
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected    6 , name T0320_D1.pdb
# PARAMETERS: T0320TS074_4-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         3.24     3.24
  LCS_AVERAGE:      2.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       224 - 227         1.90     4.74
  LCS_AVERAGE:      1.71

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         0.52     7.55
  LONGEST_CONTINUOUS_SEGMENT:     3       224 - 226         0.80     5.18
  LONGEST_CONTINUOUS_SEGMENT:     3       225 - 227         0.84     7.87
  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    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     223     S     223      3    3    6     1    3    3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     224     I     224      3    4    6     1    3    3    3    4    4    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    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:   1.97  (   1.40    1.71    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      1      3      3      3      4      4      5      5      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   0.47   1.40   1.40   1.40   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   31.63   0.49   0.49   0.49   1.90   1.90   2.64   2.64   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24
GDT RMS_ALL_CA   4.91   4.91   4.91   4.91   4.74   4.74   3.84   3.84   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24   3.24

#      Molecule1      Molecule2       DISTANCE
LGA    T     222      T     222          7.321
LGA    S     223      S     223          3.444
LGA    I     224      I     224          1.518
LGA    G     225      G     225          1.794
LGA    G     226      G     226          2.779
LGA    I     227      I     227          3.113

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  214    4.0      5    2.64     1.986     2.047     0.183

LGA_LOCAL      RMSD =  2.638  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.838  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.244  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.762294 * X  +  -0.409786 * Y  +   0.500983 * Z  +  22.174925
  Y_new =   0.134166 * X  +  -0.657180 * Y  +  -0.741696 * Z  +  25.522881
  Z_new =   0.633173 * X  +   0.632605 * Y  +  -0.445985 * Z  +   2.793483 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.184869   -0.956724  [ DEG:   125.1837    -54.8163 ]
  Theta =  -0.685646   -2.455947  [ DEG:   -39.2846   -140.7154 ]
  Phi   =   0.174218   -2.967374  [ DEG:     9.9820   -170.0180 ]
 
# 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_4-D1                               
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS074_4-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   2.64   2.047     3.24
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS074_4-D1
PFRMAT TS
TARGET T0320
MODEL  4
PARENT N/A
ATOM      1  N   THR   222      20.804  16.869  13.976  1.00  1.00
ATOM      2  CA  THR   222      22.105  17.526  13.919  1.00  1.00
ATOM      3  C   THR   222      22.388  18.383  12.678  1.00  1.00
ATOM      4  O   THR   222      23.464  18.981  12.578  1.00  1.00
ATOM      5  CB  THR   222      23.067  16.325  13.909  1.00  1.00
ATOM      6  OG1 THR   222      22.693  15.607  12.635  1.00  1.00
ATOM      7  CG2 THR   222      22.711  15.600  15.185  1.00  1.00
ATOM      8  N   SER   223      21.445  18.425  11.730  1.00  1.00
ATOM      9  CA  SER   223      21.771  19.017  10.429  1.00  1.00
ATOM     10  C   SER   223      22.033  20.515  10.453  1.00  1.00
ATOM     11  O   SER   223      22.841  21.015   9.634  1.00  1.00
ATOM     12  HN  SER   223      20.505  18.090  11.800  1.00  1.00
ATOM     13  CB  SER   223      20.754  18.654   9.352  1.00  1.00
ATOM     14  OG  SER   223      19.487  19.148   9.690  1.00  1.00
ATOM     15  N   ILE   224      21.370  21.244  11.350  1.00  1.00
ATOM     16  CA  ILE   224      21.582  22.704  11.325  1.00  1.00
ATOM     17  C   ILE   224      22.952  23.137  11.881  1.00  1.00
ATOM     18  O   ILE   224      23.622  23.972  11.258  1.00  1.00
ATOM     19  HN  ILE   224      20.731  20.938  12.057  1.00  1.00
ATOM     20  CB  ILE   224      20.401  23.510  11.883  1.00  1.00
ATOM     21  CG1 ILE   224      20.129  23.190  13.370  1.00  1.00
ATOM     22  CG2 ILE   224      19.213  23.284  10.942  1.00  1.00
ATOM     23  CD1 ILE   224      19.103  24.198  13.961  1.00  1.00
ATOM     24  N   GLY   225      23.394  22.582  13.029  1.00  1.00
ATOM     25  CA  GLY   225      24.787  22.828  13.418  1.00  1.00
ATOM     26  C   GLY   225      25.783  22.405  12.309  1.00  1.00
ATOM     27  O   GLY   225      26.771  23.098  12.078  1.00  1.00
ATOM     28  HN  GLY   225      22.888  22.008  13.673  1.00  1.00
ATOM     29  N   GLY   226      25.521  21.293  11.629  1.00  1.00
ATOM     30  CA  GLY   226      26.392  20.867  10.540  1.00  1.00
ATOM     31  C   GLY   226      26.362  21.877   9.401  1.00  1.00
ATOM     32  O   GLY   226      27.399  22.181   8.808  1.00  1.00
ATOM     33  HN  GLY   226      24.747  20.682  11.794  1.00  1.00
ATOM     34  N   ILE   227      25.174  22.400   9.105  1.00  1.00
ATOM     35  CA  ILE   227      25.029  23.380   8.032  1.00  1.00
ATOM     36  C   ILE   227      25.860  24.623   8.319  1.00  1.00
ATOM     37  O   ILE   227      26.673  25.033   7.498  1.00  1.00
ATOM     38  HN  ILE   227      24.318  22.178   9.571  1.00  1.00
ATOM     39  CB  ILE   227      23.549  23.806   7.838  1.00  1.00
ATOM     40  CG1 ILE   227      22.691  22.591   7.560  1.00  1.00
ATOM     41  CG2 ILE   227      23.547  24.900   6.772  1.00  1.00
ATOM     42  CD1 ILE   227      23.221  21.880   6.231  1.00  1.00
TER
END
