -18.491  65.220  -8.457  1.00  0.00
ATOM   2458  CD2 LEU   336     -16.196  65.772  -7.745  1.00  0.00
TER
END
