
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   21 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_2_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:    13       318 - 330         4.96     8.51
  LONGEST_CONTINUOUS_SEGMENT:    13       319 - 331         4.90     8.46
  LCS_AVERAGE:      8.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       325 - 330         1.94    12.41
  LCS_AVERAGE:      3.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       316 - 320         0.64    21.12
  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   10     3    5    5    5    6    7    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     R     317     R     317      5    5   10     3    5    5    5    5    7    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     K     318     K     318      5    5   13     3    5    5    5    5    6    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     G     319     G     319      5    5   13     3    5    5    5    6    7    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     A     320     A     320      5    5   13     3    5    5    5    5    5    7    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     A     321     A     321      3    3   13     3    3    3    3    6    7    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     L     322     L     322      3    4   13     3    3    3    3    4    4    7    8    9   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     N     323     N     323      3    4   13     3    3    3    3    4    5    7    8    9   10   12   14   15   16   18   19   20   20   21   21 
LCS_GDT     A     324     A     324      3    4   13     3    3    3    3    4    5    7    8    9   10   12   14   15   16   18   19   20   20   21   21 
LCS_GDT     V     325     V     325      4    6   13     3    3    5    5    5    6    7    8    9    9   12   13   15   16   18   19   20   20   21   21 
LCS_GDT     L     326     L     326      4    6   13     3    3    5    5    5    6    7    8    9    9   12   12   14   16   18   19   20   20   21   21 
LCS_GDT     L     327     L     327      4    6   13     3    3    5    5    5    6    7    8    9    9   12   12   14   16   18   18   20   20   21   21 
LCS_GDT     G     328     G     328      4    6   13     3    3    5    5    5    6    7    8    9    9   12   12   13   16   18   19   20   20   21   21 
LCS_GDT     E     329     E     329      4    6   13     2    3    5    5    5    6    7    8    9    9   12   12   14   16   18   18   20   20   21   21 
LCS_GDT     L     330     L     330      4    6   13     3    3    4    5    5    6    7    8    9    9   12   14   15   16   18   19   20   20   21   21 
LCS_GDT     L     331     L     331      4    4   13     3    3    4    5    6    7    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     I     332     I     332      4    5   12     3    4    4    5    6    7    8    8   10   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     K     333     K     333      4    5   12     3    4    4    5    6    7    8    9   11   12   13   14   15   16   18   19   20   20   21   21 
LCS_GDT     H     334     H     334      4    5   12     3    4    4    5    5    5    7    9   11   12   13   14   15   16   17   19   20   20   21   21 
LCS_GDT     Y     335     Y     335      4    5   12     3    4    4    5    5    5    7    9   11   12   13   14   15   16   17   19   20   20   21   21 
LCS_GDT     L     336     L     336      3    5   12     0    3    3    5    5    6    8    9   11   12   13   14   15   16   17   19   20   20   21   21 
LCS_AVERAGE  LCS_A:   4.84  (   2.70    3.38    8.43 )

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      5      5      5      6      7      8      9     11     12     13     14     15     16     18     19     20     20     21     21 
GDT PERCENT_CA   2.03   3.38   3.38   3.38   4.05   4.73   5.41   6.08   7.43   8.11   8.78   9.46  10.14  10.81  12.16  12.84  13.51  13.51  14.19  14.19
GDT RMS_LOCAL    0.07   0.64   0.64   0.64   1.81   2.03   2.27   2.63   3.25   3.47   3.69   4.18   4.29   4.67   5.62   5.73   5.97   5.98   6.20   6.20
GDT RMS_ALL_CA  11.90  21.12  21.12  21.12   7.22   7.27   7.41   7.99   7.53   7.41   7.21   7.05   6.94   6.70   6.71   6.30   6.23   6.31   6.20   6.20

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          3.718
LGA    R     317      R     317          1.433
LGA    K     318      K     318          3.723
LGA    G     319      G     319          1.707
LGA    A     320      A     320          3.402
LGA    A     321      A     321          3.305
LGA    L     322      L     322          6.430
LGA    N     323      N     323          7.370
LGA    A     324      A     324          7.442
LGA    V     325      V     325         10.324
LGA    L     326      L     326         13.277
LGA    L     327      L     327         13.518
LGA    G     328      G     328         12.973
LGA    E     329      E     329         14.759
LGA    L     330      L     330         11.752
LGA    L     331      L     331          6.303
LGA    I     332      I     332          7.453
LGA    K     333      K     333          6.447
LGA    H     334      H     334          1.906
LGA    Y     335      Y     335          0.880
LGA    L     336      L     336          1.576

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  148    4.0      9    2.63     6.419     5.625     0.330

LGA_LOCAL      RMSD =  2.625  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.987  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  6.204  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.218940 * X  +   0.270813 * Y  +   0.937404 * Z  +  -5.108107
  Y_new =  -0.813257 * X  +  -0.581490 * Y  +  -0.021954 * Z  + 123.988525
  Z_new =   0.539145 * X  +  -0.767157 * Y  +   0.347552 * Z  + -27.215187 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.145418    1.996174  [ DEG:   -65.6276    114.3724 ]
  Theta =  -0.569422   -2.572171  [ DEG:   -32.6255   -147.3745 ]
  Phi   =  -1.833775    1.307817  [ DEG:  -105.0676     74.9324 ]
 
# 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_2_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_2_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    9   2.63   5.625     6.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4d_B
ATOM   2298  N   VAL   316     -16.131  65.423   0.649  1.00  0.00
ATOM   2299  CA  VAL   316     -17.465  65.445   1.182  1.00  0.00
ATOM   2300  C   VAL   316     -17.481  64.819   2.538  1.00  0.00
ATOM   2301  O   VAL   316     -18.058  63.755   2.761  1.00  0.00
ATOM   2302  CB  VAL   316     -18.445  64.668   0.283  1.00  0.00
ATOM   2303  CG1 VAL   316     -19.855  64.732   0.852  1.00  0.00
ATOM   2304  CG2 VAL   316     -18.466  65.261  -1.118  1.00  0.00
ATOM   2305  N   ARG   317     -16.876  65.544   3.493  1.00  0.00
ATOM   2306  CA  ARG   317     -16.775  65.171   4.869  1.00  0.00
ATOM   2307  C   ARG   317     -16.466  66.454   5.562  1.00  0.00
ATOM   2308  O   ARG   317     -17.333  67.306   5.749  1.00  0.00
ATOM   2309  CB  ARG   317     -15.663  64.138   5.062  1.00  0.00
ATOM   2310  CG  ARG   317     -15.474  63.693   6.504  1.00  0.00
ATOM   2311  CD  ARG   317     -16.688  62.933   7.011  1.00  0.00
ATOM   2312  NE  ARG   317     -16.879  61.671   6.300  1.00  0.00
ATOM   2313  CZ  ARG   317     -17.954  60.899   6.423  1.00  0.00
ATOM   2314  NH1 ARG   317     -18.041  59.768   5.737  1.00  0.00
ATOM   2315  NH2 ARG   317     -18.940  61.260   7.233  1.00  0.00
ATOM   2316  N   LYS   318     -15.196  66.619   5.958  1.00  0.00
ATOM   2317  CA  LYS   318     -14.794  67.832   6.596  1.00  0.00
ATOM   2318  C   LYS   318     -15.060  68.943   5.629  1.00  0.00
ATOM   2319  O   LYS   318     -15.534  70.010   6.016  1.00  0.00
ATOM   2320  CB  LYS   318     -13.305  67.782   6.950  1.00  0.00
ATOM   2321  CG  LYS   318     -12.799  69.018   7.676  1.00  0.00
ATOM   2322  CD  LYS   318     -11.337  68.868   8.066  1.00  0.00
ATOM   2323  CE  LYS   318     -10.823  70.116   8.767  1.00  0.00
ATOM   2324  NZ  LYS   318      -9.387  69.990   9.141  1.00  0.00
ATOM   2325  N   GLY   319     -14.780  68.708   4.331  1.00  0.00
ATOM   2326  CA  GLY   319     -14.969  69.737   3.350  1.00  0.00
ATOM   2327  C   GLY   319     -16.423  69.867   3.046  1.00  0.00
ATOM   2328  O   GLY   319     -17.216  68.958   3.285  1.00  0.00
ATOM   2329  N   ALA   320     -16.805  71.025   2.476  1.00  0.00
ATOM   2330  CA  ALA   320     -18.183  71.251   2.173  1.00  0.00
ATOM   2331  C   ALA   320     -18.306  71.338   0.691  1.00  0.00
ATOM   2332  O   ALA   320     -17.392  71.789   0.002  1.00  0.00
ATOM   2333  CB  ALA   320     -18.661  72.546   2.811  1.00  0.00
ATOM   2334  N   ALA   321     -19.454  70.874   0.163  1.00  0.00
ATOM   2335  CA  ALA   321     -19.678  70.928  -1.248  1.00  0.00
ATOM   2336  C   ALA   321     -20.740  71.943  -1.472  1.00  0.00
ATOM   2337  O   ALA   321     -21.662  72.084  -0.672  1.00  0.00
ATOM   2338  CB  ALA   321     -20.124  69.568  -1.766  1.00  0.00
ATOM   2339  N   LEU   322     -20.622  72.697  -2.578  1.00  0.00
ATOM   2340  CA  LEU   322     -21.581  73.713  -2.884  1.00  0.00
ATOM   2341  C   LEU   322     -22.447  73.193  -3.984  1.00  0.00
ATOM   2342  O   LEU   322     -21.972  72.507  -4.887  1.00  0.00
ATOM   2343  CB  LEU   322     -20.878  74.996  -3.332  1.00  0.00
ATOM   2344  CG  LEU   322     -19.940  75.646  -2.314  1.00  0.00
ATOM   2345  CD1 LEU   322     -19.249  76.859  -2.917  1.00  0.00
ATOM   2346  CD2 LEU   322     -20.713  76.101  -1.085  1.00  0.00
ATOM   2347  N   ASN   323     -23.758  73.491  -3.929  1.00  0.00
ATOM   2348  CA  ASN   323     -24.613  73.017  -4.975  1.00  0.00
ATOM   2349  C   ASN   323     -24.924  74.181  -5.850  1.00  0.00
ATOM   2350  O   ASN   323     -25.569  75.140  -5.432  1.00  0.00
ATOM   2351  CB  ASN   323     -25.903  72.436  -4.392  1.00  0.00
ATOM   2352  CG  ASN   323     -26.805  71.840  -5.453  1.00  0.00
ATOM   2353  OD1 ASN   323     -26.679  72.154  -6.637  1.00  0.00
ATOM   2354  ND2 ASN   323     -27.721  70.976  -5.032  1.00  0.00
ATOM   2355  N   ALA   324     -24.450  74.120  -7.105  1.00  0.00
ATOM   2356  CA  ALA   324     -24.718  75.170  -8.037  1.00  0.00
ATOM   2357  C   ALA   324     -24.620  74.534  -9.375  1.00  0.00
ATOM   2358  O   ALA   324     -23.990  73.486  -9.512  1.00  0.00
ATOM   2359  CB  ALA   324     -23.698  76.289  -7.883  1.00  0.00
ATOM   2360  N   VAL   325     -25.251  75.125 -10.405  1.00  0.00
ATOM   2361  CA  VAL   325     -25.104  74.499 -11.681  1.00  0.00
ATOM   2362  C   VAL   325     -23.819  75.000 -12.244  1.00  0.00
ATOM   2363  O   VAL   325     -23.666  76.178 -12.565  1.00  0.00
ATOM   2364  CB  VAL   325     -26.271  74.855 -12.621  1.00  0.00
ATOM   2365  CG1 VAL   325     -26.064  74.221 -13.988  1.00  0.00
ATOM   2366  CG2 VAL   325     -27.587  74.350 -12.052  1.00  0.00
ATOM   2367  N   LEU   326     -22.834  74.093 -12.355  1.00  0.00
ATOM   2368  CA  LEU   326     -21.550  74.494 -12.834  1.00  0.00
ATOM   2369  C   LEU   326     -21.704  74.912 -14.257  1.00  0.00
ATOM   2370  O   LEU   326     -21.141  75.920 -14.678  1.00  0.00
ATOM   2371  CB  LEU   326     -20.556  73.336 -12.739  1.00  0.00
ATOM   2372  CG  LEU   326     -19.125  73.630 -13.193  1.00  0.00
ATOM   2373  CD1 LEU   326     -18.511  74.737 -12.352  1.00  0.00
ATOM   2374  CD2 LEU   326     -18.253  72.391 -13.059  1.00  0.00
ATOM   2375  N   LEU   327     -22.495  74.154 -15.039  1.00  0.00
ATOM   2376  CA  LEU   327     -22.657  74.501 -16.419  1.00  0.00
ATOM   2377  C   LEU   327     -23.465  75.752 -16.452  1.00  0.00
ATOM   2378  O   LEU   327     -24.281  75.997 -15.567  1.00  0.00
ATOM   2379  CB  LEU   327     -23.378  73.381 -17.173  1.00  0.00
ATOM   2380  CG  LEU   327     -22.642  72.042 -17.262  1.00  0.00
ATOM   2381  CD1 LEU   327     -23.518  70.991 -17.927  1.00  0.00
ATOM   2382  CD2 LEU   327     -21.366  72.183 -18.077  1.00  0.00
ATOM   2383  N   GLY   328     -23.228  76.597 -17.469  1.00  0.00
ATOM   2384  CA  GLY   328     -23.962  77.820 -17.535  1.00  0.00
ATOM   2385  C   GLY   328     -23.322  78.747 -16.561  1.00  0.00
ATOM   2386  O   GLY   328     -22.118  78.678 -16.319  1.00  0.00
ATOM   2387  N   GLU   329     -24.125  79.649 -15.972  1.00  0.00
ATOM   2388  CA  GLU   329     -23.557  80.580 -15.050  1.00  0.00
ATOM   2389  C   GLU   329     -23.081  79.813 -13.870  1.00  0.00
ATOM   2390  O   GLU   329     -23.676  78.810 -13.480  1.00  0.00
ATOM   2391  CB  GLU   329     -24.603  81.609 -14.615  1.00  0.00
ATOM   2392  CG  GLU   329     -24.062  82.694 -13.700  1.00  0.00
ATOM   2393  CD  GLU   329     -25.112  83.726 -13.335  1.00  0.00
ATOM   2394  OE1 GLU   329     -26.268  83.582 -13.787  1.00  0.00
ATOM   2395  OE2 GLU   329     -24.781  84.676 -12.596  1.00  0.00
ATOM   2396  N   LEU   330     -21.952  80.269 -13.301  1.00  0.00
ATOM   2397  CA  LEU   330     -21.374  79.642 -12.155  1.00  0.00
ATOM   2398  C   LEU   330     -22.140  80.148 -10.977  1.00  0.00
ATOM   2399  O   LEU   330     -22.730  81.225 -11.049  1.00  0.00
ATOM   2400  CB  LEU   330     -19.893  80.008 -12.035  1.00  0.00
ATOM   2401  CG  LEU   330     -18.988  79.556 -13.183  1.00  0.00
ATOM   2402  CD1 LEU   330     -17.571  80.072 -12.985  1.00  0.00
ATOM   2403  CD2 LEU   330     -18.934  78.038 -13.261  1.00  0.00
ATOM   2404  N   LEU   331     -22.144  79.358  -9.880  1.00  0.00
ATOM   2405  CA  LEU   331     -22.816  79.579  -8.622  1.00  0.00
ATOM   2406  C   LEU   331     -24.040  80.429  -8.781  1.00  0.00
ATOM   2407  O   LEU   331     -23.967  81.650  -8.893  1.00  0.00
ATOM   2408  CB  LEU   331     -21.885  80.287  -7.634  1.00  0.00
ATOM   2409  CG  LEU   331     -22.457  80.564  -6.243  1.00  0.00
ATOM   2410  CD1 LEU   331     -22.798  79.262  -5.532  1.00  0.00
ATOM   2411  CD2 LEU   331     -21.452  81.323  -5.390  1.00  0.00
ATOM   2412  N   ILE   332     -25.219  79.778  -8.736  1.00  0.00
ATOM   2413  CA  ILE   332     -26.469  80.470  -8.867  1.00  0.00
ATOM   2414  C   ILE   332     -27.203  80.297  -7.581  1.00  0.00
ATOM   2415  O   ILE   332     -27.206  79.214  -6.995  1.00  0.00
ATOM   2416  CB  ILE   332     -27.309  79.901 -10.025  1.00  0.00
ATOM   2417  CG1 ILE   332     -26.567  80.065 -11.353  1.00  0.00
ATOM   2418  CG2 ILE   332     -28.641  80.630 -10.124  1.00  0.00
ATOM   2419  CD1 ILE   332     -27.202  79.315 -12.504  1.00  0.00
ATOM   2420  N   LYS   333     -27.839  81.381  -7.097  1.00  0.00
ATOM   2421  CA  LYS   333     -28.535  81.272  -5.852  1.00  0.00
ATOM   2422  C   LYS   333     -30.005  81.342  -6.115  1.00  0.00
ATOM   2423  O   LYS   333     -30.502  82.290  -6.720  1.00  0.00
ATOM   2424  CB  LYS   333     -28.135  82.412  -4.913  1.00  0.00
ATOM   2425  CG  LYS   333     -26.672  82.391  -4.499  1.00  0.00
ATOM   2426  CD  LYS   333     -26.343  83.555  -3.578  1.00  0.00
ATOM   2427  CE  LYS   333     -24.885  83.522  -3.148  1.00  0.00
ATOM   2428  NZ  LYS   333     -24.568  84.606  -2.178  1.00  0.00
ATOM   2429  N   HIS   334     -30.725  80.293  -5.676  1.00  0.00
ATOM   2430  CA  HIS   334     -32.158  80.246  -5.698  1.00  0.00
ATOM   2431  C   HIS   334     -32.648  80.516  -7.085  1.00  0.00
ATOM   2432  O   HIS   334     -33.728  81.072  -7.273  1.00  0.00
ATOM   2433  CB  HIS   334     -32.743  81.298  -4.753  1.00  0.00
ATOM   2434  CG  HIS   334     -32.278  81.163  -3.336  1.00  0.00
ATOM   2435  ND1 HIS   334     -32.615  80.088  -2.542  1.00  0.00
ATOM   2436  CD2 HIS   334     -31.456  81.955  -2.433  1.00  0.00
ATOM   2437  CE1 HIS   334     -32.054  80.247  -1.330  1.00  0.00
ATOM   2438  NE2 HIS   334     -31.358  81.365  -1.258  1.00  0.00
ATOM   2439  N   TYR   335     -31.880  80.125  -8.116  1.00  0.00
ATOM   2440  CA  TYR   335     -32.371  80.383  -9.438  1.00  0.00
ATOM   2441  C   TYR   335     -32.141  79.171 -10.277  1.00  0.00
ATOM   2442  O   TYR   335     -31.084  78.543 -10.212  1.00  0.00
ATOM   2443  CB  TYR   335     -31.639  81.576 -10.057  1.00  0.00
ATOM   2444  CG  TYR   335     -32.092  81.909 -11.461  1.00  0.00
ATOM   2445  CD1 TYR   335     -33.290  82.578 -11.681  1.00  0.00
ATOM   2446  CD2 TYR   335     -31.320  81.556 -12.561  1.00  0.00
ATOM   2447  CE1 TYR   335     -33.712  82.887 -12.960  1.00  0.00
ATOM   2448  CE2 TYR   335     -31.726  81.858 -13.847  1.00  0.00
ATOM   2449  CZ  TYR   335     -32.933  82.529 -14.039  1.00  0.00
ATOM   2450  OH  TYR   335     -33.351  82.837 -15.314  1.00  0.00
ATOM   2451  N   LEU   336     -33.154  78.806 -11.083  1.00  0.00
ATOM   2452  CA  LEU   336     -33.017  77.686 -11.964  1.00  0.00
ATOM   2453  C   LEU   336     -33.790  78.042 -13.227  1.00  0.00
ATOM   2454  O   LEU   336     -33.701  77.264 -14.213  1.00  0.00
ATOM   2455  CB  LEU   336     -33.592  76.423 -11.318  1.00  0.00
ATOM   2456  CG  LEU   336     -32.873  75.913 -10.068  1.00  0.00
ATOM   2457  CD1 LEU   336     -33.649  74.773  -9.429  1.00  0.00
ATOM   2458  CD2 LEU   336     -31.483  75.405 -10.418  1.00  0.00
TER
END
