
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   21 , name T0298_D1.pdb
# PARAMETERS: T0298TS268_4_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:    20       316 - 335         4.96     5.13
  LCS_AVERAGE:     13.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       316 - 321         1.84    14.79
  LCS_AVERAGE:      3.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       316 - 320         0.91    19.49
  LCS_AVERAGE:      2.61

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    6   20     3    4    5    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     R     317     R     317      5    6   20     3    4    5    5    5   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     K     318     K     318      5    6   20     3    4    5    5    5    6    7   10   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     G     319     G     319      5    6   20     3    4    5    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     A     320     A     320      5    6   20     3    3    5    5    6    6    9   11   12   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     A     321     A     321      3    6   20     3    3    5    5    6    6    9   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     L     322     L     322      4    4   20     3    4    5    5    6   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     N     323     N     323      4    4   20     3    4    4    4    4    6    6    8   10   12   13   14   16   18   19   21   21   21   21   21 
LCS_GDT     A     324     A     324      4    4   20     3    4    4    4    4    6    7    8   10   12   15   17   18   18   19   21   21   21   21   21 
LCS_GDT     V     325     V     325      4    4   20     3    4    4    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     L     326     L     326      3    4   20     3    3    4    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     L     327     L     327      3    4   20     0    3    3    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     G     328     G     328      3    5   20     1    3    4    5    5    5    7    9   11   12   15   16   17   18   19   21   21   21   21   21 
LCS_GDT     E     329     E     329      4    5   20     3    3    4    5    5    5    7    8    9   12   15   16   18   18   19   21   21   21   21   21 
LCS_GDT     L     330     L     330      4    5   20     3    3    4    4    4    5    6   11   12   12   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     L     331     L     331      4    5   20     3    3    5    5    6    6    7    9   10   12   15   16   17   18   19   21   21   21   21   21 
LCS_GDT     I     332     I     332      4    5   20     3    3    4    4    6    6    7   11   12   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     K     333     K     333      3    5   20     3    3    4    5    6   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     H     334     H     334      3    4   20     3    3    4    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     Y     335     Y     335      3    4   20     3    3    4    5    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_GDT     L     336     L     336      3    3   12     0    3    4    6    8   10   11   12   13   15   16   17   18   18   19   21   21   21   21   21 
LCS_AVERAGE  LCS_A:   6.37  (   2.61    3.25   13.26 )

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      8     10     11     12     13     15     16     17     18     18     19     21     21     21     21     21 
GDT PERCENT_CA   2.03   2.70   3.38   4.05   5.41   6.76   7.43   8.11   8.78  10.14  10.81  11.49  12.16  12.16  12.84  14.19  14.19  14.19  14.19  14.19
GDT RMS_LOCAL    0.05   0.52   0.91   1.54   1.80   2.26   2.37   2.59   2.81   3.49   3.73   3.97   4.23   4.23   4.47   5.05   5.05   5.05   5.05   5.05
GDT RMS_ALL_CA   5.88  13.89  19.49   6.00   5.95   5.73   5.68   5.60   5.57   5.28   5.19   5.16   5.12   5.12   5.10   5.05   5.05   5.05   5.05   5.05

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          3.011
LGA    R     317      R     317          3.258
LGA    K     318      K     318          4.809
LGA    G     319      G     319          1.806
LGA    A     320      A     320          4.996
LGA    A     321      A     321          3.848
LGA    L     322      L     322          2.912
LGA    N     323      N     323          8.557
LGA    A     324      A     324          7.331
LGA    V     325      V     325          2.340
LGA    L     326      L     326          1.948
LGA    L     327      L     327          2.094
LGA    G     328      G     328          8.283
LGA    E     329      E     329          9.109
LGA    L     330      L     330          7.305
LGA    L     331      L     331         10.707
LGA    I     332      I     332          7.776
LGA    K     333      K     333          3.521
LGA    H     334      H     334          1.823
LGA    Y     335      Y     335          2.542
LGA    L     336      L     336          1.553

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  148    4.0     12    2.59     7.264     6.479     0.446

LGA_LOCAL      RMSD =  2.591  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.519  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  5.047  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.115980 * X  +   0.418783 * Y  +   0.900650 * Z  + -26.503122
  Y_new =  -0.955516 * X  +  -0.200523 * Y  +   0.216285 * Z  + 129.919937
  Z_new =   0.271177 * X  +  -0.885670 * Y  +   0.376897 * Z  +  -8.836427 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.168460    1.973133  [ DEG:   -66.9478    113.0522 ]
  Theta =  -0.274616   -2.866977  [ DEG:   -15.7343   -164.2657 ]
  Phi   =  -1.450007    1.691585  [ DEG:   -83.0793     96.9207 ]
 
# 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_4_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_4_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   2.59   6.479     5.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4d_B
ATOM   2298  N   VAL   316     -14.379  66.087  -0.034  1.00  0.00
ATOM   2299  CA  VAL   316     -15.596  65.421   0.335  1.00  0.00
ATOM   2300  C   VAL   316     -15.339  64.523   1.502  1.00  0.00
ATOM   2301  O   VAL   316     -15.444  63.299   1.424  1.00  0.00
ATOM   2302  CB  VAL   316     -16.147  64.568  -0.823  1.00  0.00
ATOM   2303  CG1 VAL   316     -17.450  63.898  -0.418  1.00  0.00
ATOM   2304  CG2 VAL   316     -16.412  65.436  -2.043  1.00  0.00
ATOM   2305  N   ARG   317     -15.064  65.155   2.654  1.00  0.00
ATOM   2306  CA  ARG   317     -14.775  64.485   3.882  1.00  0.00
ATOM   2307  C   ARG   317     -14.952  65.536   4.918  1.00  0.00
ATOM   2308  O   ARG   317     -16.070  65.939   5.237  1.00  0.00
ATOM   2309  CB  ARG   317     -13.346  63.939   3.872  1.00  0.00
ATOM   2310  CG  ARG   317     -13.090  62.891   2.801  1.00  0.00
ATOM   2311  CD  ARG   317     -13.769  61.574   3.143  1.00  0.00
ATOM   2312  NE  ARG   317     -13.492  60.541   2.147  1.00  0.00
ATOM   2313  CZ  ARG   317     -13.997  59.312   2.185  1.00  0.00
ATOM   2314  NH1 ARG   317     -13.690  58.440   1.237  1.00  0.00
ATOM   2315  NH2 ARG   317     -14.809  58.960   3.173  1.00  0.00
ATOM   2316  N   LYS   318     -13.821  66.012   5.460  1.00  0.00
ATOM   2317  CA  LYS   318     -13.828  67.055   6.437  1.00  0.00
ATOM   2318  C   LYS   318     -14.486  68.227   5.783  1.00  0.00
ATOM   2319  O   LYS   318     -15.257  68.951   6.411  1.00  0.00
ATOM   2320  CB  LYS   318     -12.399  67.403   6.859  1.00  0.00
ATOM   2321  CG  LYS   318     -12.312  68.476   7.933  1.00  0.00
ATOM   2322  CD  LYS   318     -10.873  68.715   8.359  1.00  0.00
ATOM   2323  CE  LYS   318     -10.784  69.809   9.412  1.00  0.00
ATOM   2324  NZ  LYS   318      -9.377  70.064   9.828  1.00  0.00
ATOM   2325  N   GLY   319     -14.208  68.425   4.479  1.00  0.00
ATOM   2326  CA  GLY   319     -14.747  69.556   3.786  1.00  0.00
ATOM   2327  C   GLY   319     -16.234  69.520   3.885  1.00  0.00
ATOM   2328  O   GLY   319     -16.884  68.581   3.428  1.00  0.00
ATOM   2329  N   ALA   320     -16.803  70.599   4.455  1.00  0.00
ATOM   2330  CA  ALA   320     -18.217  70.691   4.653  1.00  0.00
ATOM   2331  C   ALA   320     -18.870  70.850   3.324  1.00  0.00
ATOM   2332  O   ALA   320     -18.339  71.495   2.422  1.00  0.00
ATOM   2333  CB  ALA   320     -18.553  71.888   5.531  1.00  0.00
ATOM   2334  N   ALA   321     -20.055  70.228   3.176  1.00  0.00
ATOM   2335  CA  ALA   321     -20.803  70.338   1.964  1.00  0.00
ATOM   2336  C   ALA   321     -22.101  69.654   2.216  1.00  0.00
ATOM   2337  O   ALA   321     -22.241  68.905   3.181  1.00  0.00
ATOM   2338  CB  ALA   321     -20.057  69.670   0.818  1.00  0.00
ATOM   2339  N   LEU   322     -23.105  69.913   1.360  1.00  0.00
ATOM   2340  CA  LEU   322     -24.356  69.239   1.517  1.00  0.00
ATOM   2341  C   LEU   322     -24.460  68.273   0.392  1.00  0.00
ATOM   2342  O   LEU   322     -23.723  68.370  -0.588  1.00  0.00
ATOM   2343  CB  LEU   322     -25.512  70.241   1.472  1.00  0.00
ATOM   2344  CG  LEU   322     -25.476  71.366   2.507  1.00  0.00
ATOM   2345  CD1 LEU   322     -26.625  72.337   2.286  1.00  0.00
ATOM   2346  CD2 LEU   322     -25.591  70.805   3.916  1.00  0.00
ATOM   2347  N   ASN   323     -25.371  67.295   0.512  1.00  0.00
ATOM   2348  CA  ASN   323     -25.495  66.334  -0.539  1.00  0.00
ATOM   2349  C   ASN   323     -25.853  67.091  -1.772  1.00  0.00
ATOM   2350  O   ASN   323     -25.285  66.862  -2.837  1.00  0.00
ATOM   2351  CB  ASN   323     -26.585  65.314  -0.207  1.00  0.00
ATOM   2352  CG  ASN   323     -26.164  64.344   0.879  1.00  0.00
ATOM   2353  OD1 ASN   323     -24.974  64.177   1.148  1.00  0.00
ATOM   2354  ND2 ASN   323     -27.141  63.698   1.506  1.00  0.00
ATOM   2355  N   ALA   324     -26.808  68.033  -1.653  1.00  0.00
ATOM   2356  CA  ALA   324     -27.148  68.834  -2.788  1.00  0.00
ATOM   2357  C   ALA   324     -26.071  69.859  -2.911  1.00  0.00
ATOM   2358  O   ALA   324     -25.402  70.182  -1.932  1.00  0.00
ATOM   2359  CB  ALA   324     -28.500  69.499  -2.581  1.00  0.00
ATOM   2360  N   VAL   325     -25.855  70.393  -4.128  1.00  0.00
ATOM   2361  CA  VAL   325     -24.838  71.392  -4.237  1.00  0.00
ATOM   2362  C   VAL   325     -25.341  72.575  -3.485  1.00  0.00
ATOM   2363  O   VAL   325     -26.502  72.958  -3.616  1.00  0.00
ATOM   2364  CB  VAL   325     -24.570  71.768  -5.706  1.00  0.00
ATOM   2365  CG1 VAL   325     -23.569  72.910  -5.789  1.00  0.00
ATOM   2366  CG2 VAL   325     -24.007  70.578  -6.467  1.00  0.00
ATOM   2367  N   LEU   326     -24.481  73.182  -2.649  1.00  0.00
ATOM   2368  CA  LEU   326     -24.958  74.299  -1.899  1.00  0.00
ATOM   2369  C   LEU   326     -24.506  75.527  -2.605  1.00  0.00
ATOM   2370  O   LEU   326     -23.323  75.694  -2.896  1.00  0.00
ATOM   2371  CB  LEU   326     -24.394  74.271  -0.478  1.00  0.00
ATOM   2372  CG  LEU   326     -24.793  75.434   0.433  1.00  0.00
ATOM   2373  CD1 LEU   326     -26.282  75.393   0.738  1.00  0.00
ATOM   2374  CD2 LEU   326     -24.037  75.369   1.752  1.00  0.00
ATOM   2375  N   LEU   327     -25.459  76.416  -2.926  1.00  0.00
ATOM   2376  CA  LEU   327     -25.077  77.628  -3.575  1.00  0.00
ATOM   2377  C   LEU   327     -25.519  78.737  -2.686  1.00  0.00
ATOM   2378  O   LEU   327     -26.485  78.603  -1.939  1.00  0.00
ATOM   2379  CB  LEU   327     -25.752  77.737  -4.944  1.00  0.00
ATOM   2380  CG  LEU   327     -25.442  76.620  -5.944  1.00  0.00
ATOM   2381  CD1 LEU   327     -26.269  76.788  -7.209  1.00  0.00
ATOM   2382  CD2 LEU   327     -23.972  76.638  -6.331  1.00  0.00
ATOM   2383  N   GLY   328     -24.786  79.863  -2.718  1.00  0.00
ATOM   2384  CA  GLY   328     -25.187  80.990  -1.939  1.00  0.00
ATOM   2385  C   GLY   328     -25.088  80.645  -0.491  1.00  0.00
ATOM   2386  O   GLY   328     -24.111  80.054  -0.035  1.00  0.00
ATOM   2387  N   GLU   329     -26.133  81.028   0.266  1.00  0.00
ATOM   2388  CA  GLU   329     -26.176  80.849   1.685  1.00  0.00
ATOM   2389  C   GLU   329     -26.909  79.589   2.010  1.00  0.00
ATOM   2390  O   GLU   329     -27.358  78.856   1.130  1.00  0.00
ATOM   2391  CB  GLU   329     -26.894  82.025   2.352  1.00  0.00
ATOM   2392  CG  GLU   329     -26.201  83.364   2.161  1.00  0.00
ATOM   2393  CD  GLU   329     -26.899  84.491   2.894  1.00  0.00
ATOM   2394  OE1 GLU   329     -27.991  84.251   3.452  1.00  0.00
ATOM   2395  OE2 GLU   329     -26.356  85.616   2.911  1.00  0.00
ATOM   2396  N   LEU   330     -27.012  79.311   3.325  1.00  0.00
ATOM   2397  CA  LEU   330     -27.661  78.141   3.834  1.00  0.00
ATOM   2398  C   LEU   330     -29.092  78.208   3.416  1.00  0.00
ATOM   2399  O   LEU   330     -29.684  77.198   3.038  1.00  0.00
ATOM   2400  CB  LEU   330     -27.562  78.096   5.360  1.00  0.00
ATOM   2401  CG  LEU   330     -26.170  77.841   5.943  1.00  0.00
ATOM   2402  CD1 LEU   330     -26.183  78.000   7.455  1.00  0.00
ATOM   2403  CD2 LEU   330     -25.702  76.431   5.617  1.00  0.00
ATOM   2404  N   LEU   331     -29.685  79.416   3.453  1.00  0.00
ATOM   2405  CA  LEU   331     -31.061  79.521   3.084  1.00  0.00
ATOM   2406  C   LEU   331     -31.158  79.069   1.666  1.00  0.00
ATOM   2407  O   LEU   331     -30.254  79.298   0.862  1.00  0.00
ATOM   2408  CB  LEU   331     -31.543  80.967   3.217  1.00  0.00
ATOM   2409  CG  LEU   331     -31.611  81.531   4.637  1.00  0.00
ATOM   2410  CD1 LEU   331     -31.975  83.008   4.613  1.00  0.00
ATOM   2411  CD2 LEU   331     -32.660  80.796   5.458  1.00  0.00
ATOM   2412  N   ILE   332     -32.269  78.387   1.332  1.00  0.00
ATOM   2413  CA  ILE   332     -32.419  77.839   0.020  1.00  0.00
ATOM   2414  C   ILE   332     -32.545  78.962  -0.949  1.00  0.00
ATOM   2415  O   ILE   332     -33.363  79.865  -0.775  1.00  0.00
ATOM   2416  CB  ILE   332     -33.671  76.948  -0.079  1.00  0.00
ATOM   2417  CG1 ILE   332     -33.538  75.736   0.846  1.00  0.00
ATOM   2418  CG2 ILE   332     -33.857  76.449  -1.504  1.00  0.00
ATOM   2419  CD1 ILE   332     -34.815  74.937   0.991  1.00  0.00
ATOM   2420  N   LYS   333     -31.701  78.933  -1.995  1.00  0.00
ATOM   2421  CA  LYS   333     -31.763  79.911  -3.034  1.00  0.00
ATOM   2422  C   LYS   333     -32.307  79.189  -4.214  1.00  0.00
ATOM   2423  O   LYS   333     -32.135  77.978  -4.336  1.00  0.00
ATOM   2424  CB  LYS   333     -30.369  80.472  -3.324  1.00  0.00
ATOM   2425  CG  LYS   333     -29.767  81.265  -2.174  1.00  0.00
ATOM   2426  CD  LYS   333     -28.400  81.818  -2.542  1.00  0.00
ATOM   2427  CE  LYS   333     -27.802  82.616  -1.395  1.00  0.00
ATOM   2428  NZ  LYS   333     -26.471  83.185  -1.748  1.00  0.00
ATOM   2429  N   HIS   334     -33.003  79.905  -5.112  1.00  0.00
ATOM   2430  CA  HIS   334     -33.561  79.206  -6.227  1.00  0.00
ATOM   2431  C   HIS   334     -32.673  79.362  -7.409  1.00  0.00
ATOM   2432  O   HIS   334     -32.050  80.401  -7.623  1.00  0.00
ATOM   2433  CB  HIS   334     -34.945  79.762  -6.570  1.00  0.00
ATOM   2434  CG  HIS   334     -35.966  79.544  -5.497  1.00  0.00
ATOM   2435  ND1 HIS   334     -36.642  78.352  -5.345  1.00  0.00
ATOM   2436  CD2 HIS   334     -36.527  80.345  -4.419  1.00  0.00
ATOM   2437  CE1 HIS   334     -37.487  78.459  -4.304  1.00  0.00
ATOM   2438  NE2 HIS   334     -37.425  79.652  -3.744  1.00  0.00
ATOM   2439  N   TYR   335     -32.587  78.273  -8.192  1.00  0.00
ATOM   2440  CA  TYR   335     -31.854  78.238  -9.417  1.00  0.00
ATOM   2441  C   TYR   335     -32.860  77.833 -10.439  1.00  0.00
ATOM   2442  O   TYR   335     -33.697  76.970 -10.183  1.00  0.00
ATOM   2443  CB  TYR   335     -30.707  77.228  -9.327  1.00  0.00
ATOM   2444  CG  TYR   335     -29.908  77.094 -10.604  1.00  0.00
ATOM   2445  CD1 TYR   335     -28.958  78.046 -10.950  1.00  0.00
ATOM   2446  CD2 TYR   335     -30.106  76.017 -11.457  1.00  0.00
ATOM   2447  CE1 TYR   335     -28.222  77.932 -12.115  1.00  0.00
ATOM   2448  CE2 TYR   335     -29.379  75.886 -12.625  1.00  0.00
ATOM   2449  CZ  TYR   335     -28.431  76.855 -12.950  1.00  0.00
ATOM   2450  OH  TYR   335     -27.700  76.739 -14.110  1.00  0.00
ATOM   2451  N   LEU   336     -32.829  78.469 -11.622  1.00  0.00
ATOM   2452  CA  LEU   336     -33.819  78.144 -12.606  1.00  0.00
ATOM   2453  C   LEU   336     -33.630  76.669 -12.920  1.00  0.00
ATOM   2454  O   LEU   336     -34.546  75.865 -12.587  1.00  0.00
ATOM   2455  CB  LEU   336     -33.624  78.993 -13.863  1.00  0.00
ATOM   2456  CG  LEU   336     -33.691  80.511 -13.673  1.00  0.00
ATOM   2457  CD1 LEU   336     -33.361  81.230 -14.971  1.00  0.00
ATOM   2458  CD2 LEU   336     -35.085  80.937 -13.235  1.00  0.00
TER
END
