
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   18 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_5_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:    14       382 - 395         4.45     6.55
  LCS_AVERAGE:      6.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       385 - 393         1.77    11.56
  LCS_AVERAGE:      3.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       387 - 392         0.90    13.24
  LCS_AVERAGE:      2.17

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    5    9     0    3    4    4    5    5    5    5    6    6    7    7    9   12   12   15   15   17   18   18 
LCS_GDT     S     379     S     379      4    5   11     3    4    4    4    5    5    5    6    6    7   10   10   14   14   14   17   17   17   18   18 
LCS_GDT     A     380     A     380      4    5   11     3    4    4    4    5    5    5    6    6    7   10   10   14   14   14   17   17   17   18   18 
LCS_GDT     R     381     R     381      4    5   11     3    4    4    4    5    5    5    6    6    7   10   10   14   14   14   17   17   17   18   18 
LCS_GDT     I     382     I     382      4    5   14     3    4    4    4    5    5    5    6    6    7   10   10   14   14   14   17   17   17   18   18 
LCS_GDT     L     383     L     383      3    4   14     3    3    3    4    4    5    5    6    6    7    8   10   14   14   14   17   17   17   18   18 
LCS_GDT     M     384     M     384      3    7   14     3    3    5    5    6    8    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     E     385     E     385      4    9   14     3    4    5    6    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     G     386     G     386      4    9   14     3    4    6    8    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     W     387     W     387      6    9   14     3    4    6    8    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     V     388     V     388      6    9   14     3    5    6    8    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     R     389     R     389      6    9   14     3    5    6    8    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     V     390     V     390      6    9   14     3    5    6    8    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     P     391     P     391      6    9   14     3    5    6    8    8    9    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     G     392     G     392      6    9   14     3    5    6    8    8    9    9   11   12   12   12   12   13   14   14   17   17   17   18   18 
LCS_GDT     D     393     D     393      3    9   14     3    3    5    8    8    9    9   11   12   12   12   12   13   14   14   17   17   17   18   18 
LCS_GDT     A     394     A     394      3    3   14     3    3    3    3    3    5    9   11   12   12   12   12   14   14   14   17   17   17   18   18 
LCS_GDT     F     395     F     395      3    3   14     3    3    3    3    3    3    7   11   12   12   12   12   13   14   14   17   17   17   18   18 
LCS_AVERAGE  LCS_A:   4.06  (   2.17    3.42    6.61 )

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      6      8      8      9      9     11     12     12     12     12     14     14     14     17     17     17     18     18 
GDT PERCENT_CA   1.50   2.50   3.00   4.00   4.00   4.50   4.50   5.50   6.00   6.00   6.00   6.00   7.00   7.00   7.00   8.50   8.50   8.50   9.00   9.00
GDT RMS_LOCAL    0.02   0.62   0.90   1.39   1.39   1.77   1.77   2.97   3.17   3.17   3.17   3.17   5.38   4.45   4.45   5.64   5.64   5.64   6.01   6.01
GDT RMS_ALL_CA  11.23  11.98  13.24  13.19  13.19  11.56  11.56   7.25   7.01   7.01   7.01   7.01   6.41   6.55   6.55   6.08   6.08   6.08   6.01   6.01

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378         13.268
LGA    S     379      S     379         11.796
LGA    A     380      A     380         11.771
LGA    R     381      R     381         11.461
LGA    I     382      I     382         10.319
LGA    L     383      L     383          8.537
LGA    M     384      M     384          3.259
LGA    E     385      E     385          2.925
LGA    G     386      G     386          1.995
LGA    W     387      W     387          1.362
LGA    V     388      V     388          3.927
LGA    R     389      R     389          3.070
LGA    V     390      V     390          2.795
LGA    P     391      P     391          1.863
LGA    G     392      G     392          3.963
LGA    D     393      D     393          2.764
LGA    A     394      A     394          3.950
LGA    F     395      F     395          4.539

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  200    4.0     11    2.97     5.125     4.569     0.359

LGA_LOCAL      RMSD =  2.965  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.012  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  6.011  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.678700 * X  +   0.626959 * Y  +   0.382477 * Z  +  92.378716
  Y_new =   0.731018 * X  +   0.626754 * Y  +   0.269801 * Z  +   1.741954
  Z_new =  -0.070565 * X  +   0.462711 * Y  +  -0.883696 * Z  + -64.834862 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.659237   -0.482356  [ DEG:   152.3630    -27.6370 ]
  Theta =   0.070623    3.070969  [ DEG:     4.0464    175.9536 ]
  Phi   =   2.319099   -0.822493  [ DEG:   132.8746    -47.1254 ]
 
# 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_5_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_5_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   2.97   4.569     6.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      74.430  27.190  10.582  1.00  0.00
ATOM   2790  CA  ARG   378      74.002  26.663  11.872  1.00  0.00
ATOM   2791  C   ARG   378      74.530  27.516  13.018  1.00  0.00
ATOM   2792  O   ARG   378      73.862  27.682  14.039  1.00  0.00
ATOM   2793  CB  ARG   378      74.520  25.236  12.065  1.00  0.00
ATOM   2794  CG  ARG   378      73.840  24.203  11.181  1.00  0.00
ATOM   2795  CD  ARG   378      74.459  22.828  11.362  1.00  0.00
ATOM   2796  NE  ARG   378      73.831  21.828  10.501  1.00  0.00
ATOM   2797  CZ  ARG   378      74.254  20.573  10.384  1.00  0.00
ATOM   2798  NH1 ARG   378      73.621  19.733   9.575  1.00  0.00
ATOM   2799  NH2 ARG   378      75.307  20.160  11.075  1.00  0.00
ATOM   2800  N   SER   379      75.732  28.054  12.843  1.00  0.00
ATOM   2801  CA  SER   379      76.344  28.905  13.857  1.00  0.00
ATOM   2802  C   SER   379      75.589  30.218  14.005  1.00  0.00
ATOM   2803  O   SER   379      75.374  30.700  15.117  1.00  0.00
ATOM   2804  CB  SER   379      77.792  29.230  13.481  1.00  0.00
ATOM   2805  OG  SER   379      78.598  28.065  13.500  1.00  0.00
ATOM   2806  N   ALA   380      75.187  30.795  12.878  1.00  0.00
ATOM   2807  CA  ALA   380      74.429  32.040  12.881  1.00  0.00
ATOM   2808  C   ALA   380      73.054  31.845  13.508  1.00  0.00
ATOM   2809  O   ALA   380      72.601  32.669  14.303  1.00  0.00
ATOM   2810  CB  ALA   380      74.231  32.544  11.459  1.00  0.00
ATOM   2811  N   ARG   381      73.930  34.468  14.052  1.00  0.00
ATOM   2812  CA  ARG   381      73.765  34.922  15.428  1.00  0.00
ATOM   2813  C   ARG   381      72.375  35.501  15.655  1.00  0.00
ATOM   2814  O   ARG   381      71.715  35.187  16.645  1.00  0.00
ATOM   2815  CB  ARG   381      74.792  36.006  15.760  1.00  0.00
ATOM   2816  CG  ARG   381      76.220  35.497  15.871  1.00  0.00
ATOM   2817  CD  ARG   381      77.189  36.632  16.157  1.00  0.00
ATOM   2818  NE  ARG   381      78.573  36.166  16.217  1.00  0.00
ATOM   2819  CZ  ARG   381      79.622  36.963  16.397  1.00  0.00
ATOM   2820  NH1 ARG   381      80.844  36.451  16.440  1.00  0.00
ATOM   2821  NH2 ARG   381      79.446  38.270  16.536  1.00  0.00
ATOM   2822  N   ILE   382      71.936  36.350  14.731  1.00  0.00
ATOM   2823  CA  ILE   382      70.575  36.874  14.758  1.00  0.00
ATOM   2824  C   ILE   382      69.550  35.747  14.740  1.00  0.00
ATOM   2825  O   ILE   382      68.563  35.782  15.473  1.00  0.00
ATOM   2826  CB  ILE   382      70.293  37.777  13.543  1.00  0.00
ATOM   2827  CG1 ILE   382      71.122  39.060  13.628  1.00  0.00
ATOM   2828  CG2 ILE   382      68.822  38.157  13.490  1.00  0.00
ATOM   2829  CD1 ILE   382      71.113  39.879  12.355  1.00  0.00
ATOM   2830  N   LEU   383      69.792  34.748  13.898  1.00  0.00
ATOM   2831  CA  LEU   383      68.900  33.599  13.796  1.00  0.00
ATOM   2832  C   LEU   383      68.837  32.832  15.111  1.00  0.00
ATOM   2833  O   LEU   383      67.754  32.514  15.605  1.00  0.00
ATOM   2834  CB  LEU   383      69.385  32.639  12.709  1.00  0.00
ATOM   2835  CG  LEU   383      68.552  31.373  12.501  1.00  0.00
ATOM   2836  CD1 LEU   383      67.135  31.727  12.072  1.00  0.00
ATOM   2837  CD2 LEU   383      69.168  30.493  11.425  1.00  0.00
ATOM   2838  N   MET   384      70.003  32.537  15.674  1.00  0.00
ATOM   2839  CA  MET   384      70.083  31.807  16.934  1.00  0.00
ATOM   2840  C   MET   384      69.527  32.634  18.087  1.00  0.00
ATOM   2841  O   MET   384      69.048  32.088  19.079  1.00  0.00
ATOM   2842  CB  MET   384      71.536  31.457  17.259  1.00  0.00
ATOM   2843  CG  MET   384      72.154  30.435  16.319  1.00  0.00
ATOM   2844  SD  MET   384      71.260  28.869  16.307  1.00  0.00
ATOM   2845  CE  MET   384      71.603  28.272  17.960  1.00  0.00
ATOM   2846  N   GLU   385      69.592  33.953  17.946  1.00  0.00
ATOM   2847  CA  GLU   385      69.154  34.859  19.002  1.00  0.00
ATOM   2848  C   GLU   385      67.638  35.009  19.004  1.00  0.00
ATOM   2849  O   GLU   385      67.035  35.319  20.032  1.00  0.00
ATOM   2850  CB  GLU   385      69.767  36.247  18.806  1.00  0.00
ATOM   2851  CG  GLU   385      71.278  36.286  18.973  1.00  0.00
ATOM   2852  CD  GLU   385      71.853  37.672  18.751  1.00  0.00
ATOM   2853  OE1 GLU   385      71.064  38.611  18.515  1.00  0.00
ATOM   2854  OE2 GLU   385      73.091  37.818  18.812  1.00  0.00
ATOM   2855  N   GLY   386      66.745  34.719  17.884  1.00  0.00
ATOM   2856  CA  GLY   386      66.062  35.955  17.515  1.00  0.00
ATOM   2857  C   GLY   386      66.241  36.261  16.033  1.00  0.00
ATOM   2858  O   GLY   386      66.997  35.585  15.336  1.00  0.00
ATOM   2859  N   TRP   387      65.540  37.285  15.557  1.00  0.00
ATOM   2860  CA  TRP   387      65.604  37.670  14.153  1.00  0.00
ATOM   2861  C   TRP   387      65.334  39.159  13.978  1.00  0.00
ATOM   2862  O   TRP   387      64.596  39.762  14.756  1.00  0.00
ATOM   2863  CB  TRP   387      64.564  36.900  13.337  1.00  0.00
ATOM   2864  CG  TRP   387      63.153  37.155  13.772  1.00  0.00
ATOM   2865  CD1 TRP   387      62.459  36.486  14.738  1.00  0.00
ATOM   2866  CD2 TRP   387      62.262  38.151  13.253  1.00  0.00
ATOM   2867  NE1 TRP   387      61.192  37.003  14.856  1.00  0.00
ATOM   2868  CE2 TRP   387      61.046  38.027  13.954  1.00  0.00
ATOM   2869  CE3 TRP   387      62.373  39.135  12.267  1.00  0.00
ATOM   2870  CZ2 TRP   387      59.950  38.850  13.700  1.00  0.00
ATOM   2871  CZ3 TRP   387      61.285  39.948  12.018  1.00  0.00
ATOM   2872  CH2 TRP   387      60.089  39.804  12.728  1.00  0.00
ATOM   2873  N   VAL   388      65.938  39.748  12.950  1.00  0.00
ATOM   2874  CA  VAL   388      65.716  41.154  12.635  1.00  0.00
ATOM   2875  C   VAL   388      66.107  41.463  11.195  1.00  0.00
ATOM   2876  O   VAL   388      66.591  40.593  10.473  1.00  0.00
ATOM   2877  CB  VAL   388      66.545  42.075  13.549  1.00  0.00
ATOM   2878  CG1 VAL   388      66.109  41.920  14.997  1.00  0.00
ATOM   2879  CG2 VAL   388      68.023  41.730  13.453  1.00  0.00
ATOM   2880  N   ARG   389      65.893  42.710  10.785  1.00  0.00
ATOM   2881  CA  ARG   389      66.287  43.155   9.454  1.00  0.00
ATOM   2882  C   ARG   389      67.140  44.416   9.526  1.00  0.00
ATOM   2883  O   ARG   389      66.849  45.330  10.298  1.00  0.00
ATOM   2884  CB  ARG   389      65.053  43.465   8.605  1.00  0.00
ATOM   2885  CG  ARG   389      64.209  42.247   8.269  1.00  0.00
ATOM   2886  CD  ARG   389      62.987  42.629   7.451  1.00  0.00
ATOM   2887  NE  ARG   389      62.096  41.492   7.231  1.00  0.00
ATOM   2888  CZ  ARG   389      60.942  41.563   6.576  1.00  0.00
ATOM   2889  NH1 ARG   389      60.198  40.476   6.425  1.00  0.00
ATOM   2890  NH2 ARG   389      60.534  42.720   6.074  1.00  0.00
ATOM   2891  N   VAL   390      68.620  44.077   9.702  1.00  0.00
ATOM   2892  CA  VAL   390      69.485  45.217   9.423  1.00  0.00
ATOM   2893  C   VAL   390      69.450  45.587   7.945  1.00  0.00
ATOM   2894  O   VAL   390      69.655  44.738   7.078  1.00  0.00
ATOM   2895  CB  VAL   390      70.950  44.917   9.790  1.00  0.00
ATOM   2896  CG1 VAL   390      71.851  46.065   9.364  1.00  0.00
ATOM   2897  CG2 VAL   390      71.094  44.725  11.292  1.00  0.00
ATOM   2898  N   PRO   391      69.188  46.859   7.665  1.00  0.00
ATOM   2899  CA  PRO   391      69.262  47.375   6.303  1.00  0.00
ATOM   2900  C   PRO   391      70.635  47.125   5.694  1.00  0.00
ATOM   2901  O   PRO   391      71.661  47.426   6.304  1.00  0.00
ATOM   2902  CB  PRO   391      68.985  48.871   6.459  1.00  0.00
ATOM   2903  CG  PRO   391      68.186  48.975   7.714  1.00  0.00
ATOM   2904  CD  PRO   391      68.745  47.940   8.651  1.00  0.00
ATOM   2905  N   GLY   392      70.648  46.571   4.486  1.00  0.00
ATOM   2906  CA  GLY   392      71.896  46.241   3.808  1.00  0.00
ATOM   2907  C   GLY   392      71.865  46.680   2.350  1.00  0.00
ATOM   2908  O   GLY   392      70.795  46.815   1.755  1.00  0.00
ATOM   2909  N   ASP   393      73.044  46.901   1.778  1.00  0.00
ATOM   2910  CA  ASP   393      73.156  47.274   0.373  1.00  0.00
ATOM   2911  C   ASP   393      72.783  46.111  -0.537  1.00  0.00
ATOM   2912  O   ASP   393      72.957  44.947  -0.175  1.00  0.00
ATOM   2913  CB  ASP   393      74.590  47.694   0.043  1.00  0.00
ATOM   2914  CG  ASP   393      74.950  49.045   0.628  1.00  0.00
ATOM   2915  OD1 ASP   393      74.036  49.747   1.111  1.00  0.00
ATOM   2916  OD2 ASP   393      76.146  49.404   0.603  1.00  0.00
ATOM   2917  N   ALA   394      72.270  46.433  -1.720  1.00  0.00
ATOM   2918  CA  ALA   394      72.057  45.434  -2.760  1.00  0.00
ATOM   2919  C   ALA   394      73.042  45.615  -3.908  1.00  0.00
ATOM   2920  O   ALA   394      73.078  46.665  -4.548  1.00  0.00
ATOM   2921  CB  ALA   394      70.648  45.548  -3.323  1.00  0.00
ATOM   2922  N   PHE   395      73.840  44.584  -4.163  1.00  0.00
ATOM   2923  CA  PHE   395      74.901  44.665  -5.159  1.00  0.00
ATOM   2924  C   PHE   395      74.422  44.162  -6.516  1.00  0.00
ATOM   2925  O   PHE   395      73.665  43.195  -6.598  1.00  0.00
ATOM   2926  CB  PHE   395      76.101  43.816  -4.735  1.00  0.00
ATOM   2927  CG  PHE   395      76.791  44.317  -3.498  1.00  0.00
ATOM   2928  CD1 PHE   395      76.565  43.717  -2.272  1.00  0.00
ATOM   2929  CD2 PHE   395      77.664  45.388  -3.562  1.00  0.00
ATOM   2930  CE1 PHE   395      77.201  44.178  -1.134  1.00  0.00
ATOM   2931  CE2 PHE   395      78.300  45.848  -2.424  1.00  0.00
ATOM   2932  CZ  PHE   395      78.071  45.248  -1.214  1.00  0.00
TER
END
