
#######################################################
#                                                     #
#                        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   16 (  132),  selected   16 , name T0356TS105_1_1-D3
# Molecule2: number of CA atoms  120 (  972),  selected   16 , name T0356_D3.pdb
# PARAMETERS: T0356TS105_1_1-D3.T0356_D3.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:    16       348 - 363         3.55     3.55
  LCS_AVERAGE:     13.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       348 - 358         1.97     3.78
  LCS_AVERAGE:      7.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       348 - 356         0.77     5.15
  LCS_AVERAGE:      5.57

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:  120
LCS_GDT     F     348     F     348      9   11   16     4    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     P     349     P     349      9   11   16     6    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     E     350     E     350      9   11   16     6    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     I     351     I     351      9   11   16     6    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     V     352     V     352      9   11   16     6    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     D     353     D     353      9   11   16     6    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     F     354     F     354      9   11   16     4    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     Y     355     Y     355      9   11   16     6    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     L     356     L     356      9   11   16     3    7    9   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     P     357     P     357      5   11   16     3    4    6   10   10   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     P     358     P     358      5   11   16     3    4    5    6    7   10   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     E     359     E     359      4    8   16     0    4    5    6    7    9    9   10   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     G     360     G     360      3    5   16     3    3    3    4    5    5    6   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     C     361     C     361      3    5   16     3    3    3    4    5    5   11   13   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     S     362     S     362      3    5   16     3    3    3    4    5    5    7   12   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_GDT     Y     363     Y     363      3    4   16     0    3    3    4    4   10   11   12   13   13   14   15   15   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   8.87  (   5.57    7.71   13.33 )

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      6      7      9     10     10     10     11     13     13     13     14     15     15     16     16     16     16     16     16     16 
GDT PERCENT_CA   5.00   5.83   7.50   8.33   8.33   8.33   9.17  10.83  10.83  10.83  11.67  12.50  12.50  13.33  13.33  13.33  13.33  13.33  13.33  13.33
GDT RMS_LOCAL    0.31   0.39   0.77   1.30   1.30   1.30   1.86   2.53   2.42   2.42   2.75   3.12   3.12   3.55   3.55   3.55   3.55   3.55   3.55   3.55
GDT RMS_ALL_CA   5.50   5.71   5.15   4.34   4.34   4.34   4.49   3.65   4.09   4.09   3.87   3.63   3.63   3.55   3.55   3.55   3.55   3.55   3.55   3.55

#      Molecule1      Molecule2       DISTANCE
LGA    F     348      F     348          1.727
LGA    P     349      P     349          1.914
LGA    E     350      E     350          1.124
LGA    I     351      I     351          0.763
LGA    V     352      V     352          1.878
LGA    D     353      D     353          2.465
LGA    F     354      F     354          2.753
LGA    Y     355      Y     355          3.125
LGA    L     356      L     356          2.860
LGA    P     357      P     357          1.436
LGA    P     358      P     358          3.434
LGA    E     359      E     359          6.009
LGA    G     360      G     360          3.833
LGA    C     361      C     361          3.955
LGA    S     362      S     362          5.727
LGA    Y     363      Y     363          7.266

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  120    4.0     13    2.53     9.583     9.193     0.494

LGA_LOCAL      RMSD =  2.530  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.618  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  3.551  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.354429 * X  +  -0.333706 * Y  +  -0.873510 * Z  + 138.646042
  Y_new =   0.065375 * X  +  -0.923024 * Y  +   0.379147 * Z  + 182.820557
  Z_new =  -0.932795 * X  +  -0.191487 * Y  +  -0.305330 * Z  + 162.312195 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.581451    0.560141  [ DEG:  -147.9063     32.0937 ]
  Theta =   1.202091    1.939502  [ DEG:    68.8747    111.1253 ]
  Phi   =   0.182402   -2.959190  [ DEG:    10.4509   -169.5491 ]
 
# 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: T0356TS105_1_1-D3                             
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS105_1_1-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  120   4.0   13   2.53   9.193     3.55
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS105_1_1-D3
REMARK PARENT number 1
PFRMAT TS
TARGET T0356
PARENT 1pg4_A
ATOM   2713  N   PHE   348      57.822  69.189  54.491  1.00107.55           N  
ATOM   2714  CA  PHE   348      57.034  68.786  53.357  1.00107.55           C  
ATOM   2715  CB  PHE   348      55.777  67.985  53.728  1.00107.55           C  
ATOM   2716  CG  PHE   348      56.248  66.726  54.360  1.00107.55           C  
ATOM   2717  CD1 PHE   348      56.584  66.713  55.693  1.00107.55           C  
ATOM   2718  CD2 PHE   348      56.353  65.570  53.622  1.00107.55           C  
ATOM   2719  CE1 PHE   348      57.022  65.556  56.290  1.00107.55           C  
ATOM   2720  CE2 PHE   348      56.790  64.410  54.213  1.00107.55           C  
ATOM   2721  CZ  PHE   348      57.125  64.407  55.545  1.00107.55           C  
ATOM   2722  C   PHE   348      56.568  70.041  52.686  1.00107.55           C  
ATOM   2723  O   PHE   348      56.125  70.985  53.338  1.00107.55           O  
ATOM   2724  N   PRO   349      56.668  70.079  51.387  1.00 76.80           N  
ATOM   2725  CA  PRO   349      56.309  71.280  50.689  1.00 76.80           C  
ATOM   2726  CD  PRO   349      57.692  69.326  50.679  1.00 76.80           C  
ATOM   2727  CB  PRO   349      56.789  71.084  49.253  1.00 76.80           C  
ATOM   2728  CG  PRO   349      57.999  70.144  49.409  1.00 76.80           C  
ATOM   2729  C   PRO   349      54.867  71.635  50.823  1.00 76.80           C  
ATOM   2730  O   PRO   349      54.539  72.817  50.730  1.00 76.80           O  
ATOM   2731  N   GLU   350      53.987  70.635  50.995  1.00 61.93           N  
ATOM   2732  CA  GLU   350      52.586  70.902  51.120  1.00 61.93           C  
ATOM   2733  CB  GLU   350      51.694  69.663  50.934  1.00 61.93           C  
ATOM   2734  CG  GLU   350      51.650  69.177  49.482  1.00 61.93           C  
ATOM   2735  CD  GLU   350      50.481  68.215  49.335  1.00 61.93           C  
ATOM   2736  OE1 GLU   350      49.767  67.987  50.347  1.00 61.93           O1-
ATOM   2737  OE2 GLU   350      50.280  67.699  48.203  1.00 61.93           O  
ATOM   2738  C   GLU   350      52.251  71.524  52.445  1.00 61.93           C  
ATOM   2739  O   GLU   350      51.357  72.364  52.519  1.00 61.93           O  
ATOM   2740  N   ILE   351      52.955  71.142  53.530  1.00 75.85           N  
ATOM   2741  CA  ILE   351      52.546  71.586  54.839  1.00 75.85           C  
ATOM   2742  CB  ILE   351      53.033  70.680  55.932  1.00 75.85           C  
ATOM   2743  CG2 ILE   351      52.664  71.314  57.282  1.00 75.85           C  
ATOM   2744  CG1 ILE   351      52.465  69.265  55.739  1.00 75.85           C  
ATOM   2745  CD1 ILE   351      53.130  68.213  56.626  1.00 75.85           C  
ATOM   2746  C   ILE   351      53.053  72.962  55.143  1.00 75.85           C  
ATOM   2747  O   ILE   351      54.254  73.222  55.098  1.00 75.85           O  
ATOM   2748  N   VAL   352      52.114  73.899  55.410  1.00125.51           N  
ATOM   2749  CA  VAL   352      52.451  75.247  55.779  1.00125.51           C  
ATOM   2750  CB  VAL   352      51.303  76.203  55.609  1.00125.51           C  
ATOM   2751  CG1 VAL   352      50.941  76.263  54.114  1.00125.51           C  
ATOM   2752  CG2 VAL   352      50.136  75.765  56.507  1.00125.51           C  
ATOM   2753  C   VAL   352      52.952  75.354  57.199  1.00125.51           C  
ATOM   2754  O   VAL   352      54.028  75.903  57.434  1.00125.51           O  
ATOM   2755  N   ASP   353      52.196  74.823  58.191  1.00127.50           N  
ATOM   2756  CA  ASP   353      52.599  74.965  59.571  1.00127.50           C  
ATOM   2757  CB  ASP   353      51.987  76.175  60.302  1.00127.50           C  
ATOM   2758  CG  ASP   353      50.475  76.021  60.334  1.00127.50           C  
ATOM   2759  OD1 ASP   353      49.861  76.090  59.238  1.00127.50           O  
ATOM   2760  OD2 ASP   353      49.915  75.830  61.447  1.00127.50           O1-
ATOM   2761  C   ASP   353      52.212  73.734  60.327  1.00127.50           C  
ATOM   2762  O   ASP   353      51.379  72.953  59.870  1.00127.50           O  
ATOM   2763  N   PHE   354      52.820  73.527  61.518  1.00128.63           N  
ATOM   2764  CA  PHE   354      52.566  72.298  62.213  1.00128.63           C  
ATOM   2765  CB  PHE   354      53.582  71.252  61.733  1.00128.63           C  
ATOM   2766  CG  PHE   354      53.355  69.933  62.363  1.00128.63           C  
ATOM   2767  CD1 PHE   354      52.516  69.029  61.761  1.00128.63           C  
ATOM   2768  CD2 PHE   354      53.992  69.598  63.534  1.00128.63           C  
ATOM   2769  CE1 PHE   354      52.307  67.801  62.331  1.00128.63           C  
ATOM   2770  CE2 PHE   354      53.782  68.367  64.106  1.00128.63           C  
ATOM   2771  CZ  PHE   354      52.936  67.466  63.504  1.00128.63           C  
ATOM   2772  C   PHE   354      52.770  72.494  63.694  1.00128.63           C  
ATOM   2773  O   PHE   354      53.651  73.243  64.113  1.00128.63           O  
ATOM   2774  N   TYR   355      51.931  71.830  64.525  1.00133.96           N  
ATOM   2775  CA  TYR   355      52.102  71.830  65.959  1.00133.96           C  
ATOM   2776  CB  TYR   355      51.091  72.681  66.747  1.00133.96           C  
ATOM   2777  CG  TYR   355      51.351  72.349  68.178  1.00133.96           C  
ATOM   2778  CD1 TYR   355      52.388  72.939  68.863  1.00133.96           C  
ATOM   2779  CD2 TYR   355      50.559  71.435  68.833  1.00133.96           C  
ATOM   2780  CE1 TYR   355      52.637  72.622  70.178  1.00133.96           C  
ATOM   2781  CE2 TYR   355      50.802  71.113  70.147  1.00133.96           C  
ATOM   2782  CZ  TYR   355      51.842  71.705  70.821  1.00133.96           C  
ATOM   2783  OH  TYR   355      52.091  71.370  72.168  1.00133.96           O  
ATOM   2784  C   TYR   355      51.897  70.413  66.417  1.00133.96           C  
ATOM   2785  O   TYR   355      50.991  69.745  65.923  1.00133.96           O  
ATOM   2786  N   LEU   356      52.711  69.890  67.369  1.00219.85           N  
ATOM   2787  CA  LEU   356      52.414  68.518  67.694  1.00219.85           C  
ATOM   2788  CB  LEU   356      53.229  67.492  66.869  1.00219.85           C  
ATOM   2789  CG  LEU   356      54.584  67.053  67.471  1.00219.85           C  
ATOM   2790  CD1 LEU   356      55.401  68.262  67.920  1.00219.85           C  
ATOM   2791  CD2 LEU   356      54.462  65.970  68.552  1.00219.85           C  
ATOM   2792  C   LEU   356      52.607  68.173  69.150  1.00219.85           C  
ATOM   2793  O   LEU   356      53.505  68.666  69.832  1.00219.85           O  
ATOM   2794  N   PRO   357      51.666  67.401  69.654  1.00152.76           N  
ATOM   2795  CA  PRO   357      51.869  66.697  70.904  1.00152.76           C  
ATOM   2796  CD  PRO   357      50.297  67.885  69.562  1.00152.76           C  
ATOM   2797  CB  PRO   357      50.523  66.668  71.632  1.00152.76           C  
ATOM   2798  CG  PRO   357      49.497  67.023  70.549  1.00152.76           C  
ATOM   2799  C   PRO   357      52.446  65.312  70.608  1.00152.76           C  
ATOM   2800  O   PRO   357      52.191  64.805  69.519  1.00152.76           O  
ATOM   2801  N   PRO   358      53.139  64.708  71.564  1.00203.95           N  
ATOM   2802  CA  PRO   358      53.962  63.484  71.510  1.00203.95           C  
ATOM   2803  CD  PRO   358      52.968  65.184  72.924  1.00203.95           C  
ATOM   2804  CB  PRO   358      54.498  63.319  72.928  1.00203.95           C  
ATOM   2805  CG  PRO   358      53.489  64.055  73.811  1.00203.95           C  
ATOM   2806  C   PRO   358      53.720  62.079  70.939  1.00203.95           C  
ATOM   2807  O   PRO   358      54.317  61.787  69.906  1.00203.95           O  
ATOM   2808  N   GLU   359      52.945  61.160  71.585  1.00330.54           N  
ATOM   2809  CA  GLU   359      52.728  59.800  71.095  1.00330.54           C  
ATOM   2810  CB  GLU   359      53.997  59.114  70.572  1.00330.54           C  
ATOM   2811  CG  GLU   359      53.724  57.761  69.913  1.00330.54           C  
ATOM   2812  CD  GLU   359      54.996  57.314  69.205  1.00330.54           C  
ATOM   2813  OE1 GLU   359      55.911  56.799  69.901  1.00330.54           O1-
ATOM   2814  OE2 GLU   359      55.073  57.487  67.959  1.00330.54           O  
ATOM   2815  C   GLU   359      52.129  58.936  72.186  1.00330.54           C  
ATOM   2816  O   GLU   359      50.912  58.780  72.266  1.00330.54           O  
ATOM   2817  N   GLY   360      52.982  58.313  73.038  1.00217.57           N  
ATOM   2818  CA  GLY   360      52.538  57.531  74.174  1.00217.57           C  
ATOM   2819  C   GLY   360      52.949  58.273  75.421  1.00217.57           C  
ATOM   2820  O   GLY   360      53.939  58.999  75.422  1.00217.57           O  
ATOM   2821  N   CYS   361      52.188  58.096  76.530  1.00160.13           N  
ATOM   2822  CA  CYS   361      52.367  58.759  77.807  1.00160.13           C  
ATOM   2823  CB  CYS   361      53.845  58.863  78.220  1.00160.13           C  
ATOM   2824  SG  CYS   361      54.604  57.234  78.487  1.00160.13           S  
ATOM   2825  C   CYS   361      51.827  60.146  77.675  1.00160.13           C  
ATOM   2826  O   CYS   361      51.486  60.815  78.648  1.00160.13           O  
ATOM   2827  N   SER   362      51.701  60.565  76.416  1.00126.73           N  
ATOM   2828  CA  SER   362      51.105  61.758  75.934  1.00126.73           C  
ATOM   2829  CB  SER   362      51.949  63.014  76.180  1.00126.73           C  
ATOM   2830  OG  SER   362      52.048  63.266  77.574  1.00126.73           O  
ATOM   2831  C   SER   362      51.090  61.424  74.493  1.00126.73           C  
ATOM   2832  O   SER   362      52.108  60.929  74.027  1.00126.73           O  
ATOM   2833  N   TYR   363      49.966  61.667  73.785  1.00154.75           N  
ATOM   2834  CA  TYR   363      49.705  61.240  72.427  1.00154.75           C  
ATOM   2835  CB  TYR   363      48.211  61.218  72.048  1.00154.75           C  
ATOM   2836  CG  TYR   363      47.487  60.143  72.780  1.00154.75           C  
ATOM   2837  CD1 TYR   363      47.065  60.337  74.074  1.00154.75           C  
ATOM   2838  CD2 TYR   363      47.217  58.946  72.158  1.00154.75           C  
ATOM   2839  CE1 TYR   363      46.388  59.346  74.742  1.00154.75           C  
ATOM   2840  CE2 TYR   363      46.540  57.950  72.818  1.00154.75           C  
ATOM   2841  CZ  TYR   363      46.125  58.151  74.112  1.00154.75           C  
ATOM   2842  OH  TYR   363      45.429  57.130  74.789  1.00154.75           O  
ATOM   2843  C   TYR   363      50.321  62.137  71.408  1.00154.75           C  
ATOM   2844  O   TYR   363      50.512  63.330  71.636  1.00154.75           O  
TER
END
