
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   18 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_1_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       378 - 394         4.82     5.40
  LONGEST_CONTINUOUS_SEGMENT:    17       379 - 395         4.97     5.46
  LCS_AVERAGE:      8.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       384 - 390         1.94    10.90
  LONGEST_CONTINUOUS_SEGMENT:     7       388 - 394         1.42     6.10
  LCS_AVERAGE:      3.25

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       388 - 393         0.68     6.75
  LCS_AVERAGE:      2.11

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    6   17     0    2    3    5    5    6    7    8    8   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     S     379     S     379      3    6   17     3    3    3    5    5    6    7    8    8   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     A     380     A     380      3    6   17     3    3    3    5    5    7   10   10   12   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     R     381     R     381      3    6   17     3    3    3    5    5    6   10   10   12   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     I     382     I     382      3    6   17     1    3    3    4    5    6    9   11   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     L     383     L     383      3    6   17     1    3    3    5    5    6   10   11   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     M     384     M     384      4    7   17     4    4    6    7    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     E     385     E     385      4    7   17     4    4    6    7    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     G     386     G     386      4    7   17     4    4    6    7    9   10   11   12   14   14   14   15   15   15   15   16   17   18   18   18 
LCS_GDT     W     387     W     387      4    7   17     4    4    6    7    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     V     388     V     388      6    7   17     4    6    6    6    7    8   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     R     389     R     389      6    7   17     4    6    6    7    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     V     390     V     390      6    7   17     4    6    6    7    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     P     391     P     391      6    7   17     4    6    6    6    8   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     G     392     G     392      6    7   17     3    6    6    7    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     D     393     D     393      6    7   17     3    6    6    6    9   10   11   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     A     394     A     394      3    7   17     3    3    4    6    8   10   10   12   14   14   14   15   15   16   16   16   17   18   18   18 
LCS_GDT     F     395     F     395      3    4   17     3    3    6    7    9   10   11   12   14   14   14   15   15   15   15   16   17   18   18   18 
LCS_AVERAGE  LCS_A:   4.62  (   2.11    3.25    8.50 )

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      6      6      7      9     10     11     12     14     14     14     15     15     16     16     16     17     18     18     18 
GDT PERCENT_CA   2.00   3.00   3.00   3.50   4.50   5.00   5.50   6.00   7.00   7.00   7.00   7.50   7.50   8.00   8.00   8.00   8.50   9.00   9.00   9.00
GDT RMS_LOCAL    0.22   0.68   0.68   1.28   1.88   2.03   2.34   2.61   3.30   3.30   3.30   3.61   3.61   4.44   4.44   4.44   4.82   5.25   5.25   5.25
GDT RMS_ALL_CA  10.72   6.75   6.75  10.12  10.10  10.01   9.70   9.54   8.20   8.20   8.20   7.57   7.57   5.40   5.40   5.40   5.40   5.25   5.25   5.25

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378         23.109
LGA    S     379      S     379         19.372
LGA    A     380      A     380         14.395
LGA    R     381      R     381          8.531
LGA    I     382      I     382          6.227
LGA    L     383      L     383          5.719
LGA    M     384      M     384          2.027
LGA    E     385      E     385          2.976
LGA    G     386      G     386          2.672
LGA    W     387      W     387          2.249
LGA    V     388      V     388          3.889
LGA    R     389      R     389          2.756
LGA    V     390      V     390          2.121
LGA    P     391      P     391          2.859
LGA    G     392      G     392          2.280
LGA    D     393      D     393          1.621
LGA    A     394      A     394          3.019
LGA    F     395      F     395          3.822

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  200    4.0     12    2.61     5.125     4.922     0.442

LGA_LOCAL      RMSD =  2.612  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.670  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  5.247  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.606119 * X  +  -0.737485 * Y  +  -0.297885 * Z  +  45.170509
  Y_new =   0.697926 * X  +   0.672774 * Y  +  -0.245511 * Z  +  42.870888
  Z_new =   0.381470 * X  +  -0.059093 * Y  +   0.922491 * Z  +   4.902682 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.063970    3.077622  [ DEG:    -3.6652    176.3348 ]
  Theta =  -0.391386   -2.750207  [ DEG:   -22.4247   -157.5753 ]
  Phi   =   0.855683   -2.285909  [ DEG:    49.0270   -130.9730 ]
 
# 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_1_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_1_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   12   2.61   4.922     5.25
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      59.081  27.459  26.524  1.00  0.00
ATOM   2790  CA  ARG   378      60.014  27.143  25.447  1.00  0.00
ATOM   2791  C   ARG   378      59.712  27.961  24.199  1.00  0.00
ATOM   2792  O   ARG   378      58.551  28.214  23.876  1.00  0.00
ATOM   2793  CB  ARG   378      59.922  25.662  25.076  1.00  0.00
ATOM   2794  CG  ARG   378      60.394  24.718  26.171  1.00  0.00
ATOM   2795  CD  ARG   378      60.292  23.266  25.730  1.00  0.00
ATOM   2796  NE  ARG   378      60.744  22.346  26.770  1.00  0.00
ATOM   2797  CZ  ARG   378      60.703  21.021  26.665  1.00  0.00
ATOM   2798  NH1 ARG   378      61.136  20.263  27.663  1.00  0.00
ATOM   2799  NH2 ARG   378      60.229  20.458  25.562  1.00  0.00
ATOM   2800  N   SER   379      60.764  28.374  23.499  1.00  0.00
ATOM   2801  CA  SER   379      60.615  29.198  22.307  1.00  0.00
ATOM   2802  C   SER   379      61.803  29.030  21.369  1.00  0.00
ATOM   2803  O   SER   379      62.816  28.433  21.734  1.00  0.00
ATOM   2804  CB  SER   379      60.517  30.678  22.687  1.00  0.00
ATOM   2805  OG  SER   379      60.182  31.472  21.563  1.00  0.00
ATOM   2806  N   ALA   380      63.454  28.759  23.866  1.00  0.00
ATOM   2807  CA  ALA   380      63.981  30.095  23.622  1.00  0.00
ATOM   2808  C   ALA   380      65.488  30.060  23.397  1.00  0.00
ATOM   2809  O   ALA   380      66.199  29.262  24.008  1.00  0.00
ATOM   2810  CB  ALA   380      63.701  31.001  24.811  1.00  0.00
ATOM   2811  N   ARG   381      65.970  30.932  22.518  1.00  0.00
ATOM   2812  CA  ARG   381      67.400  31.041  22.253  1.00  0.00
ATOM   2813  C   ARG   381      67.667  31.882  21.011  1.00  0.00
ATOM   2814  O   ARG   381      68.650  32.620  20.949  1.00  0.00
ATOM   2815  CB  ARG   381      68.011  29.657  22.029  1.00  0.00
ATOM   2816  CG  ARG   381      67.524  28.959  20.769  1.00  0.00
ATOM   2817  CD  ARG   381      68.125  27.569  20.640  1.00  0.00
ATOM   2818  NE  ARG   381      67.688  26.895  19.420  1.00  0.00
ATOM   2819  CZ  ARG   381      68.022  25.652  19.092  1.00  0.00
ATOM   2820  NH1 ARG   381      67.577  25.120  17.962  1.00  0.00
ATOM   2821  NH2 ARG   381      68.801  24.941  19.896  1.00  0.00
ATOM   2822  N   ILE   382      66.786  31.766  20.023  1.00  0.00
ATOM   2823  CA  ILE   382      66.940  32.495  18.770  1.00  0.00
ATOM   2824  C   ILE   382      67.027  33.996  19.012  1.00  0.00
ATOM   2825  O   ILE   382      67.160  34.779  18.072  1.00  0.00
ATOM   2826  CB  ILE   382      65.751  32.247  17.823  1.00  0.00
ATOM   2827  CG1 ILE   382      65.656  30.763  17.464  1.00  0.00
ATOM   2828  CG2 ILE   382      65.918  33.044  16.538  1.00  0.00
ATOM   2829  CD1 ILE   382      64.398  30.397  16.707  1.00  0.00
ATOM   2830  N   LEU   383      68.027  34.601  20.141  1.00  0.00
ATOM   2831  CA  LEU   383      69.207  35.400  19.836  1.00  0.00
ATOM   2832  C   LEU   383      70.138  34.667  18.878  1.00  0.00
ATOM   2833  O   LEU   383      70.806  35.287  18.051  1.00  0.00
ATOM   2834  CB  LEU   383      69.990  35.709  21.114  1.00  0.00
ATOM   2835  CG  LEU   383      69.317  36.656  22.109  1.00  0.00
ATOM   2836  CD1 LEU   383      70.122  36.743  23.397  1.00  0.00
ATOM   2837  CD2 LEU   383      69.203  38.056  21.526  1.00  0.00
ATOM   2838  N   MET   384      70.175  33.344  18.996  1.00  0.00
ATOM   2839  CA  MET   384      71.001  32.521  18.120  1.00  0.00
ATOM   2840  C   MET   384      70.484  32.551  16.687  1.00  0.00
ATOM   2841  O   MET   384      71.246  32.780  15.747  1.00  0.00
ATOM   2842  CB  MET   384      71.000  31.066  18.594  1.00  0.00
ATOM   2843  CG  MET   384      71.738  30.841  19.904  1.00  0.00
ATOM   2844  SD  MET   384      71.623  29.136  20.481  1.00  0.00
ATOM   2845  CE  MET   384      72.664  28.302  19.286  1.00  0.00
ATOM   2846  N   GLU   385      69.187  32.318  16.527  1.00  0.00
ATOM   2847  CA  GLU   385      68.560  32.347  15.210  1.00  0.00
ATOM   2848  C   GLU   385      68.656  33.732  14.583  1.00  0.00
ATOM   2849  O   GLU   385      68.808  33.866  13.369  1.00  0.00
ATOM   2850  CB  GLU   385      67.079  31.975  15.313  1.00  0.00
ATOM   2851  CG  GLU   385      66.359  31.921  13.976  1.00  0.00
ATOM   2852  CD  GLU   385      64.924  31.452  14.107  1.00  0.00
ATOM   2853  OE1 GLU   385      64.156  32.089  14.858  1.00  0.00
ATOM   2854  OE2 GLU   385      64.566  30.446  13.458  1.00  0.00
ATOM   2855  N   GLY   386      67.431  34.693  14.944  1.00  0.00
ATOM   2856  CA  GLY   386      66.724  35.581  14.029  1.00  0.00
ATOM   2857  C   GLY   386      67.528  36.846  13.759  1.00  0.00
ATOM   2858  O   GLY   386      68.210  37.362  14.645  1.00  0.00
ATOM   2859  N   TRP   387      67.445  37.343  12.529  1.00  0.00
ATOM   2860  CA  TRP   387      68.027  38.634  12.183  1.00  0.00
ATOM   2861  C   TRP   387      67.283  39.775  12.866  1.00  0.00
ATOM   2862  O   TRP   387      66.082  39.954  12.663  1.00  0.00
ATOM   2863  CB  TRP   387      67.963  38.863  10.673  1.00  0.00
ATOM   2864  CG  TRP   387      68.896  37.990   9.892  1.00  0.00
ATOM   2865  CD1 TRP   387      68.574  36.857   9.202  1.00  0.00
ATOM   2866  CD2 TRP   387      70.307  38.176   9.723  1.00  0.00
ATOM   2867  NE1 TRP   387      69.696  36.325   8.613  1.00  0.00
ATOM   2868  CE2 TRP   387      70.774  37.118   8.918  1.00  0.00
ATOM   2869  CE3 TRP   387      71.221  39.133  10.173  1.00  0.00
ATOM   2870  CZ2 TRP   387      72.113  36.991   8.554  1.00  0.00
ATOM   2871  CZ3 TRP   387      72.547  39.003   9.810  1.00  0.00
ATOM   2872  CH2 TRP   387      72.984  37.942   9.009  1.00  0.00
ATOM   2873  N   VAL   388      68.003  40.544  13.676  1.00  0.00
ATOM   2874  CA  VAL   388      67.389  41.587  14.488  1.00  0.00
ATOM   2875  C   VAL   388      67.577  42.959  13.856  1.00  0.00
ATOM   2876  O   VAL   388      66.670  43.792  13.876  1.00  0.00
ATOM   2877  CB  VAL   388      68.004  41.639  15.899  1.00  0.00
ATOM   2878  CG1 VAL   388      67.442  42.816  16.682  1.00  0.00
ATOM   2879  CG2 VAL   388      67.693  40.361  16.663  1.00  0.00
ATOM   2880  N   ARG   389      68.759  43.191  13.295  1.00  0.00
ATOM   2881  CA  ARG   389      69.070  44.467  12.661  1.00  0.00
ATOM   2882  C   ARG   389      70.161  44.308  11.611  1.00  0.00
ATOM   2883  O   ARG   389      70.955  43.368  11.662  1.00  0.00
ATOM   2884  CB  ARG   389      69.555  45.478  13.702  1.00  0.00
ATOM   2885  CG  ARG   389      70.812  45.051  14.442  1.00  0.00
ATOM   2886  CD  ARG   389      71.223  46.088  15.475  1.00  0.00
ATOM   2887  NE  ARG   389      71.694  47.323  14.852  1.00  0.00
ATOM   2888  CZ  ARG   389      71.979  48.435  15.522  1.00  0.00
ATOM   2889  NH1 ARG   389      72.401  49.511  14.871  1.00  0.00
ATOM   2890  NH2 ARG   389      71.841  48.470  16.840  1.00  0.00
ATOM   2891  N   VAL   390      69.545  44.189  10.113  1.00  0.00
ATOM   2892  CA  VAL   390      70.257  43.594   8.988  1.00  0.00
ATOM   2893  C   VAL   390      70.601  44.643   7.937  1.00  0.00
ATOM   2894  O   VAL   390      70.004  45.719   7.902  1.00  0.00
ATOM   2895  CB  VAL   390      69.414  42.505   8.299  1.00  0.00
ATOM   2896  CG1 VAL   390      69.101  41.378   9.272  1.00  0.00
ATOM   2897  CG2 VAL   390      68.101  43.086   7.797  1.00  0.00
ATOM   2898  N   PRO   391      71.566  44.322   7.083  1.00  0.00
ATOM   2899  CA  PRO   391      71.988  45.233   6.026  1.00  0.00
ATOM   2900  C   PRO   391      70.811  45.647   5.152  1.00  0.00
ATOM   2901  O   PRO   391      69.979  44.819   4.782  1.00  0.00
ATOM   2902  CB  PRO   391      73.017  44.426   5.231  1.00  0.00
ATOM   2903  CG  PRO   391      73.539  43.424   6.205  1.00  0.00
ATOM   2904  CD  PRO   391      72.369  43.022   7.058  1.00  0.00
ATOM   2905  N   GLY   392      70.745  46.934   4.828  1.00  0.00
ATOM   2906  CA  GLY   392      69.667  47.461   4.000  1.00  0.00
ATOM   2907  C   GLY   392      70.108  47.611   2.550  1.00  0.00
ATOM   2908  O   GLY   392      71.294  47.503   2.238  1.00  0.00
ATOM   2909  N   ASP   393      70.686  48.140   0.168  1.00  0.00
ATOM   2910  CA  ASP   393      69.649  47.125   0.039  1.00  0.00
ATOM   2911  C   ASP   393      70.217  45.825  -0.517  1.00  0.00
ATOM   2912  O   ASP   393      69.506  44.827  -0.641  1.00  0.00
ATOM   2913  CB  ASP   393      68.545  47.604  -0.908  1.00  0.00
ATOM   2914  CG  ASP   393      69.033  47.771  -2.333  1.00  0.00
ATOM   2915  OD1 ASP   393      70.198  47.415  -2.609  1.00  0.00
ATOM   2916  OD2 ASP   393      68.250  48.259  -3.176  1.00  0.00
ATOM   2917  N   ALA   394      71.503  45.843  -0.853  1.00  0.00
ATOM   2918  CA  ALA   394      72.166  44.669  -1.408  1.00  0.00
ATOM   2919  C   ALA   394      73.320  44.218  -0.523  1.00  0.00
ATOM   2920  O   ALA   394      73.430  43.040  -0.183  1.00  0.00
ATOM   2921  CB  ALA   394      72.723  44.979  -2.790  1.00  0.00
ATOM   2922  N   PHE   395      74.179  45.162  -0.153  1.00  0.00
ATOM   2923  CA  PHE   395      75.373  44.849   0.623  1.00  0.00
ATOM   2924  C   PHE   395      75.176  45.182   2.097  1.00  0.00
ATOM   2925  O   PHE   395      74.914  46.331   2.454  1.00  0.00
ATOM   2926  CB  PHE   395      76.570  45.652   0.112  1.00  0.00
ATOM   2927  CG  PHE   395      76.993  45.287  -1.283  1.00  0.00
ATOM   2928  CD1 PHE   395      76.641  46.083  -2.359  1.00  0.00
ATOM   2929  CD2 PHE   395      77.743  44.148  -1.519  1.00  0.00
ATOM   2930  CE1 PHE   395      77.030  45.747  -3.642  1.00  0.00
ATOM   2931  CE2 PHE   395      78.132  43.812  -2.802  1.00  0.00
ATOM   2932  CZ  PHE   395      77.779  44.606  -3.861  1.00  0.00
TER
END
