
#######################################################
#                                                     #
#                        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   18 (  144),  selected   18 , name T0301TS193_3_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   18 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_3_2-D1.T0301_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:    17       379 - 395         4.48     5.31
  LCS_AVERAGE:      8.47

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       381 - 390         1.65     6.72
  LCS_AVERAGE:      4.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       383 - 390         0.90     6.05
  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:  200
LCS_GDT     R     378     R     378      3    4   16     0    3    3    3    4    4    5    5    6    7    7    8    9   13   13   13   14   14   15   17 
LCS_GDT     S     379     S     379      3    4   17     3    3    3    4    4    4    5    5    6    7    7    8   12   13   13   13   14   17   17   17 
LCS_GDT     A     380     A     380      3    4   17     3    3    3    4    4   10   10   10   11   14   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     R     381     R     381      3   10   17     3    4    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     I     382     I     382      3   10   17     3    3    4    4    6    9   10   10   11   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     L     383     L     383      8   10   17     3    3    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     M     384     M     384      8   10   17     4    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     E     385     E     385      8   10   17     4    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     G     386     G     386      8   10   17     4    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     W     387     W     387      8   10   17     4    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     V     388     V     388      8   10   17     3    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     R     389     R     389      8   10   17     3    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     V     390     V     390      8   10   17     4    5    8    9    9   10   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     P     391     P     391      3    8   17     3    3    3    4    4    8   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     G     392     G     392      3    8   17     3    3    5    7    7    8   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     D     393     D     393      3    8   17     0    3    4    7    7    8   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     A     394     A     394      3    4   17     0    3    5    7    7    8   10   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_GDT     F     395     F     395      3    4   17     0    3    3    3    4    5    5   11   13   15   15   16   16   16   16   16   16   17   17   17 
LCS_AVERAGE  LCS_A:   5.03  (   2.61    4.00    8.47 )

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      8      9      9     10     10     11     13     15     15     16     16     16     16     16     16     17     17     17 
GDT PERCENT_CA   2.00   2.50   4.00   4.50   4.50   5.00   5.00   5.50   6.50   7.50   7.50   8.00   8.00   8.00   8.00   8.00   8.00   8.50   8.50   8.50
GDT RMS_LOCAL    0.32   0.52   0.90   1.13   1.13   1.69   1.65   2.62   3.00   3.43   3.43   3.65   3.65   3.65   3.65   3.65   3.65   4.48   4.48   4.48
GDT RMS_ALL_CA   7.40   6.57   6.05   6.34   6.34   6.07   6.72   5.96   5.97   6.02   6.02   5.65   5.65   5.65   5.65   5.65   5.65   5.31   5.31   5.31

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378         14.758
LGA    S     379      S     379         11.812
LGA    A     380      A     380          6.260
LGA    R     381      R     381          6.935
LGA    I     382      I     382          8.085
LGA    L     383      L     383          3.751
LGA    M     384      M     384          0.654
LGA    E     385      E     385          1.680
LGA    G     386      G     386          0.671
LGA    W     387      W     387          1.588
LGA    V     388      V     388          2.840
LGA    R     389      R     389          3.915
LGA    V     390      V     390          4.751
LGA    P     391      P     391          3.693
LGA    G     392      G     392          1.762
LGA    D     393      D     393          2.840
LGA    A     394      A     394          2.616
LGA    F     395      F     395          5.673

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  200    4.0     11    2.62     5.125     5.197     0.405

LGA_LOCAL      RMSD =  2.617  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.963  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  5.229  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.476496 * X  +  -0.404563 * Y  +   0.780564 * Z  +  92.883064
  Y_new =   0.646883 * X  +   0.439925 * Y  +   0.622903 * Z  +  22.250376
  Z_new =  -0.595393 * X  +   0.801745 * Y  +   0.052082 * Z  +  53.097427 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.505926   -1.635666  [ DEG:    86.2832    -93.7168 ]
  Theta =   0.637755    2.503838  [ DEG:    36.5407    143.4593 ]
  Phi   =   2.205668   -0.935924  [ DEG:   126.3755    -53.6245 ]
 
# 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: T0301TS193_3_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_3_2-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18  200   4.0   11   2.62   5.197     5.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      76.116  26.491  10.021  1.00  0.00
ATOM   2790  CA  ARG   378      75.201  27.583   9.707  1.00  0.00
ATOM   2791  C   ARG   378      74.119  27.718  10.770  1.00  0.00
ATOM   2792  O   ARG   378      73.792  28.825  11.199  1.00  0.00
ATOM   2793  CB  ARG   378      74.516  27.337   8.361  1.00  0.00
ATOM   2794  CG  ARG   378      75.436  27.484   7.161  1.00  0.00
ATOM   2795  CD  ARG   378      74.711  27.155   5.866  1.00  0.00
ATOM   2796  NE  ARG   378      75.590  27.264   4.703  1.00  0.00
ATOM   2797  CZ  ARG   378      75.226  26.961   3.461  1.00  0.00
ATOM   2798  NH1 ARG   378      76.093  27.092   2.466  1.00  0.00
ATOM   2799  NH2 ARG   378      73.997  26.528   3.217  1.00  0.00
ATOM   2800  N   SER   379      73.566  26.586  11.193  1.00  0.00
ATOM   2801  CA  SER   379      72.526  26.578  12.215  1.00  0.00
ATOM   2802  C   SER   379      73.085  26.975  13.575  1.00  0.00
ATOM   2803  O   SER   379      72.404  27.616  14.374  1.00  0.00
ATOM   2804  CB  SER   379      71.913  25.182  12.343  1.00  0.00
ATOM   2805  OG  SER   379      72.861  24.251  12.835  1.00  0.00
ATOM   2806  N   ALA   380      74.331  26.590  13.832  1.00  0.00
ATOM   2807  CA  ALA   380      74.981  26.896  15.100  1.00  0.00
ATOM   2808  C   ALA   380      75.156  28.399  15.281  1.00  0.00
ATOM   2809  O   ALA   380      74.918  28.935  16.363  1.00  0.00
ATOM   2810  CB  ALA   380      76.356  26.248  15.160  1.00  0.00
ATOM   2811  N   ARG   381      77.097  28.748  15.838  1.00  0.00
ATOM   2812  CA  ARG   381      77.538  28.646  17.224  1.00  0.00
ATOM   2813  C   ARG   381      77.390  29.977  17.949  1.00  0.00
ATOM   2814  O   ARG   381      77.146  30.014  19.155  1.00  0.00
ATOM   2815  CB  ARG   381      79.009  28.230  17.290  1.00  0.00
ATOM   2816  CG  ARG   381      79.266  26.789  16.880  1.00  0.00
ATOM   2817  CD  ARG   381      80.752  26.470  16.886  1.00  0.00
ATOM   2818  NE  ARG   381      81.018  25.095  16.473  1.00  0.00
ATOM   2819  CZ  ARG   381      82.235  24.593  16.287  1.00  0.00
ATOM   2820  NH1 ARG   381      82.381  23.330  15.910  1.00  0.00
ATOM   2821  NH2 ARG   381      83.303  25.355  16.479  1.00  0.00
ATOM   2822  N   ILE   382      77.538  31.068  17.207  1.00  0.00
ATOM   2823  CA  ILE   382      77.353  32.404  17.763  1.00  0.00
ATOM   2824  C   ILE   382      75.899  32.645  18.145  1.00  0.00
ATOM   2825  O   ILE   382      75.610  33.259  19.172  1.00  0.00
ATOM   2826  CB  ILE   382      77.754  33.496  16.754  1.00  0.00
ATOM   2827  CG1 ILE   382      79.265  33.462  16.505  1.00  0.00
ATOM   2828  CG2 ILE   382      77.384  34.872  17.283  1.00  0.00
ATOM   2829  CD1 ILE   382      79.710  34.319  15.339  1.00  0.00
ATOM   2830  N   LEU   383      74.984  32.157  17.313  1.00  0.00
ATOM   2831  CA  LEU   383      73.557  32.297  17.574  1.00  0.00
ATOM   2832  C   LEU   383      73.115  31.389  18.715  1.00  0.00
ATOM   2833  O   LEU   383      72.299  31.779  19.551  1.00  0.00
ATOM   2834  CB  LEU   383      72.745  31.927  16.331  1.00  0.00
ATOM   2835  CG  LEU   383      73.018  32.755  15.073  1.00  0.00
ATOM   2836  CD1 LEU   383      72.223  32.217  13.893  1.00  0.00
ATOM   2837  CD2 LEU   383      72.623  34.208  15.289  1.00  0.00
ATOM   2838  N   MET   384      71.847  33.838  18.765  1.00  0.00
ATOM   2839  CA  MET   384      70.426  33.772  19.088  1.00  0.00
ATOM   2840  C   MET   384      69.569  34.030  17.855  1.00  0.00
ATOM   2841  O   MET   384      69.522  35.148  17.342  1.00  0.00
ATOM   2842  CB  MET   384      70.068  34.821  20.143  1.00  0.00
ATOM   2843  CG  MET   384      68.600  34.827  20.538  1.00  0.00
ATOM   2844  SD  MET   384      68.071  33.269  21.275  1.00  0.00
ATOM   2845  CE  MET   384      68.800  33.402  22.906  1.00  0.00
ATOM   2846  N   GLU   385      68.890  32.988  17.386  1.00  0.00
ATOM   2847  CA  GLU   385      68.033  33.100  16.212  1.00  0.00
ATOM   2848  C   GLU   385      66.857  34.032  16.476  1.00  0.00
ATOM   2849  O   GLU   385      66.239  33.983  17.539  1.00  0.00
ATOM   2850  CB  GLU   385      67.474  31.730  15.824  1.00  0.00
ATOM   2851  CG  GLU   385      66.614  31.742  14.570  1.00  0.00
ATOM   2852  CD  GLU   385      66.123  30.360  14.187  1.00  0.00
ATOM   2853  OE1 GLU   385      66.455  29.392  14.904  1.00  0.00
ATOM   2854  OE2 GLU   385      65.406  30.245  13.171  1.00  0.00
ATOM   2855  N   GLY   386      66.552  34.882  15.501  1.00  0.00
ATOM   2856  CA  GLY   386      65.431  35.808  15.615  1.00  0.00
ATOM   2857  C   GLY   386      65.184  36.537  14.300  1.00  0.00
ATOM   2858  O   GLY   386      66.107  36.752  13.514  1.00  0.00
ATOM   2859  N   TRP   387      66.580  38.497  14.852  1.00  0.00
ATOM   2860  CA  TRP   387      65.796  39.449  14.075  1.00  0.00
ATOM   2861  C   TRP   387      66.630  40.665  13.691  1.00  0.00
ATOM   2862  O   TRP   387      67.094  41.410  14.554  1.00  0.00
ATOM   2863  CB  TRP   387      64.591  39.937  14.883  1.00  0.00
ATOM   2864  CG  TRP   387      63.728  40.913  14.142  1.00  0.00
ATOM   2865  CD1 TRP   387      63.476  40.930  12.802  1.00  0.00
ATOM   2866  CD2 TRP   387      63.004  42.014  14.703  1.00  0.00
ATOM   2867  NE1 TRP   387      62.639  41.975  12.490  1.00  0.00
ATOM   2868  CE2 TRP   387      62.335  42.656  13.642  1.00  0.00
ATOM   2869  CE3 TRP   387      62.856  42.522  15.997  1.00  0.00
ATOM   2870  CZ2 TRP   387      61.530  43.777  13.836  1.00  0.00
ATOM   2871  CZ3 TRP   387      62.057  43.634  16.185  1.00  0.00
ATOM   2872  CH2 TRP   387      61.403  44.251  15.112  1.00  0.00
ATOM   2873  N   VAL   388      66.817  40.861  12.390  1.00  0.00
ATOM   2874  CA  VAL   388      67.612  41.975  11.890  1.00  0.00
ATOM   2875  C   VAL   388      66.727  43.056  11.281  1.00  0.00
ATOM   2876  O   VAL   388      65.860  42.769  10.455  1.00  0.00
ATOM   2877  CB  VAL   388      68.600  41.518  10.801  1.00  0.00
ATOM   2878  CG1 VAL   388      69.383  42.705  10.260  1.00  0.00
ATOM   2879  CG2 VAL   388      69.588  40.509  11.366  1.00  0.00
ATOM   2880  N   ARG   389      66.949  44.298  11.695  1.00  0.00
ATOM   2881  CA  ARG   389      66.200  45.429  11.161  1.00  0.00
ATOM   2882  C   ARG   389      67.104  46.636  10.942  1.00  0.00
ATOM   2883  O   ARG   389      67.629  47.211  11.895  1.00  0.00
ATOM   2884  CB  ARG   389      65.088  45.839  12.129  1.00  0.00
ATOM   2885  CG  ARG   389      65.586  46.273  13.498  1.00  0.00
ATOM   2886  CD  ARG   389      64.436  46.721  14.387  1.00  0.00
ATOM   2887  NE  ARG   389      64.903  47.193  15.688  1.00  0.00
ATOM   2888  CZ  ARG   389      65.152  46.402  16.726  1.00  0.00
ATOM   2889  NH1 ARG   389      65.574  46.921  17.871  1.00  0.00
ATOM   2890  NH2 ARG   389      64.980  45.091  16.616  1.00  0.00
ATOM   2891  N   VAL   390      69.421  47.760  10.649  1.00  0.00
ATOM   2892  CA  VAL   390      68.654  47.941   9.422  1.00  0.00
ATOM   2893  C   VAL   390      69.106  46.968   8.341  1.00  0.00
ATOM   2894  O   VAL   390      70.260  46.993   7.912  1.00  0.00
ATOM   2895  CB  VAL   390      68.817  49.366   8.861  1.00  0.00
ATOM   2896  CG1 VAL   390      68.088  49.502   7.532  1.00  0.00
ATOM   2897  CG2 VAL   390      68.243  50.389   9.830  1.00  0.00
ATOM   2898  N   PRO   391      68.189  46.111   7.903  1.00  0.00
ATOM   2899  CA  PRO   391      68.464  45.191   6.805  1.00  0.00
ATOM   2900  C   PRO   391      68.392  45.901   5.460  1.00  0.00
ATOM   2901  O   PRO   391      67.369  46.491   5.113  1.00  0.00
ATOM   2902  CB  PRO   391      67.373  44.126   6.933  1.00  0.00
ATOM   2903  CG  PRO   391      66.230  44.837   7.577  1.00  0.00
ATOM   2904  CD  PRO   391      66.838  45.865   8.489  1.00  0.00
ATOM   2905  N   GLY   392      69.484  45.840   4.705  1.00  0.00
ATOM   2906  CA  GLY   392      69.576  46.545   3.432  1.00  0.00
ATOM   2907  C   GLY   392      70.164  45.650   2.349  1.00  0.00
ATOM   2908  O   GLY   392      70.770  44.620   2.642  1.00  0.00
ATOM   2909  N   ASP   393      71.804  46.600   2.362  1.00  0.00
ATOM   2910  CA  ASP   393      72.222  46.315   0.995  1.00  0.00
ATOM   2911  C   ASP   393      73.671  45.844   0.950  1.00  0.00
ATOM   2912  O   ASP   393      74.540  46.417   1.606  1.00  0.00
ATOM   2913  CB  ASP   393      72.104  47.568   0.126  1.00  0.00
ATOM   2914  CG  ASP   393      70.664  47.921  -0.195  1.00  0.00
ATOM   2915  OD1 ASP   393      69.773  47.092   0.088  1.00  0.00
ATOM   2916  OD2 ASP   393      70.427  49.024  -0.729  1.00  0.00
ATOM   2917  N   ALA   394      73.923  44.797   0.172  1.00  0.00
ATOM   2918  CA  ALA   394      75.264  44.240   0.048  1.00  0.00
ATOM   2919  C   ALA   394      75.863  44.545  -1.319  1.00  0.00
ATOM   2920  O   ALA   394      75.233  44.310  -2.350  1.00  0.00
ATOM   2921  CB  ALA   394      75.230  42.729   0.224  1.00  0.00
ATOM   2922  N   PHE   395      77.085  45.069  -1.320  1.00  0.00
ATOM   2923  CA  PHE   395      77.774  45.400  -2.562  1.00  0.00
ATOM   2924  C   PHE   395      79.225  44.940  -2.525  1.00  0.00
ATOM   2925  O   PHE   395      79.759  44.620  -1.463  1.00  0.00
ATOM   2926  CB  PHE   395      77.761  46.912  -2.796  1.00  0.00
ATOM   2927  CG  PHE   395      76.382  47.508  -2.832  1.00  0.00
ATOM   2928  CD1 PHE   395      75.843  48.107  -1.708  1.00  0.00
ATOM   2929  CD2 PHE   395      75.626  47.469  -3.990  1.00  0.00
ATOM   2930  CE1 PHE   395      74.574  48.656  -1.741  1.00  0.00
ATOM   2931  CE2 PHE   395      74.359  48.018  -4.024  1.00  0.00
ATOM   2932  CZ  PHE   395      73.831  48.609  -2.906  1.00  0.00
TER
END
