
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   18 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_2_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         4.85     5.27
  LCS_AVERAGE:      8.36

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       388 - 395         1.99     9.52
  LCS_AVERAGE:      3.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       387 - 391         0.87    13.17
  LCS_AVERAGE:      1.81

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      0    4   12     0    0    0    3    3    4    4    5    8    8    8    9   11   11   12   18   18   18   18   18 
LCS_GDT     S     379     S     379      3    4   17     0    3    3    3    3    4    4    5    8    8    8    9   11   13   17   18   18   18   18   18 
LCS_GDT     A     380     A     380      3    4   17     0    3    3    3    4    5    6    6    8   11   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     R     381     R     381      3    5   17     3    3    3    3    5    5    7    8    8   10   12   14   16   16   17   18   18   18   18   18 
LCS_GDT     I     382     I     382      4    5   17     3    4    4    4    5    5    7    8   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     L     383     L     383      4    5   17     3    4    4    4    5    5    7    8   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     M     384     M     384      4    5   17     3    4    4    4    5    6    8    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     E     385     E     385      4    5   17     3    4    4    4    5    5    7    8    8   10   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     G     386     G     386      3    4   17     0    3    3    4    4    5    7    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     W     387     W     387      5    5   17     3    4    6    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     V     388     V     388      5    8   17     3    4    6    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     R     389     R     389      5    8   17     3    4    6    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     V     390     V     390      5    8   17     3    4    6    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     P     391     P     391      5    8   17     3    4    5    5    7    9    9    9   10   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     G     392     G     392      3    8   17     3    3    4    5    7    9    9    9   10   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     D     393     D     393      3    8   17     3    3    6    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     A     394     A     394      3    8   17     3    4    6    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_GDT     F     395     F     395      3    8   17     0    3    5    7    7    9    9    9   11   12   13   14   16   16   17   18   18   18   18   18 
LCS_AVERAGE  LCS_A:   4.41  (   1.81    3.06    8.36 )

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      6      7      7      9      9      9     11     12     13     14     16     16     17     18     18     18     18     18 
GDT PERCENT_CA   1.50   2.00   3.00   3.50   3.50   4.50   4.50   4.50   5.50   6.00   6.50   7.00   8.00   8.00   8.50   9.00   9.00   9.00   9.00   9.00
GDT RMS_LOCAL    0.04   0.52   1.25   1.35   1.35   2.04   2.04   2.04   3.28   3.23   3.61   3.88   4.52   4.52   4.85   5.20   5.20   5.20   5.20   5.20
GDT RMS_ALL_CA  11.43   7.43   6.29   6.28   6.28   8.16   8.16   8.16   5.88   6.63   6.16   6.07   5.42   5.42   5.27   5.20   5.20   5.20   5.20   5.20

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378         17.089
LGA    S     379      S     379         13.113
LGA    A     380      A     380         13.619
LGA    R     381      R     381         14.029
LGA    I     382      I     382         10.180
LGA    L     383      L     383          5.532
LGA    M     384      M     384          6.355
LGA    E     385      E     385          9.471
LGA    G     386      G     386          7.164
LGA    W     387      W     387          1.683
LGA    V     388      V     388          1.793
LGA    R     389      R     389          2.301
LGA    V     390      V     390          1.688
LGA    P     391      P     391          3.163
LGA    G     392      G     392          2.549
LGA    D     393      D     393          1.391
LGA    A     394      A     394          1.199
LGA    F     395      F     395          1.883

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  200    4.0      9    2.04     4.750     4.459     0.420

LGA_LOCAL      RMSD =  2.044  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.163  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  5.199  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.303834 * X  +   0.770133 * Y  +   0.560874 * Z  +  94.459465
  Y_new =   0.657012 * X  +  -0.256955 * Y  +   0.708737 * Z  +  49.843998
  Z_new =   0.689942 * X  +   0.583840 * Y  +  -0.427915 * Z  +  10.963202 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.203284   -0.938309  [ DEG:   126.2389    -53.7611 ]
  Theta =  -0.761408   -2.380184  [ DEG:   -43.6255   -136.3745 ]
  Phi   =   2.003954   -1.137639  [ DEG:   114.8181    -65.1819 ]
 
# 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_2_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_2_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    9   2.04   4.459     5.20
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      79.031  32.215  24.397  1.00  0.00
ATOM   2790  CA  ARG   378      77.965  32.735  23.549  1.00  0.00
ATOM   2791  C   ARG   378      78.124  32.260  22.110  1.00  0.00
ATOM   2792  O   ARG   378      79.197  31.804  21.712  1.00  0.00
ATOM   2793  CB  ARG   378      77.979  34.265  23.547  1.00  0.00
ATOM   2794  CG  ARG   378      77.771  34.888  24.917  1.00  0.00
ATOM   2795  CD  ARG   378      76.347  34.682  25.407  1.00  0.00
ATOM   2796  NE  ARG   378      76.109  35.340  26.691  1.00  0.00
ATOM   2797  CZ  ARG   378      76.319  34.771  27.873  1.00  0.00
ATOM   2798  NH1 ARG   378      76.075  35.447  28.987  1.00  0.00
ATOM   2799  NH2 ARG   378      76.775  33.527  27.938  1.00  0.00
ATOM   2800  N   SER   379      77.052  32.370  21.334  1.00  0.00
ATOM   2801  CA  SER   379      77.085  31.997  19.925  1.00  0.00
ATOM   2802  C   SER   379      76.839  33.204  19.029  1.00  0.00
ATOM   2803  O   SER   379      75.763  33.802  19.058  1.00  0.00
ATOM   2804  CB  SER   379      76.007  30.954  19.621  1.00  0.00
ATOM   2805  OG  SER   379      76.234  29.759  20.348  1.00  0.00
ATOM   2806  N   ALA   380      77.097  34.316  20.796  1.00  0.00
ATOM   2807  CA  ALA   380      76.207  35.347  21.318  1.00  0.00
ATOM   2808  C   ALA   380      75.995  36.459  20.300  1.00  0.00
ATOM   2809  O   ALA   380      74.863  36.856  20.027  1.00  0.00
ATOM   2810  CB  ALA   380      76.794  35.964  22.579  1.00  0.00
ATOM   2811  N   ARG   381      77.091  36.960  19.742  1.00  0.00
ATOM   2812  CA  ARG   381      77.028  38.031  18.754  1.00  0.00
ATOM   2813  C   ARG   381      76.335  37.564  17.480  1.00  0.00
ATOM   2814  O   ARG   381      75.592  38.319  16.854  1.00  0.00
ATOM   2815  CB  ARG   381      78.435  38.502  18.383  1.00  0.00
ATOM   2816  CG  ARG   381      79.140  39.279  19.483  1.00  0.00
ATOM   2817  CD  ARG   381      80.557  39.648  19.077  1.00  0.00
ATOM   2818  NE  ARG   381      81.251  40.391  20.127  1.00  0.00
ATOM   2819  CZ  ARG   381      82.525  40.765  20.060  1.00  0.00
ATOM   2820  NH1 ARG   381      83.071  41.439  21.063  1.00  0.00
ATOM   2821  NH2 ARG   381      83.248  40.464  18.991  1.00  0.00
ATOM   2822  N   ILE   382      76.581  36.314  17.102  1.00  0.00
ATOM   2823  CA  ILE   382      76.050  35.771  15.858  1.00  0.00
ATOM   2824  C   ILE   382      74.533  35.638  15.919  1.00  0.00
ATOM   2825  O   ILE   382      73.840  35.867  14.927  1.00  0.00
ATOM   2826  CB  ILE   382      76.627  34.375  15.560  1.00  0.00
ATOM   2827  CG1 ILE   382      78.122  34.472  15.250  1.00  0.00
ATOM   2828  CG2 ILE   382      75.926  33.755  14.360  1.00  0.00
ATOM   2829  CD1 ILE   382      78.823  33.131  15.204  1.00  0.00
ATOM   2830  N   LEU   383      74.023  35.266  17.088  1.00  0.00
ATOM   2831  CA  LEU   383      72.586  35.121  17.286  1.00  0.00
ATOM   2832  C   LEU   383      71.841  36.378  16.857  1.00  0.00
ATOM   2833  O   LEU   383      70.660  36.326  16.513  1.00  0.00
ATOM   2834  CB  LEU   383      72.272  34.864  18.760  1.00  0.00
ATOM   2835  CG  LEU   383      72.764  33.534  19.336  1.00  0.00
ATOM   2836  CD1 LEU   383      72.502  33.467  20.833  1.00  0.00
ATOM   2837  CD2 LEU   383      72.049  32.365  18.675  1.00  0.00
ATOM   2838  N   MET   384      72.538  37.510  16.881  1.00  0.00
ATOM   2839  CA  MET   384      71.948  38.782  16.481  1.00  0.00
ATOM   2840  C   MET   384      71.352  38.697  15.081  1.00  0.00
ATOM   2841  O   MET   384      70.425  39.434  14.745  1.00  0.00
ATOM   2842  CB  MET   384      73.006  39.887  16.479  1.00  0.00
ATOM   2843  CG  MET   384      72.460  41.270  16.166  1.00  0.00
ATOM   2844  SD  MET   384      71.298  41.858  17.413  1.00  0.00
ATOM   2845  CE  MET   384      72.409  42.212  18.772  1.00  0.00
ATOM   2846  N   GLU   385      72.595  39.090  14.258  1.00  0.00
ATOM   2847  CA  GLU   385      72.498  39.652  12.916  1.00  0.00
ATOM   2848  C   GLU   385      71.475  38.899  12.076  1.00  0.00
ATOM   2849  O   GLU   385      70.738  39.497  11.293  1.00  0.00
ATOM   2850  CB  GLU   385      73.849  39.572  12.204  1.00  0.00
ATOM   2851  CG  GLU   385      73.857  40.194  10.816  1.00  0.00
ATOM   2852  CD  GLU   385      75.225  40.147  10.164  1.00  0.00
ATOM   2853  OE1 GLU   385      76.172  39.645  10.806  1.00  0.00
ATOM   2854  OE2 GLU   385      75.350  40.613   9.012  1.00  0.00
ATOM   2855  N   GLY   386      71.435  37.581  12.242  1.00  0.00
ATOM   2856  CA  GLY   386      70.498  36.743  11.503  1.00  0.00
ATOM   2857  C   GLY   386      69.057  37.123  11.814  1.00  0.00
ATOM   2858  O   GLY   386      68.233  37.265  10.910  1.00  0.00
ATOM   2859  N   TRP   387      68.756  37.285  13.098  1.00  0.00
ATOM   2860  CA  TRP   387      67.410  37.637  13.531  1.00  0.00
ATOM   2861  C   TRP   387      67.064  39.069  13.146  1.00  0.00
ATOM   2862  O   TRP   387      65.964  39.345  12.669  1.00  0.00
ATOM   2863  CB  TRP   387      67.285  37.511  15.051  1.00  0.00
ATOM   2864  CG  TRP   387      67.399  36.103  15.547  1.00  0.00
ATOM   2865  CD1 TRP   387      67.477  34.970  14.789  1.00  0.00
ATOM   2866  CD2 TRP   387      67.450  35.675  16.914  1.00  0.00
ATOM   2867  NE1 TRP   387      67.572  33.863  15.597  1.00  0.00
ATOM   2868  CE2 TRP   387      67.557  34.270  16.908  1.00  0.00
ATOM   2869  CE3 TRP   387      67.415  36.342  18.142  1.00  0.00
ATOM   2870  CZ2 TRP   387      67.631  33.521  18.081  1.00  0.00
ATOM   2871  CZ3 TRP   387      67.487  35.596  19.303  1.00  0.00
ATOM   2872  CH2 TRP   387      67.594  34.202  19.268  1.00  0.00
ATOM   2873  N   VAL   388      68.072  39.534  11.906  1.00  0.00
ATOM   2874  CA  VAL   388      68.053  40.991  11.881  1.00  0.00
ATOM   2875  C   VAL   388      68.164  41.519  10.456  1.00  0.00
ATOM   2876  O   VAL   388      68.917  40.985   9.643  1.00  0.00
ATOM   2877  CB  VAL   388      69.222  41.585  12.688  1.00  0.00
ATOM   2878  CG1 VAL   388      69.281  43.094  12.508  1.00  0.00
ATOM   2879  CG2 VAL   388      69.054  41.284  14.169  1.00  0.00
ATOM   2880  N   ARG   389      67.410  42.572  10.160  1.00  0.00
ATOM   2881  CA  ARG   389      67.433  43.183   8.836  1.00  0.00
ATOM   2882  C   ARG   389      68.233  44.480   8.842  1.00  0.00
ATOM   2883  O   ARG   389      67.900  45.422   9.561  1.00  0.00
ATOM   2884  CB  ARG   389      66.012  43.505   8.369  1.00  0.00
ATOM   2885  CG  ARG   389      65.930  44.019   6.942  1.00  0.00
ATOM   2886  CD  ARG   389      64.489  44.272   6.528  1.00  0.00
ATOM   2887  NE  ARG   389      64.385  44.682   5.129  1.00  0.00
ATOM   2888  CZ  ARG   389      63.283  45.181   4.577  1.00  0.00
ATOM   2889  NH1 ARG   389      63.282  45.527   3.297  1.00  0.00
ATOM   2890  NH2 ARG   389      62.186  45.333   5.307  1.00  0.00
ATOM   2891  N   VAL   390      69.288  44.521   8.037  1.00  0.00
ATOM   2892  CA  VAL   390      70.154  45.693   7.968  1.00  0.00
ATOM   2893  C   VAL   390      69.938  46.462   6.671  1.00  0.00
ATOM   2894  O   VAL   390      69.873  45.872   5.592  1.00  0.00
ATOM   2895  CB  VAL   390      71.642  45.299   8.032  1.00  0.00
ATOM   2896  CG1 VAL   390      72.521  46.540   8.032  1.00  0.00
ATOM   2897  CG2 VAL   390      71.929  44.507   9.298  1.00  0.00
ATOM   2898  N   PRO   391      71.214  44.122   5.142  1.00  0.00
ATOM   2899  CA  PRO   391      72.341  44.949   4.729  1.00  0.00
ATOM   2900  C   PRO   391      71.987  45.799   3.515  1.00  0.00
ATOM   2901  O   PRO   391      72.379  46.963   3.425  1.00  0.00
ATOM   2902  CB  PRO   391      73.441  43.938   4.400  1.00  0.00
ATOM   2903  CG  PRO   391      72.710  42.750   3.869  1.00  0.00
ATOM   2904  CD  PRO   391      71.485  42.599   4.726  1.00  0.00
ATOM   2905  N   GLY   392      70.983  48.478   4.328  1.00  0.00
ATOM   2906  CA  GLY   392      69.799  47.638   4.187  1.00  0.00
ATOM   2907  C   GLY   392      69.573  47.245   2.732  1.00  0.00
ATOM   2908  O   GLY   392      69.265  46.092   2.431  1.00  0.00
ATOM   2909  N   ASP   393      69.726  48.212   1.833  1.00  0.00
ATOM   2910  CA  ASP   393      69.549  47.966   0.406  1.00  0.00
ATOM   2911  C   ASP   393      70.541  46.926  -0.100  1.00  0.00
ATOM   2912  O   ASP   393      70.174  46.011  -0.837  1.00  0.00
ATOM   2913  CB  ASP   393      69.765  49.255  -0.390  1.00  0.00
ATOM   2914  CG  ASP   393      68.625  50.241  -0.222  1.00  0.00
ATOM   2915  OD1 ASP   393      67.568  49.841   0.310  1.00  0.00
ATOM   2916  OD2 ASP   393      68.790  51.412  -0.622  1.00  0.00
ATOM   2917  N   ALA   394      71.799  47.072   0.299  1.00  0.00
ATOM   2918  CA  ALA   394      72.848  46.147  -0.117  1.00  0.00
ATOM   2919  C   ALA   394      72.567  44.736   0.381  1.00  0.00
ATOM   2920  O   ALA   394      72.809  43.758  -0.327  1.00  0.00
ATOM   2921  CB  ALA   394      74.193  46.586   0.441  1.00  0.00
ATOM   2922  N   PHE   395      72.950  44.550  -2.429  1.00  0.00
ATOM   2923  CA  PHE   395      73.902  43.536  -2.866  1.00  0.00
ATOM   2924  C   PHE   395      75.268  44.147  -3.145  1.00  0.00
ATOM   2925  O   PHE   395      75.369  45.216  -3.749  1.00  0.00
ATOM   2926  CB  PHE   395      73.414  42.860  -4.149  1.00  0.00
ATOM   2927  CG  PHE   395      72.157  42.058  -3.971  1.00  0.00
ATOM   2928  CD1 PHE   395      70.926  42.587  -4.318  1.00  0.00
ATOM   2929  CD2 PHE   395      72.205  40.774  -3.456  1.00  0.00
ATOM   2930  CE1 PHE   395      69.769  41.849  -4.155  1.00  0.00
ATOM   2931  CE2 PHE   395      71.048  40.036  -3.292  1.00  0.00
ATOM   2932  CZ  PHE   395      69.833  40.569  -3.640  1.00  0.00
TER
END
