
#######################################################
#                                                     #
#                        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    6 (   51),  selected    6 , name T0321TS074_4-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected    6 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_4-D2.T0321_D2.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:     6        97 - 102         1.96     1.96
  LCS_AVERAGE:      4.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        97 - 102         1.96     1.96
  LCS_AVERAGE:      4.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        97 - 100         0.89     2.22
  LONGEST_CONTINUOUS_SEGMENT:     4        98 - 101         0.69     2.64
  LCS_AVERAGE:      2.59

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:  148
LCS_GDT     V      97     V      97      4    6    6     3    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I      98     I      98      4    6    6     3    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F      99     F      99      4    6    6     3    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     100     S     100      4    6    6     3    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     101     D     101      4    6    6     3    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     102     A     102      3    6    6     3    3    3    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.57  (   2.59    4.05    4.05 )

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      3      4      4      5      5      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.03   2.70   2.70   3.38   3.38   3.38   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05
GDT RMS_LOCAL    0.03   0.55   0.55   1.03   1.03   1.03   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96
GDT RMS_ALL_CA   3.02   2.77   2.77   2.52   2.52   2.52   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96   1.96

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      V      97          1.589
LGA    I      98      I      98          1.147
LGA    F      99      F      99          1.447
LGA    S     100      S     100          1.205
LGA    D     101      D     101          2.188
LGA    A     102      A     102          3.308

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  148    4.0      6    1.96     3.547     3.713     0.291

LGA_LOCAL      RMSD =  1.963  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.963  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  1.963  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.886176 * X  +  -0.453989 * Y  +  -0.092662 * Z  +   0.176485
  Y_new =  -0.282832 * X  +  -0.371597 * Y  +  -0.884264 * Z  +  42.350037
  Z_new =   0.367013 * X  +   0.809821 * Y  +  -0.457702 * Z  +  74.176399 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.085227   -1.056366  [ DEG:   119.4747    -60.5253 ]
  Theta =  -0.375796   -2.765796  [ DEG:   -21.5315   -158.4685 ]
  Phi   =  -0.308941    2.832652  [ DEG:   -17.7010    162.2990 ]
 
# 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: T0321TS074_4-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_4-D2.T0321_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  148   4.0    6   1.96   3.713     1.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_4-D2
PFRMAT TS
TARGET T0321
MODEL  4
PARENT N/A
ATOM    817  N   VAL    97      -2.720  42.412  79.932  1.00  1.00
ATOM    818  CA  VAL    97      -1.918  43.562  80.319  1.00  1.00
ATOM    819  C   VAL    97      -2.702  44.305  81.387  1.00  1.00
ATOM    820  O   VAL    97      -3.877  44.610  81.196  1.00  1.00
ATOM    821  HN  VAL    97      -3.664  42.638  79.688  1.00  1.00
ATOM    822  CB  VAL    97      -1.667  44.523  79.136  1.00  1.00
ATOM    823  CG1 VAL    97      -0.934  45.763  79.616  1.00  1.00
ATOM    824  CG2 VAL    97      -2.990  44.914  78.499  1.00  1.00
ATOM    825  N   ILE    98      -2.066  44.567  82.520  1.00  1.00
ATOM    826  CA  ILE    98      -2.728  45.298  83.592  1.00  1.00
ATOM    827  C   ILE    98      -2.014  46.628  83.774  1.00  1.00
ATOM    828  O   ILE    98      -0.791  46.724  83.639  1.00  1.00
ATOM    829  HN  ILE    98      -1.125  44.300  82.730  1.00  1.00
ATOM    830  CB  ILE    98      -2.691  44.523  84.909  1.00  1.00
ATOM    831  CG1 ILE    98      -3.412  42.846  84.905  1.00  1.00
ATOM    832  CG2 ILE    98      -3.315  45.420  85.986  1.00  1.00
ATOM    833  CD1 ILE    98      -4.698  42.991  84.559  1.00  1.00
ATOM    834  N   PHE    99      -2.794  47.657  84.072  1.00  1.00
ATOM    835  CA  PHE    99      -2.261  48.991  84.274  1.00  1.00
ATOM    836  C   PHE    99      -2.636  49.518  85.648  1.00  1.00
ATOM    837  O   PHE    99      -3.805  49.481  86.036  1.00  1.00
ATOM    838  HN  PHE    99      -3.786  47.596  84.178  1.00  1.00
ATOM    839  CB  PHE    99      -2.791  49.935  83.194  1.00  1.00
ATOM    840  CG  PHE    99      -2.309  49.565  81.806  1.00  1.00
ATOM    841  CD1 PHE    99      -1.054  50.039  81.371  1.00  1.00
ATOM    842  CD2 PHE    99      -3.176  49.085  80.839  1.00  1.00
ATOM    843  CE1 PHE    99      -0.680  49.882  80.051  1.00  1.00
ATOM    844  CE2 PHE    99      -2.827  48.896  79.528  1.00  1.00
ATOM    845  CZ  PHE    99      -1.524  49.296  79.127  1.00  1.00
ATOM    846  N   SER   100      -1.629  49.989  86.382  1.00  1.00
ATOM    847  CA  SER   100      -1.838  50.545  87.709  1.00  1.00
ATOM    848  C   SER   100      -1.510  52.032  87.693  1.00  1.00
ATOM    849  O   SER   100      -0.420  52.426  87.280  1.00  1.00
ATOM    850  HN  SER   100      -0.675  49.996  86.084  1.00  1.00
ATOM    851  CB  SER   100      -0.944  49.855  88.738  1.00  1.00
ATOM    852  OG  SER   100       0.520  50.032  88.463  1.00  1.00
ATOM    853  N   ASP   101      -2.453  52.851  88.149  1.00  1.00
ATOM    854  CA  ASP   101      -2.272  54.305  88.192  1.00  1.00
ATOM    855  C   ASP   101      -1.775  54.901  86.857  1.00  1.00
ATOM    856  O   ASP   101      -1.210  55.991  86.822  1.00  1.00
ATOM    857  HN  ASP   101      -3.341  52.541  88.491  1.00  1.00
ATOM    858  CB  ASP   101      -1.380  54.711  89.379  1.00  1.00
ATOM    859  CG  ASP   101      -1.215  56.226  89.519  1.00  1.00
ATOM    860  OD1 ASP   101      -1.737  56.974  88.767  1.00  1.00
ATOM    861  OD2 ASP   101      -0.444  56.519  90.480  1.00  1.00
ATOM    862  N   ALA   102      -2.044  54.205  85.745  1.00  1.00
ATOM    863  CA  ALA   102      -1.671  54.719  84.423  1.00  1.00
ATOM    864  C   ALA   102      -2.340  56.067  84.146  1.00  1.00
ATOM    865  O   ALA   102      -1.777  56.921  83.458  1.00  1.00
ATOM    866  HN  ALA   102      -2.502  53.316  85.721  1.00  1.00
ATOM    867  CB  ALA   102      -2.065  53.725  83.323  1.00  1.00
TER
END
