
#######################################################
#                                                     #
#                        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_2_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   14 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_2_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         4.32     4.32
  LCS_AVERAGE:     11.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       316 - 325         1.45     5.42
  LCS_AVERAGE:      6.74

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       316 - 322         0.72     5.38
  LCS_AVERAGE:      4.26

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      4    4   14     2    4    4    4    4    5    6    6    9    9   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     A     315     A     315      4    5   14     3    4    4    4    4    5    6   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     I     316     I     316      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     Y     317     Y     317      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     H     318     H     318      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     S     319     S     319      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     T     320     T     320      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     Y     321     Y     321      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     T     322     T     322      7   10   14     4    6    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     G     323     G     323      5   10   14     3    3    6    8    9   10   10   10   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     R     324     R     324      3   10   14     3    3    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     P     325     P     325      3   10   14     3    3    8    9    9   10   10   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     P     326     P     326      3    4   14     3    3    4    4    4    5    9   11   12   12   12   13   13   13   13   13   13   13   14   14 
LCS_GDT     D     327     D     327      3    4   14     0    2    3    4    4    4    4    5    5    5    5    6    6    6    6    6    7    8   14   14 
LCS_AVERAGE  LCS_A:   7.43  (   4.26    6.74   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      8      9      9     10     10     11     12     12     12     13     13     13     13     13     13     13     14     14 
GDT PERCENT_CA   3.23   4.84   6.45   7.26   7.26   8.06   8.06   8.87   9.68   9.68   9.68  10.48  10.48  10.48  10.48  10.48  10.48  10.48  11.29  11.29
GDT RMS_LOCAL    0.19   0.59   0.89   1.05   1.05   1.45   1.45   2.60   2.76   2.76   2.76   3.49   3.49   3.49   3.49   3.49   3.49   3.49   4.32   4.32
GDT RMS_ALL_CA   5.89   5.68   5.13   5.27   5.27   5.42   5.42   4.57   4.65   4.65   4.65   4.40   4.40   4.40   4.40   4.40   4.40   4.40   4.32   4.32

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          6.363
LGA    A     315      A     315          3.793
LGA    I     316      I     316          3.566
LGA    Y     317      Y     317          3.287
LGA    H     318      H     318          3.284
LGA    S     319      S     319          3.296
LGA    T     320      T     320          2.866
LGA    Y     321      Y     321          1.841
LGA    T     322      T     322          2.016
LGA    G     323      G     323          4.902
LGA    R     324      R     324          3.980
LGA    P     325      P     325          1.562
LGA    P     326      P     326          2.996
LGA    D     327      D     327          9.808

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  124    4.0     11    2.60     7.863     7.889     0.407

LGA_LOCAL      RMSD =  2.603  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.336  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  4.321  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.676621 * X  +  -0.694994 * Y  +   0.243241 * Z  + 119.160851
  Y_new =  -0.135166 * X  +  -0.207497 * Y  +  -0.968853 * Z  +  75.754128
  Z_new =   0.723819 * X  +  -0.688424 * Y  +   0.046457 * Z  +  57.508350 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.503415    1.638178  [ DEG:   -86.1393     93.8607 ]
  Theta =  -0.809321   -2.332272  [ DEG:   -46.3707   -133.6293 ]
  Phi   =  -2.944422    0.197170  [ DEG:  -168.7030     11.2970 ]
 
# 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_2_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_2_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   11   2.60   7.889     4.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_2_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 1geh_A
ATOM    417  N   ASP   314      72.738  76.732  92.141  1.00  9.99
ATOM    418  CA  ASP   314      72.054  76.558  93.380  1.00  9.99
ATOM    419  CB  ASP   314      70.569  76.941  93.291  1.00  9.99
ATOM    420  CG  ASP   314      69.902  76.029  92.271  1.00  9.99
ATOM    421  OD1 ASP   314      70.628  75.286  91.559  1.00  9.99
ATOM    422  OD2 ASP   314      68.647  76.074  92.184  1.00  9.99
ATOM    423  C   ASP   314      72.128  75.150  93.909  1.00  9.99
ATOM    424  O   ASP   314      71.621  74.908  95.005  1.00  9.99
ATOM    425  N   ALA   315      72.640  74.149  93.155  1.00  9.99
ATOM    426  CA  ALA   315      72.525  72.846  93.765  1.00  9.99
ATOM    427  CB  ALA   315      71.351  72.026  93.198  1.00  9.99
ATOM    428  C   ALA   315      73.748  71.968  93.672  1.00  9.99
ATOM    429  O   ALA   315      74.556  72.070  92.750  1.00  9.99
ATOM    430  N   ILE   316      73.914  71.104  94.709  1.00  9.99
ATOM    431  CA  ILE   316      74.993  70.155  94.843  1.00  9.99
ATOM    432  CB  ILE   316      75.062  69.523  96.199  1.00  9.99
ATOM    433  CG2 ILE   316      76.107  68.398  96.113  1.00  9.99
ATOM    434  CG1 ILE   316      75.357  70.550  97.293  1.00  9.99
ATOM    435  CD1 ILE   316      76.732  71.200  97.158  1.00  9.99
ATOM    436  C   ILE   316      74.900  68.961  93.933  1.00  9.99
ATOM    437  O   ILE   316      75.771  68.716  93.100  1.00  9.99
ATOM    438  N   TYR   317      73.803  68.195  94.066  1.00  9.99
ATOM    439  CA  TYR   317      73.633  66.945  93.382  1.00  9.99
ATOM    440  CB  TYR   317      73.486  65.793  94.392  1.00  9.99
ATOM    441  CG  TYR   317      73.294  64.493  93.697  1.00  9.99
ATOM    442  CD1 TYR   317      74.369  63.795  93.198  1.00  9.99
ATOM    443  CD2 TYR   317      72.032  63.963  93.572  1.00  9.99
ATOM    444  CE1 TYR   317      74.182  62.589  92.565  1.00  9.99
ATOM    445  CE2 TYR   317      71.838  62.757  92.940  1.00  9.99
ATOM    446  CZ  TYR   317      72.916  62.068  92.438  1.00  9.99
ATOM    447  OH  TYR   317      72.722  60.829  91.791  1.00  9.99
ATOM    448  C   TYR   317      72.354  67.087  92.641  1.00  9.99
ATOM    449  O   TYR   317      71.341  67.493  93.210  1.00  9.99
ATOM    450  N   HIS   318      72.344  66.778  91.336  1.00  9.99
ATOM    451  CA  HIS   318      71.087  67.004  90.705  1.00  9.99
ATOM    452  ND1 HIS   318      69.055  67.767  88.190  1.00  9.99
ATOM    453  CG  HIS   318      69.789  68.486  89.107  1.00  9.99
ATOM    454  CB  HIS   318      71.143  68.074  89.603  1.00  9.99
ATOM    455  NE2 HIS   318      67.832  69.542  88.731  1.00  9.99
ATOM    456  CD2 HIS   318      69.029  69.570  89.425  1.00  9.99
ATOM    457  CE1 HIS   318      67.894  68.442  88.002  1.00  9.99
ATOM    458  C   HIS   318      70.598  65.738  90.102  1.00  9.99
ATOM    459  O   HIS   318      71.211  65.205  89.189  1.00  9.99
ATOM    460  N   SER   319      69.467  65.221  90.610  1.00  9.99
ATOM    461  CA  SER   319      68.845  64.058  90.071  1.00  9.99
ATOM    462  CB  SER   319      68.219  63.161  91.147  1.00  9.99
ATOM    463  OG  SER   319      67.583  62.049  90.540  1.00  9.99
ATOM    464  C   SER   319      67.731  64.553  89.218  1.00  9.99
ATOM    465  O   SER   319      67.051  65.528  89.539  1.00  9.99
ATOM    466  N   THR   320      67.531  63.885  88.075  1.00  9.99
ATOM    467  CA  THR   320      66.479  64.275  87.206  1.00  9.99
ATOM    468  CB  THR   320      66.814  64.125  85.752  1.00  9.99
ATOM    469  OG1 THR   320      67.047  62.760  85.439  1.00  9.99
ATOM    470  CG2 THR   320      68.076  64.955  85.464  1.00  9.99
ATOM    471  C   THR   320      65.348  63.366  87.517  1.00  9.99
ATOM    472  O   THR   320      65.465  62.418  88.293  1.00  9.99
ATOM    473  N   TYR   321      64.220  63.650  86.869  1.00  9.99
ATOM    474  CA  TYR   321      62.972  63.016  87.115  1.00  9.99
ATOM    475  CB  TYR   321      61.877  64.071  87.262  1.00  9.99
ATOM    476  CG  TYR   321      61.911  64.888  85.996  1.00  9.99
ATOM    477  CD1 TYR   321      62.868  65.856  85.761  1.00  9.99
ATOM    478  CD2 TYR   321      61.003  64.668  84.993  1.00  9.99
ATOM    479  CE1 TYR   321      62.891  66.597  84.607  1.00  9.99
ATOM    480  CE2 TYR   321      61.005  65.394  83.829  1.00  9.99
ATOM    481  CZ  TYR   321      61.953  66.364  83.634  1.00  9.99
ATOM    482  OH  TYR   321      61.965  67.118  82.441  1.00  9.99
ATOM    483  C   TYR   321      62.577  62.259  85.895  1.00  9.99
ATOM    484  O   TYR   321      63.224  62.335  84.851  1.00  9.99
ATOM    485  N   THR   322      61.525  61.431  86.051  1.00  9.99
ATOM    486  CA  THR   322      60.920  60.793  84.927  1.00  9.99
ATOM    487  CB  THR   322      60.122  59.576  85.279  1.00  9.99
ATOM    488  OG1 THR   322      60.936  58.623  85.939  1.00  9.99
ATOM    489  CG2 THR   322      59.571  58.976  83.976  1.00  9.99
ATOM    490  C   THR   322      59.939  61.822  84.460  1.00  9.99
ATOM    491  O   THR   322      59.365  62.531  85.287  1.00  9.99
ATOM    492  N   GLY   323      59.710  61.939  83.138  1.00  9.99
ATOM    493  CA  GLY   323      58.827  62.968  82.674  1.00  9.99
ATOM    494  C   GLY   323      57.490  62.378  82.364  1.00  9.99
ATOM    495  O   GLY   323      57.383  61.369  81.667  1.00  9.99
ATOM    496  N   ARG   324      56.420  63.019  82.881  1.00  9.99
ATOM    497  CA  ARG   324      55.104  62.543  82.594  1.00  9.99
ATOM    498  CB  ARG   324      54.279  62.180  83.844  1.00  9.99
ATOM    499  CG  ARG   324      54.816  60.951  84.582  1.00  9.99
ATOM    500  CD  ARG   324      56.073  61.223  85.412  1.00  9.99
ATOM    501  NE  ARG   324      55.690  61.156  86.852  1.00  9.99
ATOM    502  CZ  ARG   324      55.742  59.956  87.502  1.00  9.99
ATOM    503  NH1 ARG   324      56.146  58.838  86.830  1.00  9.99
ATOM    504  NH2 ARG   324      55.405  59.873  88.821  1.00  9.99
ATOM    505  C   ARG   324      54.379  63.624  81.862  1.00  9.99
ATOM    506  O   ARG   324      54.196  64.737  82.356  1.00  9.99
ATOM    507  N   PRO   325      54.001  63.291  80.659  1.00  9.99
ATOM    508  CA  PRO   325      53.252  64.188  79.819  1.00  9.99
ATOM    509  CD  PRO   325      54.810  62.369  79.875  1.00  9.99
ATOM    510  CB  PRO   325      53.576  63.803  78.373  1.00  9.99
ATOM    511  CG  PRO   325      54.172  62.389  78.478  1.00  9.99
ATOM    512  C   PRO   325      51.792  64.121  80.120  1.00  9.99
ATOM    513  O   PRO   325      51.332  63.148  80.714  1.00  9.99
ATOM    514  N   PRO   326      51.084  65.134  79.705  1.00  9.99
ATOM    515  CA  PRO   326      49.661  65.179  79.893  1.00  9.99
ATOM    516  CD  PRO   326      51.669  66.464  79.656  1.00  9.99
ATOM    517  CB  PRO   326      49.249  66.623  79.620  1.00  9.99
ATOM    518  CG  PRO   326      50.514  67.437  79.950  1.00  9.99
ATOM    519  C   PRO   326      49.049  64.206  78.948  1.00  9.99
ATOM    520  O   PRO   326      49.756  63.727  78.064  1.00  9.99
ATOM    521  N   ASP   327      47.753  63.883  79.133  1.00  9.99
ATOM    522  CA  ASP   327      47.078  62.951  78.276  1.00  9.99
ATOM    523  CB  ASP   327      45.550  62.961  78.454  1.00  9.99
ATOM    524  CG  ASP   327      45.209  62.375  79.816  1.00  9.99
ATOM    525  OD1 ASP   327      45.550  61.186  80.057  1.00  9.99
ATOM    526  OD2 ASP   327      44.596  63.113  80.633  1.00  9.99
ATOM    527  C   ASP   327      47.352  63.310  76.815  1.00  9.99
ATOM    528  O   ASP   327      47.766  64.470  76.541  1.00  9.99
ATOM    529  OXT ASP   327      47.130  62.423  75.947  1.00  9.99
TER
END
