
#######################################################
#                                                     #
#                        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   14 (  113),  selected   14 , name T0356TS249_3_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   14 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_3_3-D1.T0356_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       314 - 327         3.77     3.77
  LCS_AVERAGE:     11.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       314 - 323         1.76     4.42
  LCS_AVERAGE:      7.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       317 - 323         0.83     4.83
  LCS_AVERAGE:      4.38

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:  124
LCS_GDT     D     314     D     314      3   10   14     3    3    3    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     A     315     A     315      4   10   14     3    3    4    6    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     I     316     I     316      5   10   14     3    3    5    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     Y     317     Y     317      7   10   14     3    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     H     318     H     318      7   10   14     3    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     319     S     319      7   10   14     4    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     T     320     T     320      7   10   14     4    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     Y     321     Y     321      7   10   14     4    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     T     322     T     322      7   10   14     4    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     G     323     G     323      7   10   14     4    6    7    9    9   10   10   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     R     324     R     324      5    8   14     3    3    5    5    5    6    8   10   11   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     P     325     P     325      5    6   14     3    3    5    5    5    6    7    8   10   12   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     P     326     P     326      5    6   14     0    3    5    5    5    6    7    8    9   11   13   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     327     D     327      0    6   14     0    0    3    4    4    5    7    7    9    9   12   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   7.64  (   4.38    7.26   11.29 )

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      7      9      9     10     10     10     11     12     13     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   3.23   4.84   5.65   7.26   7.26   8.06   8.06   8.06   8.87   9.68  10.48  11.29  11.29  11.29  11.29  11.29  11.29  11.29  11.29  11.29
GDT RMS_LOCAL    0.39   0.64   0.83   1.42   1.42   1.76   1.76   1.76   2.39   2.91   3.39   3.77   3.77   3.77   3.77   3.77   3.77   3.77   3.77   3.77
GDT RMS_ALL_CA   5.37   5.28   4.83   4.53   4.53   4.42   4.42   4.42   4.14   3.99   3.82   3.77   3.77   3.77   3.77   3.77   3.77   3.77   3.77   3.77

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          1.848
LGA    A     315      A     315          3.056
LGA    I     316      I     316          1.316
LGA    Y     317      Y     317          2.434
LGA    H     318      H     318          1.415
LGA    S     319      S     319          0.561
LGA    T     320      T     320          1.149
LGA    Y     321      Y     321          1.121
LGA    T     322      T     322          1.666
LGA    G     323      G     323          1.661
LGA    R     324      R     324          6.066
LGA    P     325      P     325          7.237
LGA    P     326      P     326          8.326
LGA    D     327      D     327          9.207

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  124    4.0     10    1.76     7.863     8.033     0.539

LGA_LOCAL      RMSD =  1.756  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.425  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  3.774  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.115986 * X  +   0.017435 * Y  +  -0.993098 * Z  +  58.566170
  Y_new =  -0.914454 * X  +   0.392162 * Y  +  -0.099916 * Z  +  42.563271
  Z_new =   0.387713 * X  +   0.919731 * Y  +   0.061429 * Z  +  -1.086838 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.504105   -1.637488  [ DEG:    86.1789    -93.8211 ]
  Theta =  -0.398150   -2.743443  [ DEG:   -22.8123   -157.1877 ]
  Phi   =  -1.444634    1.696959  [ DEG:   -82.7714     97.2286 ]
 
# 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: T0356TS249_3_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_3_3-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  124   4.0   10   1.76   8.033     3.77
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_3_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1g5h_A
ATOM    417  N   ASP   314      76.892  75.214  95.040  1.00  9.99
ATOM    418  CA  ASP   314      75.904  74.590  95.874  1.00  9.99
ATOM    419  CB  ASP   314      74.579  75.368  96.030  1.00  9.99
ATOM    420  CG  ASP   314      73.827  75.472  94.708  1.00  9.99
ATOM    421  OD1 ASP   314      74.438  75.239  93.634  1.00  9.99
ATOM    422  OD2 ASP   314      72.612  75.805  94.763  1.00  9.99
ATOM    423  C   ASP   314      75.619  73.278  95.216  1.00  9.99
ATOM    424  O   ASP   314      75.792  73.139  94.016  1.00  9.99
ATOM    425  N   ALA   315      75.163  72.288  95.994  1.00  9.99
ATOM    426  CA  ALA   315      74.964  70.925  95.577  1.00  9.99
ATOM    427  CB  ALA   315      74.574  70.007  96.749  1.00  9.99
ATOM    428  C   ALA   315      73.915  70.749  94.518  1.00  9.99
ATOM    429  O   ALA   315      73.929  69.738  93.823  1.00  9.99
ATOM    430  N   ILE   316      72.936  71.661  94.403  1.00  9.99
ATOM    431  CA  ILE   316      71.803  71.401  93.557  1.00  9.99
ATOM    432  CB  ILE   316      70.666  72.318  93.882  1.00  9.99
ATOM    433  CG2 ILE   316      69.507  72.021  92.916  1.00  9.99
ATOM    434  CG1 ILE   316      70.295  72.170  95.364  1.00  9.99
ATOM    435  CD1 ILE   316      69.416  73.304  95.882  1.00  9.99
ATOM    436  C   ILE   316      72.084  71.557  92.099  1.00  9.99
ATOM    437  O   ILE   316      72.330  72.646  91.590  1.00  9.99
ATOM    438  N   TYR   317      71.881  70.442  91.379  1.00  9.99
ATOM    439  CA  TYR   317      72.059  70.292  89.971  1.00  9.99
ATOM    440  CB  TYR   317      72.558  68.886  89.577  1.00  9.99
ATOM    441  CG  TYR   317      73.965  68.673  90.000  1.00  9.99
ATOM    442  CD1 TYR   317      74.313  68.482  91.314  1.00  9.99
ATOM    443  CD2 TYR   317      74.941  68.606  89.044  1.00  9.99
ATOM    444  CE1 TYR   317      75.627  68.286  91.673  1.00  9.99
ATOM    445  CE2 TYR   317      76.256  68.422  89.399  1.00  9.99
ATOM    446  CZ  TYR   317      76.608  68.256  90.714  1.00  9.99
ATOM    447  OH  TYR   317      77.959  68.060  91.075  1.00  9.99
ATOM    448  C   TYR   317      70.649  70.284  89.489  1.00  9.99
ATOM    449  O   TYR   317      69.736  70.538  90.271  1.00  9.99
ATOM    450  N   HIS   318      70.425  70.061  88.185  1.00  9.99
ATOM    451  CA  HIS   318      69.075  70.001  87.724  1.00  9.99
ATOM    452  ND1 HIS   318      68.652  73.073  86.690  1.00  9.99
ATOM    453  CG  HIS   318      69.380  71.989  86.254  1.00  9.99
ATOM    454  CB  HIS   318      68.902  70.569  86.311  1.00  9.99
ATOM    455  NE2 HIS   318      70.600  73.865  85.965  1.00  9.99
ATOM    456  CD2 HIS   318      70.567  72.491  85.815  1.00  9.99
ATOM    457  CE1 HIS   318      69.428  74.170  86.494  1.00  9.99
ATOM    458  C   HIS   318      68.702  68.553  87.718  1.00  9.99
ATOM    459  O   HIS   318      69.405  67.716  87.153  1.00  9.99
ATOM    460  N   SER   319      67.580  68.224  88.378  1.00  9.99
ATOM    461  CA  SER   319      67.174  66.856  88.472  1.00  9.99
ATOM    462  CB  SER   319      66.766  66.444  89.896  1.00  9.99
ATOM    463  OG  SER   319      66.376  65.079  89.927  1.00  9.99
ATOM    464  C   SER   319      65.975  66.673  87.605  1.00  9.99
ATOM    465  O   SER   319      65.075  67.509  87.569  1.00  9.99
ATOM    466  N   THR   320      65.941  65.550  86.862  1.00  9.99
ATOM    467  CA  THR   320      64.807  65.307  86.025  1.00  9.99
ATOM    468  CB  THR   320      65.122  65.028  84.592  1.00  9.99
ATOM    469  OG1 THR   320      65.939  63.875  84.510  1.00  9.99
ATOM    470  CG2 THR   320      65.830  66.236  83.975  1.00  9.99
ATOM    471  C   THR   320      64.125  64.078  86.522  1.00  9.99
ATOM    472  O   THR   320      64.758  63.092  86.898  1.00  9.99
ATOM    473  N   TYR   321      62.783  64.130  86.493  1.00  9.99
ATOM    474  CA  TYR   321      61.918  63.096  86.966  1.00  9.99
ATOM    475  CB  TYR   321      60.802  63.605  87.898  1.00  9.99
ATOM    476  CG  TYR   321      61.443  64.170  89.123  1.00  9.99
ATOM    477  CD1 TYR   321      61.825  65.491  89.170  1.00  9.99
ATOM    478  CD2 TYR   321      61.665  63.376  90.225  1.00  9.99
ATOM    479  CE1 TYR   321      62.414  66.014  90.297  1.00  9.99
ATOM    480  CE2 TYR   321      62.254  63.891  91.354  1.00  9.99
ATOM    481  CZ  TYR   321      62.630  65.213  91.392  1.00  9.99
ATOM    482  OH  TYR   321      63.235  65.743  92.551  1.00  9.99
ATOM    483  C   TYR   321      61.252  62.478  85.769  1.00  9.99
ATOM    484  O   TYR   321      61.030  63.134  84.753  1.00  9.99
ATOM    485  N   THR   322      60.993  61.159  85.877  1.00  9.99
ATOM    486  CA  THR   322      60.491  60.275  84.848  1.00  9.99
ATOM    487  CB  THR   322      60.388  58.852  85.318  1.00  9.99
ATOM    488  OG1 THR   322      61.612  58.376  85.848  1.00  9.99
ATOM    489  CG2 THR   322      59.965  57.995  84.113  1.00  9.99
ATOM    490  C   THR   322      59.094  60.454  84.321  1.00  9.99
ATOM    491  O   THR   322      58.904  60.639  83.118  1.00  9.99
ATOM    492  N   GLY   323      58.076  60.341  85.202  1.00  9.99
ATOM    493  CA  GLY   323      56.718  60.242  84.733  1.00  9.99
ATOM    494  C   GLY   323      56.311  61.494  84.044  1.00  9.99
ATOM    495  O   GLY   323      55.767  61.466  82.940  1.00  9.99
ATOM    496  N   ARG   324      56.571  62.634  84.697  1.00  9.99
ATOM    497  CA  ARG   324      56.251  63.895  84.116  1.00  9.99
ATOM    498  CB  ARG   324      55.416  64.795  85.053  1.00  9.99
ATOM    499  CG  ARG   324      56.046  65.050  86.426  1.00  9.99
ATOM    500  CD  ARG   324      55.139  65.837  87.380  1.00  9.99
ATOM    501  NE  ARG   324      55.819  65.919  88.707  1.00  9.99
ATOM    502  CZ  ARG   324      55.552  64.996  89.677  1.00  9.99
ATOM    503  NH1 ARG   324      54.650  63.996  89.443  1.00  9.99
ATOM    504  NH2 ARG   324      56.183  65.068  90.886  1.00  9.99
ATOM    505  C   ARG   324      57.571  64.534  83.846  1.00  9.99
ATOM    506  O   ARG   324      58.458  64.550  84.693  1.00  9.99
ATOM    507  N   PRO   325      57.700  65.061  82.666  1.00  9.99
ATOM    508  CA  PRO   325      58.922  65.694  82.245  1.00  9.99
ATOM    509  CD  PRO   325      56.961  64.507  81.542  1.00  9.99
ATOM    510  CB  PRO   325      58.782  65.888  80.735  1.00  9.99
ATOM    511  CG  PRO   325      57.839  64.752  80.306  1.00  9.99
ATOM    512  C   PRO   325      59.293  66.964  82.971  1.00  9.99
ATOM    513  O   PRO   325      60.317  67.517  82.574  1.00  9.99
ATOM    514  N   PRO   326      58.596  67.507  83.940  1.00  9.99
ATOM    515  CA  PRO   326      59.089  68.726  84.516  1.00  9.99
ATOM    516  CD  PRO   326      57.140  67.526  83.934  1.00  9.99
ATOM    517  CB  PRO   326      57.909  69.396  85.227  1.00  9.99
ATOM    518  CG  PRO   326      56.771  68.369  85.156  1.00  9.99
ATOM    519  C   PRO   326      60.300  68.618  85.383  1.00  9.99
ATOM    520  O   PRO   326      60.724  67.517  85.745  1.00  9.99
ATOM    521  N   ASP   327      60.895  69.788  85.680  1.00  9.99
ATOM    522  CA  ASP   327      62.032  69.874  86.537  1.00  9.99
ATOM    523  CB  ASP   327      62.974  71.037  86.178  1.00  9.99
ATOM    524  CG  ASP   327      64.202  70.963  87.076  1.00  9.99
ATOM    525  OD1 ASP   327      64.239  70.069  87.963  1.00  9.99
ATOM    526  OD2 ASP   327      65.120  71.807  86.890  1.00  9.99
ATOM    527  C   ASP   327      61.498  70.139  87.937  1.00  9.99
ATOM    528  O   ASP   327      60.913  71.238  88.147  1.00  9.99
ATOM    529  OXT ASP   327      61.670  69.253  88.814  1.00  9.99
TER
END
