
#######################################################
#                                                     #
#                        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   15 (  120),  selected   15 , name T0333TS174_1u-D1
# Molecule2: number of CA atoms  206 ( 1581),  selected   15 , name T0333_D1.pdb
# PARAMETERS: T0333TS174_1u-D1.T0333_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:    15       361 - 375         2.06     2.06
  LCS_AVERAGE:      7.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       361 - 374         1.91     2.12
  LONGEST_CONTINUOUS_SEGMENT:    14       362 - 375         1.09     2.25
  LCS_AVERAGE:      6.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       362 - 374         0.62     2.30
  LCS_AVERAGE:      5.70

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:  206
LCS_GDT     P     361     P     361      3   14   15     0    3    3    3    4    5    6    9   13   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     T     362     T     362     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P     363     P     363     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     A     364     A     364     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     365     E     365     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     T     366     T     366     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     367     V     367     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     368     R     368     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     369     R     369     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I     370     I     370     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     V     371     V     371     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     372     E     372     13   14   15    11   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     373     R     373     13   14   15     9   12   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I     374     I     374     13   14   15     4    5   13   13   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     S     375     S     375      4   14   15     0    4    5    5   14   14   14   14   14   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   6.59  (   5.70    6.80    7.28 )

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     11     12     13     13     14     14     14     14     14     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   5.34   5.83   6.31   6.31   6.80   6.80   6.80   6.80   6.80   7.28   7.28   7.28   7.28   7.28   7.28   7.28   7.28   7.28   7.28   7.28
GDT RMS_LOCAL    0.27   0.37   0.62   0.62   1.09   1.09   1.09   1.09   1.09   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06
GDT RMS_ALL_CA   2.25   2.28   2.30   2.30   2.25   2.25   2.25   2.25   2.25   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06

#      Molecule1      Molecule2       DISTANCE
LGA    P     361      P     361          7.707
LGA    T     362      T     362          0.832
LGA    P     363      P     363          0.600
LGA    A     364      A     364          0.317
LGA    E     365      E     365          0.413
LGA    T     366      T     366          0.536
LGA    V     367      V     367          0.620
LGA    R     368      R     368          0.448
LGA    R     369      R     369          0.269
LGA    I     370      I     370          0.801
LGA    V     371      V     371          1.107
LGA    E     372      E     372          0.890
LGA    R     373      R     373          0.983
LGA    I     374      I     374          1.398
LGA    S     375      S     375          2.976

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  206    4.0     14    1.09     6.553     6.766     1.174

LGA_LOCAL      RMSD =  1.092  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.252  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  2.059  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.377536 * X  +  -0.584541 * Y  +   0.718177 * Z  +  63.283905
  Y_new =  -0.863917 * X  +  -0.056845 * Y  +  -0.500416 * Z  +  85.110420
  Z_new =   0.333339 * X  +  -0.809370 * Y  +  -0.483534 * Z  +  67.121475 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.109317    1.032276  [ DEG:  -120.8549     59.1451 ]
  Theta =  -0.339843   -2.801750  [ DEG:   -19.4715   -160.5284 ]
  Phi   =  -1.982791    1.158802  [ DEG:  -113.6055     66.3945 ]
 
# 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: T0333TS174_1u-D1                              
REMARK     2: T0333_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0333TS174_1u-D1.T0333_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  206   4.0   14   1.09   6.766     2.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0333TS174_1u-D1
PFRMAT TS
TARGET T0333
MODEL 1  UNREFINED
PARENT 1iir_A 
ATOM   2717  N   PRO   361      52.027  16.220   2.265  1.00  1.00
ATOM   2718  CA  PRO   361      52.503  16.891   3.468  1.00  1.00
ATOM   2719  C   PRO   361      52.318  18.402   3.455  1.00  1.00
ATOM   2720  O   PRO   361      52.939  19.111   4.242  1.00  1.00
ATOM   2721  CB  PRO   361      53.986  16.551   3.680  1.00  1.00
ATOM   2722  CG  PRO   361      54.387  16.375   2.208  1.00  1.00
ATOM   2723  CD  PRO   361      53.276  15.751   1.532  1.00  1.00
ATOM   2724  N   THR   362      51.446  18.889   2.579  1.00  1.00
ATOM   2725  CA  THR   362      51.225  20.323   2.473  1.00  1.00
ATOM   2726  C   THR   362      50.841  21.044   3.752  1.00  1.00
ATOM   2727  O   THR   362      51.299  22.163   3.997  1.00  1.00
ATOM   2728  CB  THR   362      50.204  20.890   1.560  1.00  1.00
ATOM   2729  OG1 THR   362      50.170  22.317   1.458  1.00  1.00
ATOM   2730  CG2 THR   362      48.877  20.344   2.024  1.00  1.00
ATOM   2731  N   PRO   363      49.985  20.430   4.560  1.00  1.00
ATOM   2732  CA  PRO   363      49.563  21.060   5.806  1.00  1.00
ATOM   2733  C   PRO   363      50.756  21.182   6.755  1.00  1.00
ATOM   2734  O   PRO   363      50.898  22.184   7.463  1.00  1.00
ATOM   2735  CB  PRO   363      48.435  20.252   6.456  1.00  1.00
ATOM   2736  CG  PRO   363      48.858  18.871   5.932  1.00  1.00
ATOM   2737  CD  PRO   363      49.379  19.058   4.601  1.00  1.00
ATOM   2738  N   ALA   364      51.620  20.167   6.757  1.00  1.00
ATOM   2739  CA  ALA   364      52.804  20.179   7.611  1.00  1.00
ATOM   2740  C   ALA   364      53.770  21.252   7.111  1.00  1.00
ATOM   2741  O   ALA   364      54.407  21.952   7.904  1.00  1.00
ATOM   2742  CB  ALA   364      53.477  18.802   7.596  1.00  1.00
ATOM   2743  N   GLU   365      53.883  21.374   5.792  1.00  1.00
ATOM   2744  CA  GLU   365      54.750  22.381   5.191  1.00  1.00
ATOM   2745  C   GLU   365      54.274  23.766   5.633  1.00  1.00
ATOM   2746  O   GLU   365      55.075  24.620   6.021  1.00  1.00
ATOM   2747  CB  GLU   365      54.706  22.294   3.646  1.00  1.00
ATOM   2748  CG  GLU   365      55.310  21.026   3.096  1.00  1.00
ATOM   2749  CD  GLU   365      55.265  20.960   1.584  1.00  1.00
ATOM   2750  OE1 GLU   365      55.791  21.766   0.879  1.00  1.00
ATOM   2751  OE2 GLU   365      54.577  19.938   1.158  1.00  1.00
ATOM   2752  N   THR   366      52.964  23.986   5.575  1.00  1.00
ATOM   2753  CA  THR   366      52.404  25.274   5.968  1.00  1.00
ATOM   2754  C   THR   366      52.580  25.517   7.466  1.00  1.00
ATOM   2755  O   THR   366      52.898  26.630   7.887  1.00  1.00
ATOM   2756  CB  THR   366      50.922  25.337   5.597  1.00  1.00
ATOM   2757  OG1 THR   366      50.906  25.291   4.169  1.00  1.00
ATOM   2758  CG2 THR   366      50.287  26.606   6.099  1.00  1.00
ATOM   2759  N   VAL   367      52.369  24.477   8.266  1.00  1.00
ATOM   2760  CA  VAL   367      52.501  24.596   9.713  1.00  1.00
ATOM   2761  C   VAL   367      53.898  25.079  10.088  1.00  1.00
ATOM   2762  O   VAL   367      54.052  25.931  10.962  1.00  1.00
ATOM   2763  CB  VAL   367      52.211  23.257  10.379  1.00  1.00
ATOM   2764  CG1 VAL   367      50.805  22.769  10.083  1.00  1.00
ATOM   2765  CG2 VAL   367      52.439  23.396  11.868  1.00  1.00
ATOM   2766  N   ARG   368      54.913  24.536   9.423  1.00  1.00
ATOM   2767  CA  ARG   368      56.293  24.929   9.699  1.00  1.00
ATOM   2768  C   ARG   368      56.556  26.374   9.293  1.00  1.00
ATOM   2769  O   ARG   368      57.190  27.130  10.034  1.00  1.00
ATOM   2770  CB  ARG   368      57.272  23.994   8.973  1.00  1.00
ATOM   2771  CG  ARG   368      58.736  24.422   9.070  1.00  1.00
ATOM   2772  CD  ARG   368      59.148  24.689  10.513  1.00  1.00
ATOM   2773  NE  ARG   368      59.052  23.492  11.342  1.00  1.00
ATOM   2774  CZ  ARG   368      59.168  23.488  12.666  1.00  1.00
ATOM   2775  NH1 ARG   368      59.385  24.622  13.320  1.00  1.00
ATOM   2776  NH2 ARG   368      59.073  22.349  13.336  1.00  1.00
ATOM   2777  N   ARG   369      56.073  26.761   8.117  1.00  1.00
ATOM   2778  CA  ARG   369      56.264  28.125   7.645  1.00  1.00
ATOM   2779  C   ARG   369      55.572  29.110   8.582  1.00  1.00
ATOM   2780  O   ARG   369      56.063  30.217   8.809  1.00  1.00
ATOM   2781  CB  ARG   369      55.709  28.287   6.227  1.00  1.00
ATOM   2782  CG  ARG   369      54.344  28.042   6.231  1.00  1.00
ATOM   2783  CD  ARG   369      53.757  28.204   4.828  1.00  1.00
ATOM   2784  NE  ARG   369      53.816  29.425   4.338  1.00  1.00
ATOM   2785  CZ  ARG   369      52.891  30.384   4.576  1.00  1.00
ATOM   2786  NH1 ARG   369      53.050  31.572   4.035  1.00  1.00
ATOM   2787  NH2 ARG   369      51.822  29.880   5.463  1.00  1.00
ATOM   2788  N   ILE   370      54.430  28.699   9.125  1.00  1.00
ATOM   2789  CA  ILE   370      53.666  29.541  10.035  1.00  1.00
ATOM   2790  C   ILE   370      54.425  29.780  11.341  1.00  1.00
ATOM   2791  O   ILE   370      54.612  30.924  11.764  1.00  1.00
ATOM   2792  CB  ILE   370      52.314  28.890  10.338  1.00  1.00
ATOM   2793  CG1 ILE   370      51.442  28.827   9.093  1.00  1.00
ATOM   2794  CG2 ILE   370      51.621  29.744  11.380  1.00  1.00
ATOM   2795  CD1 ILE   370      50.149  28.033   9.250  1.00  1.00
ATOM   2796  N   VAL   371      54.862  28.697  11.979  1.00  1.00
ATOM   2797  CA  VAL   371      55.592  28.818  13.236  1.00  1.00
ATOM   2798  C   VAL   371      56.883  29.609  13.075  1.00  1.00
ATOM   2799  O   VAL   371      57.244  30.392  13.953  1.00  1.00
ATOM   2800  CB  VAL   371      55.896  27.438  13.819  1.00  1.00
ATOM   2801  CG1 VAL   371      56.798  26.625  12.910  1.00  1.00
ATOM   2802  CG2 VAL   371      54.593  26.719  14.088  1.00  1.00
ATOM   2803  N   GLU   372      57.583  29.411  11.964  1.00  1.00
ATOM   2804  CA  GLU   372      58.818  30.156  11.741  1.00  1.00
ATOM   2805  C   GLU   372      58.492  31.642  11.615  1.00  1.00
ATOM   2806  O   GLU   372      59.226  32.495  12.116  1.00  1.00
ATOM   2807  CB  GLU   372      59.527  29.682  10.471  1.00  1.00
ATOM   2808  CG  GLU   372      58.719  29.883   9.215  1.00  1.00
ATOM   2809  CD  GLU   372      59.434  29.402   7.972  1.00  1.00
ATOM   2810  OE1 GLU   372      60.489  29.839   7.614  1.00  1.00
ATOM   2811  OE2 GLU   372      58.764  28.468   7.358  1.00  1.00
ATOM   2812  N   ARG   373      57.389  31.950  10.939  1.00  1.00
ATOM   2813  CA  ARG   373      56.975  33.336  10.761  1.00  1.00
ATOM   2814  C   ARG   373      56.610  33.963  12.103  1.00  1.00
ATOM   2815  O   ARG   373      56.978  35.103  12.387  1.00  1.00
ATOM   2816  CB  ARG   373      55.787  33.410   9.811  1.00  1.00
ATOM   2817  CG  ARG   373      56.184  33.039   8.528  1.00  1.00
ATOM   2818  CD  ARG   373      55.019  33.122   7.545  1.00  1.00
ATOM   2819  NE  ARG   373      54.029  32.279   7.783  1.00  1.00
ATOM   2820  CZ  ARG   373      52.841  32.636   8.324  1.00  1.00
ATOM   2821  NH1 ARG   373      51.918  31.711   8.508  1.00  1.00
ATOM   2822  NH2 ARG   373      52.800  34.089   8.608  1.00  1.00
ATOM   2823  N   ILE   374      55.884  33.213  12.925  1.00  1.00
ATOM   2824  CA  ILE   374      55.466  33.702  14.232  1.00  1.00
ATOM   2825  C   ILE   374      56.676  33.913  15.136  1.00  1.00
ATOM   2826  O   ILE   374      56.676  34.795  15.995  1.00  1.00
ATOM   2827  CB  ILE   374      54.489  32.716  14.904  1.00  1.00
ATOM   2828  CG1 ILE   374      55.163  31.377  15.156  1.00  1.00
ATOM   2829  CG2 ILE   374      53.263  32.487  14.043  1.00  1.00
ATOM   2830  CD1 ILE   374      55.689  31.171  16.573  1.00  1.00
ATOM   2831  N   SER   375      57.711  33.107  14.930  1.00  1.00
ATOM   2832  CA  SER   375      58.928  33.217  15.724  1.00  1.00
ATOM   2833  C   SER   375      59.715  34.469  15.351  1.00  1.00
ATOM   2834  O   SER   375      60.615  34.885  16.083  1.00  1.00
ATOM   2835  CB  SER   375      59.802  31.978  15.527  1.00  1.00
ATOM   2836  OG  SER   375      59.126  30.815  15.969  1.00  1.00
TER
END
