
#######################################################
#                                                     #
#                        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_4_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected   14 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_4_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         3.28     3.28
  LCS_AVERAGE:     11.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       314 - 325         1.44     3.57
  LCS_AVERAGE:      8.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       315 - 323         0.92     4.92
  LCS_AVERAGE:      6.05

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      8   12   14     3    4    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     A     315     A     315      9   12   14     5    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     I     316     I     316      9   12   14     5    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     Y     317     Y     317      9   12   14     5    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     H     318     H     318      9   12   14     3    6    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     S     319     S     319      9   12   14     4    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     T     320     T     320      9   12   14     5    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     Y     321     Y     321      9   12   14     5    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     T     322     T     322      9   12   14     3    5    9   10   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     G     323     G     323      9   12   14     3    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     R     324     R     324      4   12   14     3    3    8   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     P     325     P     325      4   12   14     3    7    9   11   12   12   12   12   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     P     326     P     326      4    4   14     1    3    4    4    4    7    9   10   12   13   13   13   13   13   13   13   14   14   14   14 
LCS_GDT     D     327     D     327      4    4   14     0    3    4    4    4    5    5    5    5    5    6    6    6    8    9   11   14   14   14   14 
LCS_AVERAGE  LCS_A:   8.70  (   6.05    8.76   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      5      7      9     11     12     12     12     12     12     13     13     13     13     13     13     13     14     14     14     14 
GDT PERCENT_CA   4.03   5.65   7.26   8.87   9.68   9.68   9.68   9.68   9.68  10.48  10.48  10.48  10.48  10.48  10.48  10.48  11.29  11.29  11.29  11.29
GDT RMS_LOCAL    0.32   0.50   0.92   1.30   1.44   1.44   1.44   1.44   1.44   2.24   2.24   2.24   2.24   2.24   2.24   2.24   3.28   3.28   3.28   3.28
GDT RMS_ALL_CA   4.23   4.10   4.92   3.52   3.57   3.57   3.57   3.57   3.57   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.28   3.28   3.28   3.28

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          1.708
LGA    A     315      A     315          0.328
LGA    I     316      I     316          0.872
LGA    Y     317      Y     317          1.614
LGA    H     318      H     318          1.858
LGA    S     319      S     319          1.143
LGA    T     320      T     320          0.508
LGA    Y     321      Y     321          1.120
LGA    T     322      T     322          2.339
LGA    G     323      G     323          0.733
LGA    R     324      R     324          1.991
LGA    P     325      P     325          1.527
LGA    P     326      P     326          7.211
LGA    D     327      D     327         10.054

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  124    4.0     12    1.44     8.669     9.107     0.778

LGA_LOCAL      RMSD =  1.442  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.566  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  3.277  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.906369 * X  +   0.122390 * Y  +  -0.404371 * Z  +  75.678749
  Y_new =   0.422459 * X  +   0.273416 * Y  +  -0.864160 * Z  +  62.736275
  Z_new =   0.004797 * X  +  -0.954078 * Y  +  -0.299521 * Z  +  90.743500 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.874990    1.266603  [ DEG:  -107.4290     72.5710 ]
  Theta =  -0.004797   -3.136796  [ DEG:    -0.2748   -179.7252 ]
  Phi   =   2.705430   -0.436162  [ DEG:   155.0097    -24.9903 ]
 
# 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_4_3-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_4_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   12   1.44   9.107     3.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_4_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0356
PARENT 2gm2_A
ATOM    417  N   ASP   314      74.740  75.940  97.391  1.00  9.99
ATOM    418  CA  ASP   314      75.468  74.758  97.037  1.00  9.99
ATOM    419  CB  ASP   314      74.792  73.429  97.436  1.00  9.99
ATOM    420  CG  ASP   314      74.962  73.154  98.913  1.00  9.99
ATOM    421  OD1 ASP   314      76.014  73.561  99.471  1.00  9.99
ATOM    422  OD2 ASP   314      74.043  72.527  99.503  1.00  9.99
ATOM    423  C   ASP   314      75.525  74.634  95.557  1.00  9.99
ATOM    424  O   ASP   314      75.010  75.457  94.801  1.00  9.99
ATOM    425  N   ALA   315      76.222  73.571  95.119  1.00  9.99
ATOM    426  CA  ALA   315      76.159  73.186  93.753  1.00  9.99
ATOM    427  CB  ALA   315      77.424  72.475  93.245  1.00  9.99
ATOM    428  C   ALA   315      75.052  72.189  93.812  1.00  9.99
ATOM    429  O   ALA   315      75.138  71.184  94.516  1.00  9.99
ATOM    430  N   ILE   316      73.948  72.459  93.108  1.00  9.99
ATOM    431  CA  ILE   316      72.864  71.546  93.242  1.00  9.99
ATOM    432  CB  ILE   316      71.638  72.179  93.835  1.00  9.99
ATOM    433  CG2 ILE   316      70.524  71.122  93.878  1.00  9.99
ATOM    434  CG1 ILE   316      71.974  72.753  95.222  1.00  9.99
ATOM    435  CD1 ILE   316      70.886  73.660  95.792  1.00  9.99
ATOM    436  C   ILE   316      72.543  71.047  91.879  1.00  9.99
ATOM    437  O   ILE   316      72.544  71.789  90.899  1.00  9.99
ATOM    438  N   TYR   317      72.318  69.736  91.755  1.00  9.99
ATOM    439  CA  TYR   317      71.957  69.321  90.447  1.00  9.99
ATOM    440  CB  TYR   317      73.017  68.449  89.769  1.00  9.99
ATOM    441  CG  TYR   317      74.053  69.445  89.373  1.00  9.99
ATOM    442  CD1 TYR   317      74.986  69.923  90.264  1.00  9.99
ATOM    443  CD2 TYR   317      74.061  69.924  88.086  1.00  9.99
ATOM    444  CE1 TYR   317      75.922  70.851  89.863  1.00  9.99
ATOM    445  CE2 TYR   317      74.993  70.848  87.680  1.00  9.99
ATOM    446  CZ  TYR   317      75.928  71.315  88.570  1.00  9.99
ATOM    447  OH  TYR   317      76.885  72.265  88.155  1.00  9.99
ATOM    448  C   TYR   317      70.663  68.632  90.557  1.00  9.99
ATOM    449  O   TYR   317      70.544  67.679  91.312  1.00  9.99
ATOM    450  N   HIS   318      69.640  69.112  89.833  1.00  9.99
ATOM    451  CA  HIS   318      68.368  68.482  90.004  1.00  9.99
ATOM    452  ND1 HIS   318      65.719  67.723  91.616  1.00  9.99
ATOM    453  CG  HIS   318      65.953  68.786  90.773  1.00  9.99
ATOM    454  CB  HIS   318      67.294  69.431  90.575  1.00  9.99
ATOM    455  NE2 HIS   318      63.773  68.215  90.660  1.00  9.99
ATOM    456  CD2 HIS   318      64.752  69.076  90.199  1.00  9.99
ATOM    457  CE1 HIS   318      64.400  67.421  91.509  1.00  9.99
ATOM    458  C   HIS   318      67.887  67.981  88.693  1.00  9.99
ATOM    459  O   HIS   318      67.654  68.767  87.791  1.00  9.99
ATOM    460  N   SER   319      67.706  66.660  88.525  1.00  9.99
ATOM    461  CA  SER   319      67.187  66.247  87.245  1.00  9.99
ATOM    462  CB  SER   319      68.053  65.194  86.535  1.00  9.99
ATOM    463  OG  SER   319      69.316  65.756  86.211  1.00  9.99
ATOM    464  C   SER   319      65.853  65.642  87.503  1.00  9.99
ATOM    465  O   SER   319      65.710  64.856  88.425  1.00  9.99
ATOM    466  N   THR   320      64.815  65.965  86.712  1.00  9.99
ATOM    467  CA  THR   320      63.556  65.387  87.090  1.00  9.99
ATOM    468  CB  THR   320      62.490  66.429  87.253  1.00  9.99
ATOM    469  OG1 THR   320      62.908  67.385  88.214  1.00  9.99
ATOM    470  CG2 THR   320      61.184  65.758  87.712  1.00  9.99
ATOM    471  C   THR   320      63.120  64.445  86.022  1.00  9.99
ATOM    472  O   THR   320      63.165  64.786  84.851  1.00  9.99
ATOM    473  N   TYR   321      62.699  63.213  86.361  1.00  9.99
ATOM    474  CA  TYR   321      62.237  62.399  85.271  1.00  9.99
ATOM    475  CB  TYR   321      63.027  61.086  85.090  1.00  9.99
ATOM    476  CG  TYR   321      62.689  60.545  83.739  1.00  9.99
ATOM    477  CD1 TYR   321      63.290  61.079  82.620  1.00  9.99
ATOM    478  CD2 TYR   321      61.797  59.510  83.577  1.00  9.99
ATOM    479  CE1 TYR   321      62.997  60.603  81.364  1.00  9.99
ATOM    480  CE2 TYR   321      61.499  59.028  82.322  1.00  9.99
ATOM    481  CZ  TYR   321      62.099  59.576  81.213  1.00  9.99
ATOM    482  OH  TYR   321      61.794  59.082  79.926  1.00  9.99
ATOM    483  C   TYR   321      60.811  62.059  85.591  1.00  9.99
ATOM    484  O   TYR   321      60.524  61.491  86.644  1.00  9.99
ATOM    485  N   THR   322      59.866  62.404  84.688  1.00  9.99
ATOM    486  CA  THR   322      58.482  62.157  84.991  1.00  9.99
ATOM    487  CB  THR   322      57.629  63.392  84.926  1.00  9.99
ATOM    488  OG1 THR   322      58.127  64.381  85.816  1.00  9.99
ATOM    489  CG2 THR   322      56.189  63.014  85.320  1.00  9.99
ATOM    490  C   THR   322      57.921  61.165  84.011  1.00  9.99
ATOM    491  O   THR   322      58.111  61.281  82.802  1.00  9.99
ATOM    492  N   GLY   323      57.234  60.143  84.566  1.00  9.99
ATOM    493  CA  GLY   323      56.569  59.025  83.943  1.00  9.99
ATOM    494  C   GLY   323      55.312  59.413  83.220  1.00  9.99
ATOM    495  O   GLY   323      54.884  58.719  82.300  1.00  9.99
ATOM    496  N   ARG   324      54.677  60.518  83.644  1.00  9.99
ATOM    497  CA  ARG   324      53.372  60.971  83.231  1.00  9.99
ATOM    498  CB  ARG   324      52.948  62.286  83.909  1.00  9.99
ATOM    499  CG  ARG   324      52.830  62.190  85.433  1.00  9.99
ATOM    500  CD  ARG   324      52.066  63.360  86.063  1.00  9.99
ATOM    501  NE  ARG   324      52.231  63.278  87.545  1.00  9.99
ATOM    502  CZ  ARG   324      51.424  64.016  88.361  1.00  9.99
ATOM    503  NH1 ARG   324      50.369  64.709  87.842  1.00  9.99
ATOM    504  NH2 ARG   324      51.692  64.088  89.698  1.00  9.99
ATOM    505  C   ARG   324      53.213  61.199  81.752  1.00  9.99
ATOM    506  O   ARG   324      52.071  61.114  81.304  1.00  9.99
ATOM    507  N   PRO   325      54.192  61.484  80.934  1.00  9.99
ATOM    508  CA  PRO   325      53.896  61.826  79.569  1.00  9.99
ATOM    509  CD  PRO   325      55.450  62.083  81.362  1.00  9.99
ATOM    510  CB  PRO   325      55.241  62.171  78.941  1.00  9.99
ATOM    511  CG  PRO   325      56.039  62.762  80.117  1.00  9.99
ATOM    512  C   PRO   325      53.063  60.874  78.765  1.00  9.99
ATOM    513  O   PRO   325      52.495  61.348  77.782  1.00  9.99
ATOM    514  N   PRO   326      52.944  59.613  79.058  1.00  9.99
ATOM    515  CA  PRO   326      52.071  58.818  78.245  1.00  9.99
ATOM    516  CD  PRO   326      54.048  58.837  79.597  1.00  9.99
ATOM    517  CB  PRO   326      52.348  57.374  78.643  1.00  9.99
ATOM    518  CG  PRO   326      53.826  57.405  79.077  1.00  9.99
ATOM    519  C   PRO   326      50.671  59.277  78.476  1.00  9.99
ATOM    520  O   PRO   326      50.351  59.669  79.597  1.00  9.99
ATOM    521  N   ASP   327      49.820  59.253  77.433  1.00  9.99
ATOM    522  CA  ASP   327      48.483  59.725  77.626  1.00  9.99
ATOM    523  CB  ASP   327      48.168  60.974  76.789  1.00  9.99
ATOM    524  CG  ASP   327      46.897  61.598  77.339  1.00  9.99
ATOM    525  OD1 ASP   327      46.407  61.099  78.387  1.00  9.99
ATOM    526  OD2 ASP   327      46.406  62.585  76.730  1.00  9.99
ATOM    527  C   ASP   327      47.524  58.628  77.178  1.00  9.99
ATOM    528  O   ASP   327      46.600  58.947  76.382  1.00  9.99
ATOM    529  OXT ASP   327      47.700  57.464  77.624  1.00  9.99
TER
END
