
#######################################################
#                                                     #
#                        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   28 (   28),  selected   28 , name T0320TS464_4_2-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   28 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_4_2-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:    19        27 - 45          4.51     7.39
  LCS_AVERAGE:      7.53

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        28 - 41          1.72     8.53
  LONGEST_CONTINUOUS_SEGMENT:    14        29 - 42          1.51     8.76
  LCS_AVERAGE:      4.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        29 - 41          0.39     8.67
  LCS_AVERAGE:      3.87

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     I      27     I      27      3    3   19     0    3    3    3    3    5    6   14   16   17   17   19   21   22   24   25   26   26   26   27 
LCS_GDT     A      28     A      28      3   14   19     3    3    3    3    3    4   10   14   14   17   19   20   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   25   26   26   26   27 
LCS_GDT     Y      40     Y      40     13   14   19     8   13   13   13   15   15   16   16   18   19   20   20   21   22   24   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   21   22   24   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   21   22   24   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   21   22   24   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   20   22   24   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   24   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   17   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   21   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   21   22   24   25   26   26   26   27 
LCS_GDT     I     163     I     163      5    7    7     4    5    6    7    7    7    7    7   18   19   20   20   21   22   24   25   26   26   26   27 
LCS_GDT     G     164     G     164      5    7    7     4    5    6   12   15   15   16   16   18   19   20   20   21   22   24   25   26   26   26   27 
LCS_GDT     I     165     I     165      5    7    7     3    5    6    7    7    7    7    7    7   19   20   20   21   22   24   25   26   26   26   27 
LCS_GDT     R     166     R     166      5    7    7     3    3    6    7   13   15   16   16   18   19   20   20   21   22   24   25   26   26   26   27 
LCS_GDT     H     167     H     167      5    7    7     0    3    6    7    7    7    7    7    7    7   20   20   21   21   23   25   26   26   26   27 
LCS_AVERAGE  LCS_A:   5.37  (   3.87    4.71    7.53 )

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     21     22     24     25     26     26     26     27 
GDT PERCENT_CA   5.14   6.07   6.07   6.07   7.01   7.01   7.48   7.48   8.41   8.88   9.35   9.35   9.81  10.28  11.21  11.68  12.15  12.15  12.15  12.62
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   3.14   3.66   4.74   4.92   5.02   5.02   5.02   5.55
GDT RMS_ALL_CA   8.75   8.67   8.67   8.67   7.69   7.69   7.58   7.58   7.65   7.64   7.73   7.73   7.59   7.28   6.64   6.64   6.70   6.70   6.70   6.57

#      Molecule1      Molecule2       DISTANCE
LGA    I      27      I      27          8.927
LGA    A      28      A      28          6.765
LGA    S      29      S      29          0.868
LGA    T      30      T      30          1.883
LGA    Q      31      Q      31          2.792
LGA    E      32      E      32          1.734
LGA    A      33      A      33          1.297
LGA    I      34      I      34          1.972
LGA    R      35      R      35          2.281
LGA    L      36      L      36          1.604
LGA    T      37      T      37          1.255
LGA    R      38      R      38          1.774
LGA    K      39      K      39          1.615
LGA    Y      40      Y      40          1.343
LGA    L      41      L      41          2.168
LGA    L      42      L      42          6.698
LGA    S      43      S      43         10.274
LGA    E      44      E      44         12.436
LGA    I      45      I      45         11.781
LGA    F      46      F      46         16.362
LGA    V      47      V      47         22.336
LGA    I     161      I     161          4.658
LGA    V     162      V     162          1.816
LGA    I     163      I     163          4.675
LGA    G     164      G     164          1.946
LGA    I     165      I     165          5.749
LGA    R     166      R     166          3.870
LGA    H     167      H     167          7.324

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28  214    4.0     16    1.85     7.827     7.081     0.822

LGA_LOCAL      RMSD =  1.847  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.393  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  6.509  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.003907 * X  +   0.953089 * Y  +  -0.302665 * Z  + -70.654533
  Y_new =  -0.322116 * X  +  -0.285336 * Y  +  -0.902677 * Z  +  37.322342
  Z_new =  -0.946692 * X  +   0.101020 * Y  +   0.305890 * Z  +  83.497276 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.318971   -2.822622  [ DEG:    18.2757   -161.7243 ]
  Theta =   1.242808    1.898785  [ DEG:    71.2076    108.7924 ]
  Phi   =  -1.558669    1.582924  [ DEG:   -89.3052     90.6948 ]
 
# 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-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_4_2-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28  214   4.0   16   1.85   7.081     6.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  ILE    27       2.710   6.497  19.940  1.00  0.00
ATOM      2  CA  ALA    28       3.776   8.990  22.578  1.00  0.00
ATOM      3  CA  SER    29       2.052  12.321  23.131  1.00  0.00
ATOM      4  CA  THR    30       4.571  15.174  22.898  1.00  0.00
ATOM      5  CA  GLN    31       2.263  17.866  24.334  1.00  0.00
ATOM      6  CA  GLU    32       2.205  15.716  27.460  1.00  0.00
ATOM      7  CA  ALA    33       6.016  15.728  28.006  1.00  0.00
ATOM      8  CA  ILE    34       6.102  19.507  27.645  1.00  0.00
ATOM      9  CA  ARG    35       3.648  20.222  30.519  1.00  0.00
ATOM     10  CA  LEU    36       5.327  17.709  32.862  1.00  0.00
ATOM     11  CA  THR    37       8.726  19.134  31.915  1.00  0.00
ATOM     12  CA  ARG    38       7.680  22.616  32.949  1.00  0.00
ATOM     13  CA  LYS    39       6.085  21.357  36.122  1.00  0.00
ATOM     14  CA  TYR    40       9.393  19.559  36.751  1.00  0.00
ATOM     15  CA  LEU    41      11.229  22.888  36.869  1.00  0.00
ATOM     16  CA  LEU    42      12.570  23.461  33.349  1.00  0.00
ATOM     17  CA  SER    43      12.687  27.237  32.723  1.00  0.00
ATOM     18  CA  GLU    44      12.449  26.686  28.941  1.00  0.00
ATOM     19  CA  ILE    45      11.681  23.672  26.796  1.00  0.00
ATOM     20  CA  PHE    46      12.729  23.630  23.133  1.00  0.00
ATOM     21  CA  VAL    47      11.356  20.699  21.182  1.00  0.00
ATOM     22  CA  ILE   161      17.406  25.669  33.094  1.00  0.00
ATOM     23  CA  VAL   162      17.034  24.684  29.446  1.00  0.00
ATOM     24  CA  ILE   163      15.406  21.377  28.510  1.00  0.00
ATOM     25  CA  GLY   164      15.885  20.109  24.959  1.00  0.00
ATOM     26  CA  ILE   165      13.165  17.712  23.958  1.00  0.00
ATOM     27  CA  ARG   166      14.051  15.293  21.162  1.00  0.00
ATOM     28  CA  HIS   167      10.924  13.398  20.043  1.00  0.00
TER
END
