
#######################################################
#                                                     #
#                        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    5 (   39),  selected    5 , name T0378TS186_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected    5 , name T0378_D1.pdb
# PARAMETERS: T0378TS186_3-D1.T0378_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:     5        85 - 89          3.01     3.01
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 87          0.78     6.01
  LONGEST_CONTINUOUS_SEGMENT:     3        86 - 88          0.60     4.50
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.79     4.89
  LCS_AVERAGE:      3.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3        85 - 87          0.78     6.01
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.79     4.89
  LCS_AVERAGE:      3.37

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:   89
LCS_GDT     M      85     M      85      3    3    5     0    3    3    3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A      86     A      86      3    3    5     0    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     V      87     V      87      3    3    5     0    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F      88     F      88      3    3    5     0    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D      89     D      89      3    3    5     0    3    3    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   4.12  (   3.37    3.37    5.62 )

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      0      3      3      3      3      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   0.00   3.37   3.37   3.37   3.37   4.49   4.49   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62
GDT RMS_LOCAL  1000.00   0.60   0.60   0.60   0.60   2.18   2.18   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01
GDT RMS_ALL_CA 1000.00   4.50   4.50   4.50   4.50   3.77   3.77   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01   3.01

#      Molecule1      Molecule2       DISTANCE
LGA    M      85      M      85          3.790
LGA    A      86      A      86          3.370
LGA    V      87      V      87          1.881
LGA    F      88      F      88          2.071
LGA    D      89      D      89          3.438

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   89    4.0      5    3.01     4.494     4.273     0.161

LGA_LOCAL      RMSD =  3.012  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.012  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  3.012  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.423974 * X  +   0.880022 * Y  +   0.214027 * Z  +  22.429428
  Y_new =   0.289965 * X  +   0.355776 * Y  +  -0.888450 * Z  +  18.022087
  Z_new =  -0.858001 * X  +  -0.314619 * Y  +  -0.406016 * Z  +  83.889206 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.482349    0.659244  [ DEG:  -142.2281     37.7719 ]
  Theta =   1.031365    2.110227  [ DEG:    59.0929    120.9071 ]
  Phi   =   2.541739   -0.599854  [ DEG:   145.6309    -34.3691 ]
 
# 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: T0378TS186_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS186_3-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   89   4.0    5   3.01   4.273     3.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS186_3-D1
PFRMAT TS
TARGET T0378
MODEL  3
PARENT 1v2x_A
ATOM      1  N   MET    85       4.162  21.160  48.901  1.00  0.00
ATOM      2  CA  MET    85       5.317  20.382  48.357  1.00  0.00
ATOM      3  C   MET    85       6.636  20.723  49.042  1.00  0.00
ATOM      4  O   MET    85       7.401  19.827  49.403  1.00  0.00
ATOM      5  CB  MET    85       5.466  20.625  46.854  1.00  0.00
ATOM      6  CG  MET    85       6.709  19.976  46.259  1.00  0.00
ATOM      7  SD  MET    85       7.065  20.515  44.575  1.00  0.00
ATOM      8  CE  MET    85       6.568  19.057  43.629  1.00  0.00
ATOM      9  N   ALA    86       6.915  22.013  49.207  1.00  0.00
ATOM     10  CA  ALA    86       8.159  22.409  49.850  1.00  0.00
ATOM     11  C   ALA    86       7.977  22.360  51.366  1.00  0.00
ATOM     12  O   ALA    86       8.943  22.310  52.122  1.00  0.00
ATOM     13  CB  ALA    86       8.543  23.822  49.438  1.00  0.00
ATOM     14  N   VAL    87       6.731  22.365  51.815  1.00  0.00
ATOM     15  CA  VAL    87       6.462  22.291  53.243  1.00  0.00
ATOM     16  C   VAL    87       6.803  20.851  53.650  1.00  0.00
ATOM     17  O   VAL    87       7.325  20.578  54.735  1.00  0.00
ATOM     18  CB  VAL    87       4.988  22.606  53.557  1.00  0.00
ATOM     19  CG1 VAL    87       4.687  22.338  55.024  1.00  0.00
ATOM     20  CG2 VAL    87       4.680  24.065  53.262  1.00  0.00
ATOM     21  N   PHE    88       6.513  19.941  52.729  1.00  0.00
ATOM     22  CA  PHE    88       6.803  18.359  52.900  1.00  0.00
ATOM     23  C   PHE    88       8.276  17.988  52.912  1.00  0.00
ATOM     24  O   PHE    88       8.641  16.849  52.619  1.00  0.00
ATOM     25  CB  PHE    88       6.170  17.571  51.751  1.00  0.00
ATOM     26  CG  PHE    88       4.668  17.562  51.777  1.00  0.00
ATOM     27  CD1 PHE    88       3.942  18.419  50.969  1.00  0.00
ATOM     28  CD2 PHE    88       3.982  16.696  52.611  1.00  0.00
ATOM     29  CE1 PHE    88       2.560  18.410  50.994  1.00  0.00
ATOM     30  CE2 PHE    88       2.600  16.688  52.635  1.00  0.00
ATOM     31  CZ  PHE    88       1.889  17.540  51.832  1.00  0.00
ATOM     32  N   ASP    89       8.916  18.713  53.168  1.00  0.00
ATOM     33  CA  ASP    89      10.317  18.467  53.209  1.00  0.00
ATOM     34  C   ASP    89      10.727  17.657  54.428  1.00  0.00
ATOM     35  O   ASP    89      10.150  17.808  55.506  1.00  0.00
ATOM     36  CB  ASP    89      11.092  19.786  53.252  1.00  0.00
ATOM     37  CG  ASP    89      11.048  20.531  51.933  1.00  0.00
ATOM     38  OD1 ASP    89      10.623  19.929  50.925  1.00  0.00
ATOM     39  OD2 ASP    89      11.439  21.717  51.908  1.00  0.00
TER
END
