
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   18 , name T0301_D1.pdb
# PARAMETERS: T0301TS193_4_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       381 - 394         4.97     8.36
  LONGEST_CONTINUOUS_SEGMENT:    14       382 - 395         4.91     8.92
  LCS_AVERAGE:      6.67

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       389 - 395         1.25    13.13
  LCS_AVERAGE:      2.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       389 - 394         0.92    12.50
  LONGEST_CONTINUOUS_SEGMENT:     6       390 - 395         0.72    15.09
  LCS_AVERAGE:      2.08

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    8     0    3    4    5    5    5    5    5    6    6    6    6    7    8    9    9   10   10   11   11 
LCS_GDT     S     379     S     379      3    5    9     0    3    4    5    5    5    5    5    6    6    6    6    7    8    9    9   10   10   11   11 
LCS_GDT     A     380     A     380      3    5   13     0    3    4    5    5    5    5    5    6    7    8    8    9   11   12   12   13   15   15   16 
LCS_GDT     R     381     R     381      3    5   14     3    3    4    5    5    5    7    8    8   10   11   11   12   13   14   15   15   15   15   16 
LCS_GDT     I     382     I     382      3    5   14     3    3    3    5    5    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     L     383     L     383      3    4   14     3    3    3    4    4    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     M     384     M     384      3    4   14     3    3    3    4    4    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     E     385     E     385      3    4   14     3    3    3    4    4    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     G     386     G     386      3    5   14     1    3    3    4    5    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     W     387     W     387      3    5   14     3    3    3    4    5    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     V     388     V     388      3    6   14     3    3    3    4    5    6    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     R     389     R     389      6    7   14     3    3    6    6    7    7    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     V     390     V     390      6    7   14     5    5    6    6    7    7    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     P     391     P     391      6    7   14     5    5    6    6    7    7    7    8    9   10   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     G     392     G     392      6    7   14     5    5    6    6    7    7    7    8    8    9   11   12   13   14   14   15   15   15   15   16 
LCS_GDT     D     393     D     393      6    7   14     5    5    6    6    7    7    7    8    8    9   10   12   13   14   14   15   15   15   15   16 
LCS_GDT     A     394     A     394      6    7   14     5    5    6    6    7    7    7    7    8    9   10   12   13   14   14   15   15   15   15   16 
LCS_GDT     F     395     F     395      6    7   14     3    3    6    6    7    7    7    7    8    9   10   12   13   14   14   15   15   15   15   16 
LCS_AVERAGE  LCS_A:   3.86  (   2.08    2.83    6.67 )

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      5      5      6      6      7      7      7      8      9     10     11     12     13     14     14     15     15     15     15     16 
GDT PERCENT_CA   2.50   2.50   3.00   3.00   3.50   3.50   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.00   7.50   7.50   7.50   7.50   8.00
GDT RMS_LOCAL    0.08   0.08   0.72   0.72   1.25   1.25   1.25   2.79   3.35   3.56   3.79   4.54   4.72   4.91   4.91   5.20   5.20   5.20   5.20   5.74
GDT RMS_ALL_CA  14.16  14.16  15.09  15.09  13.13  13.13  13.13  15.83   9.17   9.47   9.23   9.66   9.18   8.92   8.92   8.54   8.54   8.54   8.54   8.30

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378         36.824
LGA    S     379      S     379         30.481
LGA    A     380      A     380         26.948
LGA    R     381      R     381         23.031
LGA    I     382      I     382         17.195
LGA    L     383      L     383         15.184
LGA    M     384      M     384         11.614
LGA    E     385      E     385          7.732
LGA    G     386      G     386          2.846
LGA    W     387      W     387          2.900
LGA    V     388      V     388          3.155
LGA    R     389      R     389          2.393
LGA    V     390      V     390          1.732
LGA    P     391      P     391          2.881
LGA    G     392      G     392          2.045
LGA    D     393      D     393          3.796
LGA    A     394      A     394          8.100
LGA    F     395      F     395         10.903

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18  200    4.0      8    2.79     4.250     3.925     0.277

LGA_LOCAL      RMSD =  2.786  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.828  Number of atoms =   18 
Std_ALL_ATOMS  RMSD =  7.954  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.102144 * X  +   0.428975 * Y  +   0.897523 * Z  +  59.868893
  Y_new =  -0.162246 * X  +   0.897345 * Y  +  -0.410425 * Z  +  67.540024
  Z_new =  -0.981449 * X  +  -0.103697 * Y  +   0.161258 * Z  + -16.859373 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.571476    2.570117  [ DEG:   -32.7432    147.2568 ]
  Theta =   1.377880    1.763712  [ DEG:    78.9467    101.0533 ]
  Phi   =  -1.008924    2.132669  [ DEG:   -57.8071    122.1929 ]
 
# 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_4_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS193_4_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    8   2.79   3.925     7.95
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS193_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM   2789  N   ARG   378      60.515  47.823   9.963  1.00  0.00
ATOM   2790  CA  ARG   378      59.906  46.810  10.815  1.00  0.00
ATOM   2791  C   ARG   378      60.957  45.871  11.394  1.00  0.00
ATOM   2792  O   ARG   378      61.996  45.633  10.778  1.00  0.00
ATOM   2793  CB  ARG   378      58.907  45.969  10.018  1.00  0.00
ATOM   2794  CG  ARG   378      59.548  45.063   8.980  1.00  0.00
ATOM   2795  CD  ARG   378      58.507  44.209   8.274  1.00  0.00
ATOM   2796  NE  ARG   378      59.115  43.268   7.337  1.00  0.00
ATOM   2797  CZ  ARG   378      59.621  42.089   7.684  1.00  0.00
ATOM   2798  NH1 ARG   378      60.154  41.299   6.761  1.00  0.00
ATOM   2799  NH2 ARG   378      59.593  41.704   8.952  1.00  0.00
ATOM   2800  N   SER   379      60.680  45.341  12.580  1.00  0.00
ATOM   2801  CA  SER   379      61.525  44.313  13.176  1.00  0.00
ATOM   2802  C   SER   379      61.321  42.967  12.491  1.00  0.00
ATOM   2803  O   SER   379      60.252  42.693  11.947  1.00  0.00
ATOM   2804  CB  SER   379      61.198  44.144  14.660  1.00  0.00
ATOM   2805  OG  SER   379      61.443  45.342  15.376  1.00  0.00
ATOM   2806  N   ALA   380      58.097  42.380  12.511  1.00  0.00
ATOM   2807  CA  ALA   380      58.321  42.594  13.935  1.00  0.00
ATOM   2808  C   ALA   380      59.236  41.523  14.516  1.00  0.00
ATOM   2809  O   ALA   380      59.971  41.772  15.472  1.00  0.00
ATOM   2810  CB  ALA   380      57.002  42.551  14.691  1.00  0.00
ATOM   2811  N   ARG   381      57.942  42.425  16.192  1.00  0.00
ATOM   2812  CA  ARG   381      58.260  42.243  17.602  1.00  0.00
ATOM   2813  C   ARG   381      58.415  40.767  17.946  1.00  0.00
ATOM   2814  O   ARG   381      59.249  40.395  18.771  1.00  0.00
ATOM   2815  CB  ARG   381      57.150  42.821  18.481  1.00  0.00
ATOM   2816  CG  ARG   381      57.082  44.339  18.478  1.00  0.00
ATOM   2817  CD  ARG   381      55.914  44.842  19.310  1.00  0.00
ATOM   2818  NE  ARG   381      55.818  46.299  19.295  1.00  0.00
ATOM   2819  CZ  ARG   381      54.845  46.990  19.881  1.00  0.00
ATOM   2820  NH1 ARG   381      54.840  48.315  19.815  1.00  0.00
ATOM   2821  NH2 ARG   381      53.881  46.356  20.533  1.00  0.00
ATOM   2822  N   ILE   382      57.605  39.928  17.308  1.00  0.00
ATOM   2823  CA  ILE   382      57.644  38.491  17.552  1.00  0.00
ATOM   2824  C   ILE   382      58.873  37.857  16.912  1.00  0.00
ATOM   2825  O   ILE   382      59.365  36.828  17.375  1.00  0.00
ATOM   2826  CB  ILE   382      56.404  37.786  16.972  1.00  0.00
ATOM   2827  CG1 ILE   382      55.148  38.192  17.747  1.00  0.00
ATOM   2828  CG2 ILE   382      56.559  36.275  17.062  1.00  0.00
ATOM   2829  CD1 ILE   382      53.858  37.757  17.089  1.00  0.00
ATOM   2830  N   LEU   383      59.367  38.479  15.846  1.00  0.00
ATOM   2831  CA  LEU   383      60.533  37.970  15.136  1.00  0.00
ATOM   2832  C   LEU   383      61.820  38.572  15.686  1.00  0.00
ATOM   2833  O   LEU   383      62.914  38.264  15.211  1.00  0.00
ATOM   2834  CB  LEU   383      60.447  38.315  13.647  1.00  0.00
ATOM   2835  CG  LEU   383      59.217  37.795  12.901  1.00  0.00
ATOM   2836  CD1 LEU   383      59.240  38.243  11.448  1.00  0.00
ATOM   2837  CD2 LEU   383      59.173  36.275  12.930  1.00  0.00
ATOM   2838  N   MET   384      62.386  40.413  14.804  1.00  0.00
ATOM   2839  CA  MET   384      63.170  40.489  13.577  1.00  0.00
ATOM   2840  C   MET   384      64.653  40.285  13.857  1.00  0.00
ATOM   2841  O   MET   384      65.336  39.558  13.137  1.00  0.00
ATOM   2842  CB  MET   384      62.996  41.858  12.915  1.00  0.00
ATOM   2843  CG  MET   384      63.762  42.017  11.611  1.00  0.00
ATOM   2844  SD  MET   384      63.542  43.647  10.872  1.00  0.00
ATOM   2845  CE  MET   384      64.530  44.656  11.973  1.00  0.00
ATOM   2846  N   GLU   385      65.146  40.930  14.909  1.00  0.00
ATOM   2847  CA  GLU   385      66.547  40.809  15.295  1.00  0.00
ATOM   2848  C   GLU   385      66.857  39.409  15.808  1.00  0.00
ATOM   2849  O   GLU   385      67.933  38.867  15.551  1.00  0.00
ATOM   2850  CB  GLU   385      66.885  41.806  16.406  1.00  0.00
ATOM   2851  CG  GLU   385      66.712  43.262  16.005  1.00  0.00
ATOM   2852  CD  GLU   385      66.922  44.214  17.166  1.00  0.00
ATOM   2853  OE1 GLU   385      67.179  43.733  18.290  1.00  0.00
ATOM   2854  OE2 GLU   385      66.830  45.441  16.951  1.00  0.00
ATOM   2855  N   GLY   386      67.449  36.814  14.767  1.00  0.00
ATOM   2856  CA  GLY   386      66.426  37.285  13.843  1.00  0.00
ATOM   2857  C   GLY   386      67.019  37.594  12.474  1.00  0.00
ATOM   2858  O   GLY   386      68.216  37.415  12.251  1.00  0.00
ATOM   2859  N   TRP   387      66.174  38.059  11.559  1.00  0.00
ATOM   2860  CA  TRP   387      66.564  38.207  10.162  1.00  0.00
ATOM   2861  C   TRP   387      66.161  39.573   9.620  1.00  0.00
ATOM   2862  O   TRP   387      65.219  40.194  10.113  1.00  0.00
ATOM   2863  CB  TRP   387      65.888  37.138   9.301  1.00  0.00
ATOM   2864  CG  TRP   387      66.239  35.737   9.700  1.00  0.00
ATOM   2865  CD1 TRP   387      65.439  34.846  10.355  1.00  0.00
ATOM   2866  CD2 TRP   387      67.484  35.065   9.469  1.00  0.00
ATOM   2867  NE1 TRP   387      66.107  33.661  10.547  1.00  0.00
ATOM   2868  CE2 TRP   387      67.365  33.770  10.011  1.00  0.00
ATOM   2869  CE3 TRP   387      68.686  35.431   8.857  1.00  0.00
ATOM   2870  CZ2 TRP   387      68.403  32.841   9.960  1.00  0.00
ATOM   2871  CZ3 TRP   387      69.712  34.507   8.808  1.00  0.00
ATOM   2872  CH2 TRP   387      69.568  33.227   9.355  1.00  0.00
ATOM   2873  N   VAL   388      65.942  42.317  10.296  1.00  0.00
ATOM   2874  CA  VAL   388      67.311  41.940  10.630  1.00  0.00
ATOM   2875  C   VAL   388      68.082  43.122  11.204  1.00  0.00
ATOM   2876  O   VAL   388      67.690  44.276  11.030  1.00  0.00
ATOM   2877  CB  VAL   388      68.078  41.443   9.391  1.00  0.00
ATOM   2878  CG1 VAL   388      69.565  41.336   9.692  1.00  0.00
ATOM   2879  CG2 VAL   388      67.574  40.072   8.967  1.00  0.00
ATOM   2880  N   ARG   389      69.183  42.827  11.889  1.00  0.00
ATOM   2881  CA  ARG   389      70.085  43.864  12.373  1.00  0.00
ATOM   2882  C   ARG   389      71.074  44.282  11.292  1.00  0.00
ATOM   2883  O   ARG   389      71.883  43.476  10.833  1.00  0.00
ATOM   2884  CB  ARG   389      70.883  43.361  13.577  1.00  0.00
ATOM   2885  CG  ARG   389      70.041  43.107  14.817  1.00  0.00
ATOM   2886  CD  ARG   389      70.894  42.606  15.971  1.00  0.00
ATOM   2887  NE  ARG   389      70.088  42.262  17.139  1.00  0.00
ATOM   2888  CZ  ARG   389      70.588  41.813  18.287  1.00  0.00
ATOM   2889  NH1 ARG   389      69.777  41.525  19.295  1.00  0.00
ATOM   2890  NH2 ARG   389      71.897  41.654  18.422  1.00  0.00
ATOM   2891  N   VAL   390      71.564  45.451   9.804  1.00  0.00
ATOM   2892  CA  VAL   390      70.580  44.930   8.862  1.00  0.00
ATOM   2893  C   VAL   390      70.865  45.412   7.445  1.00  0.00
ATOM   2894  O   VAL   390      70.945  46.614   7.192  1.00  0.00
ATOM   2895  CB  VAL   390      69.154  45.381   9.228  1.00  0.00
ATOM   2896  CG1 VAL   390      68.159  44.908   8.179  1.00  0.00
ATOM   2897  CG2 VAL   390      68.742  44.805  10.575  1.00  0.00
ATOM   2898  N   PRO   391      71.017  44.467   6.524  1.00  0.00
ATOM   2899  CA  PRO   391      71.266  44.794   5.125  1.00  0.00
ATOM   2900  C   PRO   391      70.181  45.707   4.571  1.00  0.00
ATOM   2901  O   PRO   391      68.991  45.475   4.786  1.00  0.00
ATOM   2902  CB  PRO   391      71.265  43.435   4.421  1.00  0.00
ATOM   2903  CG  PRO   391      71.641  42.462   5.487  1.00  0.00
ATOM   2904  CD  PRO   391      70.992  42.955   6.751  1.00  0.00
ATOM   2905  N   GLY   392      70.598  46.747   3.856  1.00  0.00
ATOM   2906  CA  GLY   392      69.690  47.814   3.453  1.00  0.00
ATOM   2907  C   GLY   392      68.706  47.329   2.395  1.00  0.00
ATOM   2908  O   GLY   392      67.665  47.946   2.172  1.00  0.00
ATOM   2909  N   ASP   393      69.044  46.221   1.744  1.00  0.00
ATOM   2910  CA  ASP   393      68.190  45.649   0.710  1.00  0.00
ATOM   2911  C   ASP   393      67.267  44.583   1.286  1.00  0.00
ATOM   2912  O   ASP   393      66.616  43.846   0.545  1.00  0.00
ATOM   2913  CB  ASP   393      69.037  45.002  -0.388  1.00  0.00
ATOM   2914  CG  ASP   393      69.857  43.834   0.123  1.00  0.00
ATOM   2915  OD1 ASP   393      69.784  43.540   1.335  1.00  0.00
ATOM   2916  OD2 ASP   393      70.574  43.211  -0.689  1.00  0.00
ATOM   2917  N   ALA   394      67.213  44.506   2.611  1.00  0.00
ATOM   2918  CA  ALA   394      66.351  43.545   3.289  1.00  0.00
ATOM   2919  C   ALA   394      65.380  44.245   4.230  1.00  0.00
ATOM   2920  O   ALA   394      64.533  43.604   4.852  1.00  0.00
ATOM   2921  CB  ALA   394      67.185  42.571   4.107  1.00  0.00
ATOM   2922  N   PHE   395      65.507  45.564   4.331  1.00  0.00
ATOM   2923  CA  PHE   395      64.668  46.348   5.229  1.00  0.00
ATOM   2924  C   PHE   395      63.200  46.250   4.836  1.00  0.00
ATOM   2925  O   PHE   395      62.313  46.328   5.687  1.00  0.00
ATOM   2926  CB  PHE   395      65.072  47.823   5.188  1.00  0.00
ATOM   2927  CG  PHE   395      66.431  48.096   5.770  1.00  0.00
ATOM   2928  CD1 PHE   395      67.057  47.156   6.570  1.00  0.00
ATOM   2929  CD2 PHE   395      67.081  49.292   5.518  1.00  0.00
ATOM   2930  CE1 PHE   395      68.307  47.407   7.105  1.00  0.00
ATOM   2931  CE2 PHE   395      68.329  49.542   6.054  1.00  0.00
ATOM   2932  CZ  PHE   395      68.943  48.606   6.844  1.00  0.00
TER
END
