
#######################################################
#                                                     #
#                        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    3 (   23),  selected    3 , name T0320TS550_1_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected    3 , name T0320_D2.pdb
# PARAMETERS: T0320TS550_1_1-D2.T0320_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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       228 - 230         0.22     0.22
  LCS_AVERAGE:      4.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       228 - 230         0.22     0.22
  LCS_AVERAGE:      4.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       228 - 230         0.22     0.22
  LCS_AVERAGE:      4.11

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:   73
LCS_GDT     N     228     N     228      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     N     229     N     229      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     S     230     S     230      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   4.11  (   4.11    4.11    4.11 )

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      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11
GDT RMS_LOCAL    0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22
GDT RMS_ALL_CA   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22   0.22

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          0.203
LGA    N     229      N     229          0.253
LGA    S     230      S     230          0.198

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3   73    4.0      3    0.22     4.110     4.110     0.939

LGA_LOCAL      RMSD =  0.219  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.219  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.219  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.024748 * X  +  -0.888225 * Y  +   0.458742 * Z  +  77.126892
  Y_new =  -0.826614 * X  +  -0.276256 * Y  +  -0.490297 * Z  +  71.768578
  Z_new =   0.562224 * X  +  -0.367069 * Y  +  -0.741056 * Z  +  62.189419 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.681686    0.459907  [ DEG:  -153.6493     26.3507 ]
  Theta =  -0.597073   -2.544519  [ DEG:   -34.2098   -145.7902 ]
  Phi   =  -1.540866    1.600726  [ DEG:   -88.2851     91.7149 ]
 
# 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: T0320TS550_1_1-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS550_1_1-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3   73   4.0    3   0.22   4.110     0.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS550_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 1zun_A
ATOM   1865  N   ASN   228      31.333  21.115   5.460  1.00  0.00
ATOM   1866  CA  ASN   228      30.485  21.414   6.572  1.00  0.00
ATOM   1867  CB  ASN   228      29.527  22.590   6.325  1.00  0.00
ATOM   1868  CG  ASN   228      30.357  23.863   6.239  1.00  0.00
ATOM   1869  OD1 ASN   228      31.555  23.863   6.520  1.00  0.00
ATOM   1870  ND2 ASN   228      29.700  24.988   5.848  1.00  0.00
ATOM   1871  C   ASN   228      29.648  20.211   6.849  1.00  0.00
ATOM   1872  O   ASN   228      29.237  19.495   5.937  1.00  0.00
ATOM   1873  N   ASN   229      29.399  19.946   8.146  1.00  0.00
ATOM   1874  CA  ASN   229      28.583  18.833   8.516  1.00  0.00
ATOM   1875  CB  ASN   229      28.810  18.351   9.959  1.00  0.00
ATOM   1876  CG  ASN   229      27.921  17.140  10.212  1.00  0.00
ATOM   1877  OD1 ASN   229      26.923  17.226  10.923  1.00  0.00
ATOM   1878  ND2 ASN   229      28.290  15.978   9.605  1.00  0.00
ATOM   1879  C   ASN   229      27.163  19.271   8.395  1.00  0.00
ATOM   1880  O   ASN   229      26.855  20.458   8.499  1.00  0.00
ATOM   1881  N   SER   230      26.257  18.311   8.142  1.00  0.00
ATOM   1882  CA  SER   230      24.872  18.642   8.028  1.00  0.00
ATOM   1883  CB  SER   230      24.018  17.489   7.471  1.00  0.00
ATOM   1884  OG  SER   230      24.048  16.382   8.361  1.00  0.00
ATOM   1885  C   SER   230      24.382  18.945   9.440  1.00  0.00
ATOM   1886  O   SER   230      23.914  20.092   9.674  1.00  0.00
ATOM   1887  OXT SER   230      24.469  18.032  10.305  1.00  0.00
TER
END
