
#######################################################
#                                                     #
#                        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   33 (   33),  selected   33 , name T0320TS464_4_2
# Molecule2: number of CA atoms  287 ( 2364),  selected   33 , name T0320.pdb
# PARAMETERS: T0320TS464_4_2.T0320.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:    19        27 - 45          4.51    15.39
  LCS_AVERAGE:      5.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        28 - 41          1.72    16.92
  LONGEST_CONTINUOUS_SEGMENT:    14        29 - 42          1.51    15.94
  LCS_AVERAGE:      3.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        29 - 41          0.39    16.60
  LCS_AVERAGE:      2.61

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:  287
LCS_GDT     I      27     I      27      3    3   19     0    3    3    3    3    5    6   14   16   17   19   19   22   22   23   25   26   26   26   27 
LCS_GDT     A      28     A      28      3   14   19     3    3    3    3    3    4   10   14   17   18   19   20   22   22   23   25   26   26   26   27 
LCS_GDT     S      29     S      29     13   14   19     9   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     T      30     T      30     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     Q      31     Q      31     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     E      32     E      32     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     A      33     A      33     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     I      34     I      34     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     R      35     R      35     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     L      36     L      36     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     T      37     T      37     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     R      38     R      38     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     K      39     K      39     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     Y      40     Y      40     13   14   19    10   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     L      41     L      41     13   14   19    11   13   13   13   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     L      42     L      42      4   14   19     4    4    4    4    7   13   14   14   16   16   18   20   22   22   23   25   26   26   26   27 
LCS_GDT     S      43     S      43      4    4   19     4    4    4    4    5    8    8   12   16   16   17   18   22   22   23   25   26   26   26   27 
LCS_GDT     E      44     E      44      4    4   19     4    4    4    4    4    4    5    7    9   10   12   16   18   22   23   25   26   26   26   27 
LCS_GDT     I      45     I      45      4    4   19     4    4    4    4    4    5    5    7    9   10   12   14   18   22   23   25   26   26   26   27 
LCS_GDT     F      46     F      46      3    4   18     3    3    3    3    4    4    5    7    9   10   11   14   14   16   18   20   22   24   26   27 
LCS_GDT     V      47     V      47      3    4   13     1    3    3    3    4    4    5    5    7    9    9   11   12   13   14   15   15   16   17   17 
LCS_GDT     I     161     I     161      5    7   12     4    5    6    7    7    7    7    7   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     V     162     V     162      5    7   12     4    5    6   12   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     I     163     I     163      5    7    8     4    5    6    7    7    7    7    7   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     G     164     G     164      5    7    8     4    5    6   12   15   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     I     165     I     165      5    7    8     3    5    6    7    7    7    7    7    7   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     R     166     R     166      5    7    8     3    4    6    7   13   15   16   16   18   19   20   20   22   22   23   25   26   26   26   27 
LCS_GDT     H     167     H     167      5    7    8     0    4    6    7    7    7    7    7    7    7   20   20   21   21   23   25   26   26   26   27 
LCS_GDT     I     272     I     272      3    4    8     3    3    4    4    4    4    4    4    4    5    5    5    5    8    8    8   10   10   11   11 
LCS_GDT     S     273     S     273      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    6    8    8    9   10   10   11   11 
LCS_GDT     V     274     V     274      3    4    5     3    3    4    4    4    4    4    4    4    5    5    5    6    8    8    8    8   10   11   11 
LCS_GDT     V     275     V     275      3    4    5     1    3    4    4    4    4    4    4    4    5    5    5    6    8    8    9   10   10   11   11 
LCS_GDT     D     276     D     276      3    3    5     0    3    3    3    3    3    4    4    4    5    5    6    6    8    8    9   10   10   11   11 
LCS_AVERAGE  LCS_A:   3.63  (   2.61    3.18    5.11 )

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     11     13     13     13     15     15     16     16     18     19     20     20     22     22     23     25     26     26     26     27 
GDT PERCENT_CA   3.83   4.53   4.53   4.53   5.23   5.23   5.57   5.57   6.27   6.62   6.97   6.97   7.67   7.67   8.01   8.71   9.06   9.06   9.06   9.41
GDT RMS_LOCAL    0.34   0.39   0.39   0.39   1.50   1.50   1.85   1.85   2.35   2.60   2.84   2.84   3.66   3.66   4.08   4.92   5.02   5.02   5.02   5.55
GDT RMS_ALL_CA  16.56  16.60  16.60  16.60  17.43  17.43  17.69  17.69  17.69  17.67  17.85  17.85  17.35  17.35  17.14  17.14  17.14  17.14  17.14  16.91

#      Molecule1      Molecule2       DISTANCE
LGA    I      27      I      27         10.062
LGA    A      28      A      28          7.684
LGA    S      29      S      29          0.817
LGA    T      30      T      30          2.348
LGA    Q      31      Q      31          2.697
LGA    E      32      E      32          1.298
LGA    A      33      A      33          1.430
LGA    I      34      I      34          2.113
LGA    R      35      R      35          2.022
LGA    L      36      L      36          1.127
LGA    T      37      T      37          1.203
LGA    R      38      R      38          1.831
LGA    K      39      K      39          1.407
LGA    Y      40      Y      40          0.860
LGA    L      41      L      41          1.928
LGA    L      42      L      42          7.174
LGA    S      43      S      43         10.799
LGA    E      44      E      44         12.983
LGA    I      45      I      45         12.317
LGA    F      46      F      46         16.976
LGA    V      47      V      47         22.853
LGA    I     161      I     161          4.392
LGA    V     162      V     162          2.073
LGA    I     163      I     163          4.398
LGA    G     164      G     164          1.890
LGA    I     165      I     165          5.591
LGA    R     166      R     166          3.861
LGA    H     167      H     167          6.939
LGA    I     272      I     272         38.343
LGA    S     273      S     273         40.538
LGA    V     274      V     274         43.794
LGA    V     275      V     275         44.800
LGA    D     276      D     276         40.552

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  287    4.0     16    1.85     5.836     5.200     0.822

LGA_LOCAL      RMSD =  1.847  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.685  Number of atoms =   33 
Std_ALL_ATOMS  RMSD = 12.144  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.004575 * X  +   0.968249 * Y  +  -0.249946 * Z  + -69.744553
  Y_new =  -0.358292 * X  +  -0.234941 * Y  +  -0.903565 * Z  +  35.299507
  Z_new =  -0.933598 * X  +   0.085420 * Y  +   0.347991 * Z  +  84.659241 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.240707   -2.900885  [ DEG:    13.7915   -166.2085 ]
  Theta =   1.204327    1.937266  [ DEG:    69.0029    110.9971 ]
  Phi   =  -1.583564    1.558028  [ DEG:   -90.7315     89.2685 ]
 
# 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: T0320TS464_4_2                                
REMARK     2: T0320.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_2.T0320.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  287   4.0   16   1.85   5.200    12.14
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  ILE    27       3.390   5.584  20.314  1.00  0.00
ATOM      2  CA  ALA    28       4.400   8.226  22.825  1.00  0.00
ATOM      3  CA  SER    29       2.529  11.489  23.299  1.00  0.00
ATOM      4  CA  THR    30       4.898  14.449  22.890  1.00  0.00
ATOM      5  CA  GLN    31       2.498  17.080  24.286  1.00  0.00
ATOM      6  CA  GLU    32       2.626  15.055  27.492  1.00  0.00
ATOM      7  CA  ALA    33       6.445  15.271  27.931  1.00  0.00
ATOM      8  CA  ILE    34       6.335  19.033  27.426  1.00  0.00
ATOM      9  CA  ARG    35       3.923  19.740  30.337  1.00  0.00
ATOM     10  CA  LEU    36       5.783  17.405  32.726  1.00  0.00
ATOM     11  CA  THR    37       9.084  18.954  31.633  1.00  0.00
ATOM     12  CA  ARG    38       7.894  22.419  32.563  1.00  0.00
ATOM     13  CA  LYS    39       6.445  21.209  35.824  1.00  0.00
ATOM     14  CA  TYR    40       9.853  19.599  36.429  1.00  0.00
ATOM     15  CA  LEU    41      11.525  23.015  36.371  1.00  0.00
ATOM     16  CA  LEU    42      12.745  23.514  32.796  1.00  0.00
ATOM     17  CA  SER    43      12.660  27.263  32.024  1.00  0.00
ATOM     18  CA  GLU    44      12.353  26.555  28.274  1.00  0.00
ATOM     19  CA  ILE    45      11.679  23.425  26.267  1.00  0.00
ATOM     20  CA  PHE    46      12.634  23.291  22.580  1.00  0.00
ATOM     21  CA  VAL    47      11.356  20.224  20.780  1.00  0.00
ATOM     22  CA  ILE   161      17.459  25.940  32.325  1.00  0.00
ATOM     23  CA  VAL   162      17.042  24.797  28.728  1.00  0.00
ATOM     24  CA  ILE   163      15.555  21.381  27.962  1.00  0.00
ATOM     25  CA  GLY   164      16.005  20.000  24.451  1.00  0.00
ATOM     26  CA  ILE   165      13.381  17.437  23.615  1.00  0.00
ATOM     27  CA  ARG   166      14.312  14.957  20.890  1.00  0.00
ATOM     28  CA  HIS   167      11.255  12.871  19.930  1.00  0.00
ATOM     29  CA  ILE   272      11.166  10.860  35.301  1.00  0.00
ATOM     30  CA  SER   273      10.747   7.841  33.003  1.00  0.00
ATOM     31  CA  VAL   274       8.024   6.424  30.753  1.00  0.00
ATOM     32  CA  VAL   275       7.835   2.836  29.539  1.00  0.00
ATOM     33  CA  ASP   276       5.475   2.456  26.582  1.00  0.00
TER
END
