
#######################################################
#                                                     #
#                        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 (   53),  selected    6 , name T0347TS671_5-D1
# Molecule2: number of CA atoms   89 (  730),  selected    6 , name T0347_D1.pdb
# PARAMETERS: T0347TS671_5-D1.T0347_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:     6       103 - 108         3.99     3.99
  LCS_AVERAGE:      6.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       103 - 106         1.49     6.19
  LONGEST_CONTINUOUS_SEGMENT:     4       105 - 108         0.48     5.48
  LCS_AVERAGE:      4.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       105 - 108         0.48     5.48
  LCS_AVERAGE:      4.12

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     103     M     103      3    4    6     3    3    3    3    4    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     104     D     104      3    4    6     3    3    3    3    4    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     H     105     H     105      4    4    6     3    4    4    4    4    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     R     106     R     106      4    4    6     3    4    4    4    4    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     N     107     N     107      4    4    6     3    4    4    4    4    4    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     L     108     L     108      4    4    6     3    4    4    4    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   5.12  (   4.12    4.49    6.74 )

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      4      4      4      4      5      5      5      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   3.37   4.49   4.49   4.49   4.49   4.49   4.49   5.62   5.62   5.62   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74   6.74
GDT RMS_LOCAL    0.25   0.48   0.48   0.48   0.48   0.48   0.48   2.84   2.61   2.61   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99
GDT RMS_ALL_CA   5.48   5.48   5.48   5.48   5.48   5.48   5.48   4.70   4.59   4.59   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99   3.99

#      Molecule1      Molecule2       DISTANCE
LGA    M     103      M     103          2.411
LGA    D     104      D     104          2.436
LGA    H     105      H     105          1.536
LGA    R     106      R     106          3.499
LGA    N     107      N     107          3.740
LGA    L     108      L     108          9.610

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   89    4.0      5    2.84     5.337     5.101     0.170

LGA_LOCAL      RMSD =  2.840  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.703  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.986  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.760919 * X  +   0.376490 * Y  +   0.528449 * Z  +  25.321676
  Y_new =   0.591361 * X  +   0.737557 * Y  +   0.326039 * Z  +  36.860371
  Z_new =  -0.267011 * X  +   0.560593 * Y  +  -0.783862 * Z  +  44.213249 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.520759   -0.620833  [ DEG:   144.4289    -35.5711 ]
  Theta =   0.270290    2.871302  [ DEG:    15.4865    164.5135 ]
  Phi   =   2.480930   -0.660663  [ DEG:   142.1468    -37.8532 ]
 
# 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: T0347TS671_5-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347TS671_5-D1.T0347_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   89   4.0    5   2.84   5.101     3.99
REMARK  ---------------------------------------------------------- 
MOLECULE T0347TS671_5-D1
PFRMAT TS
TARGET T0347
MODEL  5  REFINED
PARENT 1VZ0_A
ATOM      1  N   MET   103       3.275  32.756   7.536  1.00  0.00
ATOM      2  CA  MET   103       3.280  34.188   7.181  1.00  0.00
ATOM      3  C   MET   103       3.646  35.162   8.354  1.00  0.00
ATOM      4  O   MET   103       3.659  36.378   8.090  1.00  0.00
ATOM      5  CB  MET   103       1.850  34.509   6.723  1.00  0.00
ATOM      6  CG  MET   103       1.581  34.056   5.316  1.00  0.00
ATOM      7  SD  MET   103      -0.147  34.361   4.879  1.00  0.00
ATOM      8  CE  MET   103      -0.408  32.783   4.190  1.00  0.00
ATOM      9  N   ASP   104       3.977  34.692   9.543  1.00  0.00
ATOM     10  CA  ASP   104       4.272  35.619  10.630  1.00  0.00
ATOM     11  C   ASP   104       5.788  35.674  11.031  1.00  0.00
ATOM     12  O   ASP   104       6.097  36.430  11.968  1.00  0.00
ATOM     13  CB  ASP   104       3.439  35.146  11.809  1.00  0.00
ATOM     14  CG  ASP   104       2.328  36.091  12.222  1.00  0.00
ATOM     15  OD1 ASP   104       1.814  35.961  13.358  1.00  0.00
ATOM     16  OD2 ASP   104       1.939  36.943  11.381  1.00  0.00
ATOM     17  N   HIS   105       6.696  35.238  10.164  1.00  0.00
ATOM     18  CA  HIS   105       8.065  35.169  10.445  1.00  0.00
ATOM     19  C   HIS   105       8.903  36.223   9.681  1.00  0.00
ATOM     20  O   HIS   105       8.951  36.245   8.443  1.00  0.00
ATOM     21  CB  HIS   105       8.516  33.788   9.929  1.00  0.00
ATOM     22  CG  HIS   105       8.321  32.739  11.011  1.00  0.00
ATOM     23  ND1 HIS   105       7.290  31.876  11.219  1.00  0.00
ATOM     24  CD2 HIS   105       9.214  32.564  12.014  1.00  0.00
ATOM     25  CE1 HIS   105       7.573  31.256  12.328  1.00  0.00
ATOM     26  NE2 HIS   105       8.698  31.645  12.779  1.00  0.00
ATOM     27  N   ARG   106       9.798  36.789  10.459  1.00  0.00
ATOM     28  CA  ARG   106      10.791  37.744  10.023  1.00  0.00
ATOM     29  C   ARG   106      11.994  36.858   9.554  1.00  0.00
ATOM     30  O   ARG   106      12.240  35.780  10.149  1.00  0.00
ATOM     31  CB  ARG   106      11.175  38.521  11.283  1.00  0.00
ATOM     32  CG  ARG   106      12.066  39.728  10.999  1.00  0.00
ATOM     33  CD  ARG   106      12.066  40.577  12.256  1.00  0.00
ATOM     34  NE  ARG   106      10.762  41.200  12.405  1.00  0.00
ATOM     35  CZ  ARG   106      10.498  42.103  13.353  1.00  0.00
ATOM     36  NH1 ARG   106      11.413  42.499  14.250  1.00  0.00
ATOM     37  NH2 ARG   106       9.279  42.641  13.374  1.00  0.00
ATOM     38  N   ASN   107      12.709  37.165   8.444  1.00  0.00
ATOM     39  CA  ASN   107      13.874  36.423   7.958  1.00  0.00
ATOM     40  C   ASN   107      14.734  36.002   9.199  1.00  0.00
ATOM     41  O   ASN   107      15.335  34.946   9.109  1.00  0.00
ATOM     42  CB  ASN   107      14.654  37.367   7.001  1.00  0.00
ATOM     43  CG  ASN   107      15.821  36.682   6.338  1.00  0.00
ATOM     44  OD1 ASN   107      16.902  36.472   6.915  1.00  0.00
ATOM     45  ND2 ASN   107      15.688  36.496   5.070  1.00  0.00
ATOM     46  N   LEU   108      14.907  36.818  10.189  1.00  0.00
ATOM     47  CA  LEU   108      15.659  36.520  11.403  1.00  0.00
ATOM     48  C   LEU   108      15.363  35.051  11.990  1.00  0.00
ATOM     49  O   LEU   108      16.328  34.262  12.046  1.00  0.00
ATOM     50  CB  LEU   108      15.201  37.562  12.442  1.00  0.00
ATOM     51  CG  LEU   108      15.321  39.041  12.131  1.00  0.00
ATOM     52  CD1 LEU   108      14.926  39.886  13.370  1.00  0.00
ATOM     53  CD2 LEU   108      16.782  39.382  11.718  1.00  0.00
TER
END
