
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected    6 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_3-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         3.02     3.02
  LCS_AVERAGE:      2.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       223 - 226         1.94     3.86
  LONGEST_CONTINUOUS_SEGMENT:     4       224 - 227         1.83     3.99
  LCS_AVERAGE:      1.79

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       222 - 224         0.87     7.02
  LONGEST_CONTINUOUS_SEGMENT:     3       223 - 225         0.65     4.49
  LONGEST_CONTINUOUS_SEGMENT:     3       224 - 226         0.72     4.47
  LONGEST_CONTINUOUS_SEGMENT:     3       225 - 227         0.85     6.87
  LCS_AVERAGE:      1.40

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      3    3    6     0    3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     223     S     223      3    4    6     0    3    3    3    3    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     224     I     224      3    4    6     0    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     225     G     225      3    4    6     0    3    3    3    4    5    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    5    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    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   2.00  (   1.40    1.79    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      0      3      3      3      4      5      5      5      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   0.00   1.40   1.40   1.40   1.87   2.34   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  1000.00   0.65   0.65   0.65   1.83   2.32   2.32   2.32   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02
GDT RMS_ALL_CA 1000.00   4.49   4.49   4.49   3.99   3.52   3.52   3.52   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02   3.02

#      Molecule1      Molecule2       DISTANCE
LGA    T     222      T     222          6.892
LGA    S     223      S     223          2.852
LGA    I     224      I     224          1.586
LGA    G     225      G     225          1.499
LGA    G     226      G     226          2.648
LGA    I     227      I     227          2.651

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  214    4.0      5    2.32     1.986     2.096     0.207

LGA_LOCAL      RMSD =  2.321  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.522  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.023  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.234526 * X  +  -0.901276 * Y  +  -0.364279 * Z  +  23.842052
  Y_new =   0.044863 * X  +  -0.384366 * Y  +   0.922090 * Z  +  30.890272
  Z_new =  -0.971074 * X  +   0.199911 * Y  +   0.130578 * Z  +  17.602190 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.992189   -2.149404  [ DEG:    56.8482   -123.1518 ]
  Theta =   1.329689    1.811904  [ DEG:    76.1856    103.8144 ]
  Phi   =   2.952582   -0.189010  [ DEG:   169.1705    -10.8295 ]
 
# 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_3-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_3-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   2.32   2.096     3.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_3-D1
PFRMAT TS
TARGET T0320
MODEL  3
PARENT N/A
ATOM      1  N   THR   222      21.353  19.470  15.894  1.00  1.00
ATOM      2  CA  THR   222      20.546  19.338  14.689  1.00  1.00
ATOM      3  C   THR   222      21.385  19.306  13.426  1.00  1.00
ATOM      4  O   THR   222      22.565  19.634  13.448  1.00  1.00
ATOM      5  CB  THR   222      19.540  20.499  14.566  1.00  1.00
ATOM      6  OG1 THR   222      20.252  21.738  14.463  1.00  1.00
ATOM      7  CG2 THR   222      18.627  20.542  15.783  1.00  1.00
ATOM      8  N   SER   223      20.760  18.913  12.323  1.00  1.00
ATOM      9  CA  SER   223      21.452  18.849  11.050  1.00  1.00
ATOM     10  C   SER   223      21.891  20.263  10.694  1.00  1.00
ATOM     11  O   SER   223      22.856  20.462   9.955  1.00  1.00
ATOM     12  HN  SER   223      19.800  18.638  12.278  1.00  1.00
ATOM     13  CB  SER   223      20.526  18.292   9.965  1.00  1.00
ATOM     14  OG  SER   223      19.401  19.138   9.773  1.00  1.00
ATOM     15  N   ILE   224      21.182  21.245  11.239  1.00  1.00
ATOM     16  CA  ILE   224      21.507  22.640  10.994  1.00  1.00
ATOM     17  C   ILE   224      22.853  23.022  11.601  1.00  1.00
ATOM     18  O   ILE   224      23.474  23.985  11.169  1.00  1.00
ATOM     19  HN  ILE   224      20.395  21.110  11.841  1.00  1.00
ATOM     20  CB  ILE   224      20.413  23.552  11.563  1.00  1.00
ATOM     21  CG1 ILE   224      20.236  23.448  13.080  1.00  1.00
ATOM     22  CG2 ILE   224      19.132  23.276  10.768  1.00  1.00
ATOM     23  CD1 ILE   224      19.333  24.513  13.658  1.00  1.00
ATOM     24  N   GLY   225      23.299  22.279  12.613  1.00  1.00
ATOM     25  CA  GLY   225      24.588  22.591  13.235  1.00  1.00
ATOM     26  C   GLY   225      25.716  22.314  12.243  1.00  1.00
ATOM     27  O   GLY   225      26.742  22.989  12.251  1.00  1.00
ATOM     28  HN  GLY   225      22.832  21.494  13.018  1.00  1.00
ATOM     29  N   GLY   226      25.527  21.307  11.394  1.00  1.00
ATOM     30  CA  GLY   226      26.545  20.963  10.405  1.00  1.00
ATOM     31  C   GLY   226      26.642  22.094   9.398  1.00  1.00
ATOM     32  O   GLY   226      27.736  22.487   8.991  1.00  1.00
ATOM     33  HN  GLY   226      24.713  20.727  11.358  1.00  1.00
ATOM     34  N   ILE   227      25.491  22.643   9.015  1.00  1.00
ATOM     35  CA  ILE   227      25.471  23.753   8.061  1.00  1.00
ATOM     36  C   ILE   227      26.095  25.008   8.656  1.00  1.00
ATOM     37  O   ILE   227      26.805  25.767   7.972  1.00  1.00
ATOM     38  HN  ILE   227      24.585  22.360   9.329  1.00  1.00
ATOM     39  CB  ILE   227      24.026  23.971   7.598  1.00  1.00
ATOM     40  CG1 ILE   227      23.461  22.803   6.813  1.00  1.00
ATOM     41  CG2 ILE   227      23.984  25.312   6.855  1.00  1.00
ATOM     42  CD1 ILE   227      21.951  22.920   6.564  1.00  1.00
TER
END
