
#######################################################
#                                                     #
#                        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 (   42),  selected    6 , name T0320TS074_5-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected    6 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_5-D1.T0320_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       222 - 227         3.11     3.11
  LCS_AVERAGE:      2.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       222 - 225         0.99     4.14
  LONGEST_CONTINUOUS_SEGMENT:     4       224 - 227         1.77     5.22
  LCS_AVERAGE:      1.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       222 - 225         0.99     4.14
  LCS_AVERAGE:      1.71

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:  214
LCS_GDT     T     222     T     222      4    4    6     3    3    4    4    4    4    4    4    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     223     S     223      4    4    6     3    3    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     224     I     224      4    4    6     3    3    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     225     G     225      4    4    6     0    3    4    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     226     G     226      3    4    6     0    3    3    3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     227     I     227      3    4    6     0    3    3    3    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   2.13  (   1.71    1.87    2.80 )

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      4      4      4      4      5      5      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   1.40   1.40   1.87   1.87   1.87   1.87   2.34   2.34   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80   2.80
GDT RMS_LOCAL    0.03   0.03   0.99   0.99   0.99   0.99   2.47   2.47   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11
GDT RMS_ALL_CA   4.86   4.86   4.14   4.14   4.14   4.14   3.73   3.73   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11   3.11

#      Molecule1      Molecule2       DISTANCE
LGA    T     222      T     222          7.272
LGA    S     223      S     223          3.282
LGA    I     224      I     224          1.586
LGA    G     225      G     225          1.516
LGA    G     226      G     226          2.548
LGA    I     227      I     227          2.883

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  214    4.0      5    2.47     2.103     2.154     0.195

LGA_LOCAL      RMSD =  2.465  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.725  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.108  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.526043 * X  +   0.654115 * Y  +   0.543518 * Z  +  17.665915
  Y_new =   0.803019 * X  +   0.592491 * Y  +   0.064148 * Z  +  23.493919
  Z_new =  -0.280070 * X  +   0.470200 * Y  +  -0.836943 * Z  +   1.566568 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.629730   -0.511863  [ DEG:   150.6724    -29.3276 ]
  Theta =   0.283867    2.857726  [ DEG:    16.2644    163.7356 ]
  Phi   =   2.150736   -0.990857  [ DEG:   123.2281    -56.7719 ]
 
# 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: T0320TS074_5-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_5-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  214   4.0    5   2.47   2.154     3.11
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_5-D1
PFRMAT TS
TARGET T0320
MODEL  5
PARENT N/A
ATOM      1  N   THR   222      21.920  16.834   6.374  1.00  1.00
ATOM      2  CA  THR   222      22.752  17.223   7.507  1.00  1.00
ATOM      3  C   THR   222      21.990  18.156   8.435  1.00  1.00
ATOM      4  O   THR   222      21.080  18.865   8.010  1.00  1.00
ATOM      5  CB  THR   222      24.133  17.832   7.096  1.00  1.00
ATOM      6  OG1 THR   222      25.013  18.108   8.317  1.00  1.00
ATOM      7  CG2 THR   222      23.937  19.107   6.317  1.00  1.00
ATOM      8  N   SER   223      22.361  18.123   9.710  1.00  1.00
ATOM      9  CA  SER   223      21.764  18.969  10.739  1.00  1.00
ATOM     10  C   SER   223      22.056  20.440  10.496  1.00  1.00
ATOM     11  O   SER   223      23.007  20.783   9.777  1.00  1.00
ATOM     12  HN  SER   223      23.077  17.513  10.049  1.00  1.00
ATOM     13  CB  SER   223      22.315  18.592  12.114  1.00  1.00
ATOM     14  OG  SER   223      21.911  17.267  12.450  1.00  1.00
ATOM     15  N   ILE   224      21.235  21.293  11.118  1.00  1.00
ATOM     16  CA  ILE   224      21.444  22.754  11.141  1.00  1.00
ATOM     17  C   ILE   224      22.822  23.106  11.709  1.00  1.00
ATOM     18  O   ILE   224      23.486  24.005  11.212  1.00  1.00
ATOM     19  HN  ILE   224      20.420  20.991  11.612  1.00  1.00
ATOM     20  CB  ILE   224      20.356  23.447  11.966  1.00  1.00
ATOM     21  CG1 ILE   224      18.932  23.151  11.466  1.00  1.00
ATOM     22  CG2 ILE   224      20.708  24.939  12.025  1.00  1.00
ATOM     23  CD1 ILE   224      18.723  23.608  10.019  1.00  1.00
ATOM     24  N   GLY   225      23.225  22.377  12.750  1.00  1.00
ATOM     25  CA  GLY   225      24.534  22.487  13.381  1.00  1.00
ATOM     26  C   GLY   225      25.664  22.388  12.346  1.00  1.00
ATOM     27  O   GLY   225      26.538  23.259  12.276  1.00  1.00
ATOM     28  HN  GLY   225      22.629  21.692  13.167  1.00  1.00
ATOM     29  N   GLY   226      25.614  21.320  11.546  1.00  1.00
ATOM     30  CA  GLY   226      26.600  21.049  10.504  1.00  1.00
ATOM     31  C   GLY   226      26.557  22.058   9.367  1.00  1.00
ATOM     32  O   GLY   226      27.594  22.410   8.811  1.00  1.00
ATOM     33  HN  GLY   226      24.891  20.631  11.611  1.00  1.00
ATOM     34  N   ILE   227      25.361  22.507   9.003  1.00  1.00
ATOM     35  CA  ILE   227      25.220  23.536   7.979  1.00  1.00
ATOM     36  C   ILE   227      25.926  24.829   8.379  1.00  1.00
ATOM     37  O   ILE   227      26.649  25.404   7.559  1.00  1.00
ATOM     38  HN  ILE   227      24.491  22.191   9.385  1.00  1.00
ATOM     39  CB  ILE   227      23.733  23.788   7.606  1.00  1.00
ATOM     40  CG1 ILE   227      23.073  22.482   7.137  1.00  1.00
ATOM     41  CG2 ILE   227      23.726  24.949   6.614  1.00  1.00
ATOM     42  CD1 ILE   227      23.862  21.958   5.866  1.00  1.00
TER
END
