
#######################################################
#                                                     #
#                        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_3-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected    6 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_3-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         2.54     2.54
  LCS_AVERAGE:      4.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        97 - 101         0.92     3.24
  LCS_AVERAGE:      3.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        97 - 101         0.92     3.24
  LCS_AVERAGE:      3.15

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      5    5    6     3    4    4    5    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I      98     I      98      5    5    6     3    4    4    5    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F      99     F      99      5    5    6     3    3    4    5    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     100     S     100      5    5    6     3    4    4    5    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     101     D     101      5    5    6     3    4    4    5    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     102     A     102      3    3    6     3    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.45  (   3.15    3.15    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      5      5      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   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
GDT RMS_LOCAL    0.11   0.48   0.48   0.92   0.92   0.92   0.92   0.92   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54
GDT RMS_ALL_CA   9.27   3.37   3.37   3.24   3.24   3.24   3.24   3.24   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54   2.54

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      V      97          0.539
LGA    I      98      I      98          0.473
LGA    F      99      F      99          1.618
LGA    S     100      S     100          0.692
LGA    D     101      D     101          0.792
LGA    A     102      A     102          7.654

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  148    4.0      5    0.92     3.378     3.414     0.490

LGA_LOCAL      RMSD =  0.921  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.236  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.545  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.351300 * X  +  -0.801796 * Y  +  -0.483437 * Z  +   5.613091
  Y_new =  -0.677194 * X  +   0.574159 * Y  +  -0.460162 * Z  +  54.988659
  Z_new =   0.646526 * X  +   0.165726 * Y  +  -0.744674 * Z  +  72.757355 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.922613   -0.218980  [ DEG:   167.4534    -12.5466 ]
  Theta =  -0.703022   -2.438571  [ DEG:   -40.2802   -139.7198 ]
  Phi   =  -2.049338    1.092255  [ DEG:  -117.4184     62.5816 ]
 
# 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_3-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_3-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    5   0.92   3.414     2.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_3-D2
PFRMAT TS
TARGET T0321
MODEL  3
PARENT N/A
ATOM    817  N   VAL    97      -4.109  42.382  80.701  1.00  1.00
ATOM    818  CA  VAL    97      -2.977  43.294  80.559  1.00  1.00
ATOM    819  C   VAL    97      -2.936  44.096  81.854  1.00  1.00
ATOM    820  O   VAL    97      -3.905  44.762  82.206  1.00  1.00
ATOM    821  HN  VAL    97      -4.918  42.654  80.181  1.00  1.00
ATOM    822  CB  VAL    97      -3.187  44.268  79.393  1.00  1.00
ATOM    823  CG1 VAL    97      -3.351  43.604  78.051  1.00  1.00
ATOM    824  CG2 VAL    97      -2.058  45.244  79.187  1.00  1.00
ATOM    825  N   ILE    98      -1.819  44.036  82.593  1.00  1.00
ATOM    826  CA  ILE    98      -1.730  44.794  83.848  1.00  1.00
ATOM    827  C   ILE    98      -1.734  46.306  83.600  1.00  1.00
ATOM    828  O   ILE    98      -0.991  46.805  82.756  1.00  1.00
ATOM    829  HN  ILE    98      -0.998  43.508  82.378  1.00  1.00
ATOM    830  CB  ILE    98      -0.422  44.296  84.455  1.00  1.00
ATOM    831  CG1 ILE    98       0.599  44.713  83.434  1.00  1.00
ATOM    832  CG2 ILE    98      -0.602  42.808  84.786  1.00  1.00
ATOM    833  CD1 ILE    98       2.127  44.376  84.342  1.00  1.00
ATOM    834  N   PHE    99      -2.573  47.027  84.337  1.00  1.00
ATOM    835  CA  PHE    99      -2.679  48.477  84.184  1.00  1.00
ATOM    836  C   PHE    99      -2.375  49.170  85.507  1.00  1.00
ATOM    837  O   PHE    99      -3.124  49.040  86.475  1.00  1.00
ATOM    838  HN  PHE    99      -3.180  46.646  85.034  1.00  1.00
ATOM    839  CB  PHE    99      -4.093  48.877  83.729  1.00  1.00
ATOM    840  CG  PHE    99      -4.362  48.326  82.339  1.00  1.00
ATOM    841  CD1 PHE    99      -3.261  48.169  81.462  1.00  1.00
ATOM    842  CD2 PHE    99      -5.609  48.496  81.741  1.00  1.00
ATOM    843  CE1 PHE    99      -3.480  47.924  80.121  1.00  1.00
ATOM    844  CE2 PHE    99      -5.861  48.237  80.419  1.00  1.00
ATOM    845  CZ  PHE    99      -4.754  47.922  79.585  1.00  1.00
ATOM    846  N   SER   100      -1.284  49.927  85.534  1.00  1.00
ATOM    847  CA  SER   100      -0.863  50.629  86.751  1.00  1.00
ATOM    848  C   SER   100      -1.684  51.895  87.028  1.00  1.00
ATOM    849  O   SER   100      -1.605  52.452  88.122  1.00  1.00
ATOM    850  HN  SER   100      -0.680  50.075  84.751  1.00  1.00
ATOM    851  CB  SER   100       0.628  50.989  86.669  1.00  1.00
ATOM    852  OG  SER   100       0.887  51.869  85.586  1.00  1.00
ATOM    853  N   ASP   101      -2.444  52.358  86.034  1.00  1.00
ATOM    854  CA  ASP   101      -3.391  53.479  86.204  1.00  1.00
ATOM    855  C   ASP   101      -4.816  53.038  86.599  1.00  1.00
ATOM    856  O   ASP   101      -5.707  53.884  86.726  1.00  1.00
ATOM    857  HN  ASP   101      -2.425  51.977  85.110  1.00  1.00
ATOM    858  CB  ASP   101      -3.465  54.328  84.918  1.00  1.00
ATOM    859  CG  ASP   101      -3.979  53.536  83.709  1.00  1.00
ATOM    860  OD1 ASP   101      -4.766  52.603  83.835  1.00  1.00
ATOM    861  OD2 ASP   101      -3.509  53.786  82.596  1.00  1.00
ATOM    862  N   ALA   102      -5.033  51.733  86.776  1.00  1.00
ATOM    863  CA  ALA   102      -6.336  51.217  87.204  1.00  1.00
ATOM    864  C   ALA   102      -6.740  51.893  88.500  1.00  1.00
ATOM    865  O   ALA   102      -5.923  52.014  89.413  1.00  1.00
ATOM    866  HN  ALA   102      -4.342  51.024  86.632  1.00  1.00
ATOM    867  CB  ALA   102      -6.288  49.708  87.395  1.00  1.00
TER
END
