
#######################################################
#                                                     #
#                        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   34 (   34),  selected   28 , name T0365TS464_2_2
# Molecule2: number of CA atoms  214 ( 1638),  selected   28 , name T0365.pdb
# PARAMETERS: T0365TS464_2_2.T0365.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:    26         7 - 161         4.96     5.55
  LCS_AVERAGE:     12.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        12 - 29          1.32     7.02
  LCS_AVERAGE:      6.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17        13 - 29          0.69     7.11
  LCS_AVERAGE:      5.84

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     L       7     L       7      6    6   26     5    5    6    9   12   15   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     G       8     G       8      6    6   26     5    6    6    9   12   15   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     V       9     V       9      6    6   26     5    6    6    9   12   15   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     F      10     F      10      6    6   26     5    6    6    9   12   15   18   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     A      11     A      11      6    6   26     5    6    6    9   12   15   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     K      12     K      12      6   18   26     3    5    6    6   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     S      13     S      13     17   18   26     0   12   14   17   17   17   18   18   18   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     P      14     P      14     17   18   26     3   16   16   17   17   17   18   18   18   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     I      15     I      15     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     K      16     K      16     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     P      17     P      17     17   18   26     5   16   16   17   17   17   18   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     L      18     L      18     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     Q      19     Q      19     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     E      20     E      20     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     H      21     H      21     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     M      22     M      22     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     D      23     D      23     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     K      24     K      24     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     V      25     V      25     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     Y      26     Y      26     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     D      27     D      27     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     C      28     C      28     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     A      29     A      29     17   18   26    14   16   16   17   17   17   19   20   21   23   23   23   23   23   24   24   24   25   27   27 
LCS_GDT     A     159     A     159      5    5   26     0    4    5    5    5    5    5    5    5    5    8   13   17   21   22   22   23   23   26   27 
LCS_GDT     K     160     K     160      5    5   26     4    4    5    5    5    5    5    5    5    5   10   14   19   21   22   22   23   24   27   27 
LCS_GDT     M     161     M     161      5    5   26     4    4    5    5    5    5    5    5    5    5    6   12   16   21   24   24   24   25   27   27 
LCS_GDT     I     162     I     162      5    5   24     4    4    5    5    5    5    5    5    5    5    5    5   10   13   17   22   23   23   27   27 
LCS_GDT     N     163     N     163      5    5   24     4    4    5    5    5    5    5    5    5    5   10   18   19   21   22   22   24   25   27   27 
LCS_AVERAGE  LCS_A:   8.08  (   5.84    6.33   12.08 )

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     14     16     16     17     17     17     19     20     21     23     23     23     23     23     24     24     24     25     27     27 
GDT PERCENT_CA   6.54   7.48   7.48   7.94   7.94   7.94   8.88   9.35   9.81  10.75  10.75  10.75  10.75  10.75  11.21  11.21  11.21  11.68  12.62  12.62
GDT RMS_LOCAL    0.38   0.46   0.46   0.69   0.69   0.69   2.70   2.72   2.83   3.15   3.15   3.15   3.15   3.15   3.78   3.78   3.78   4.44   5.15   5.15
GDT RMS_ALL_CA   7.22   7.12   7.12   7.11   7.11   7.11   6.98   6.92   6.85   7.02   7.02   7.02   7.02   7.02   6.31   6.31   6.31   5.67   5.49   5.49

#      Molecule1      Molecule2       DISTANCE
LGA    L       7      L       7          3.052
LGA    G       8      G       8          2.588
LGA    V       9      V       9          2.869
LGA    F      10      F      10          3.107
LGA    A      11      A      11          2.979
LGA    K      12      K      12          2.457
LGA    S      13      S      13          5.959
LGA    P      14      P      14          6.031
LGA    I      15      I      15          3.824
LGA    K      16      K      16          2.985
LGA    P      17      P      17          4.337
LGA    L      18      L      18          3.723
LGA    Q      19      Q      19          1.755
LGA    E      20      E      20          2.753
LGA    H      21      H      21          3.286
LGA    M      22      M      22          1.887
LGA    D      23      D      23          0.932
LGA    K      24      K      24          1.493
LGA    V      25      V      25          1.381
LGA    Y      26      Y      26          2.729
LGA    D      27      D      27          3.277
LGA    C      28      C      28          1.607
LGA    A      29      A      29          3.487
LGA    A     159      A     159         16.819
LGA    K     160      K     160         14.042
LGA    M     161      M     161         11.204
LGA    I     162      I     162         14.888
LGA    N     163      N     163         15.684

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  214    4.0     20    2.72     8.995     8.402     0.709

LGA_LOCAL      RMSD =  2.721  Number of atoms =   20  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.848  Number of atoms =   28 
Std_ALL_ATOMS  RMSD =  5.461  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.668928 * X  +  -0.731639 * Y  +   0.131300 * Z  +  17.615711
  Y_new =   0.138654 * X  +   0.296352 * Y  +   0.944961 * Z  +  -0.228739
  Z_new =  -0.730281 * X  +  -0.613905 * Y  +   0.299682 * Z  +  27.069088 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.116668    2.024925  [ DEG:   -63.9803    116.0197 ]
  Theta =   0.818734    2.322859  [ DEG:    46.9100    133.0900 ]
  Phi   =   0.204383   -2.937209  [ DEG:    11.7103   -168.2897 ]
 
# 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: T0365TS464_2_2                                
REMARK     2: T0365.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0365TS464_2_2.T0365.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  214   4.0   20   2.72   8.402     5.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0365TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0365
PARENT N/A
ATOM      1  CA  MET     1      37.778  12.378  18.707  1.00  0.00
ATOM      2  CA  PRO     2      38.460   9.485  21.050  1.00  0.00
ATOM      3  CA  VAL     3      34.873   9.524  22.383  1.00  0.00
ATOM      4  CA  ASN     4      33.418   9.057  18.860  1.00  0.00
ATOM      5  CA  SER     5      35.879   6.210  18.306  1.00  0.00
ATOM      6  CA  ILE     6      35.362   4.140  21.449  1.00  0.00
ATOM      7  CA  LEU     7      31.561   4.662  21.472  1.00  0.00
ATOM      8  CA  GLY     8      30.724   5.346  17.836  1.00  0.00
ATOM      9  CA  VAL     9      29.049   8.681  18.596  1.00  0.00
ATOM     10  CA  PHE    10      28.259  11.822  16.609  1.00  0.00
ATOM     11  CA  ALA    11      30.604  14.733  17.344  1.00  0.00
ATOM     12  CA  LYS    12      27.764  16.506  19.236  1.00  0.00
ATOM     13  CA  SER    13      26.969  13.547  21.588  1.00  0.00
ATOM     14  CA  PRO    14      30.706  13.459  22.425  1.00  0.00
ATOM     15  CA  ILE    15      31.698  16.527  24.487  1.00  0.00
ATOM     16  CA  LYS    16      28.452  15.977  26.416  1.00  0.00
ATOM     17  CA  PRO    17      29.957  12.819  27.960  1.00  0.00
ATOM     18  CA  LEU    18      32.763  14.937  29.395  1.00  0.00
ATOM     19  CA  GLN    19      30.165  17.489  30.546  1.00  0.00
ATOM     20  CA  GLU    20      28.299  15.072  32.827  1.00  0.00
ATOM     21  CA  HIS    21      31.486  13.793  34.482  1.00  0.00
ATOM     22  CA  MET    22      32.905  17.330  34.728  1.00  0.00
ATOM     23  CA  ASP    23      29.870  18.489  36.729  1.00  0.00
ATOM     24  CA  LYS    24      30.207  15.500  39.063  1.00  0.00
ATOM     25  CA  VAL    25      33.896  16.204  39.754  1.00  0.00
ATOM     26  CA  TYR    26      33.273  19.958  40.040  1.00  0.00
ATOM     27  CA  ASP    27      30.757  19.386  42.845  1.00  0.00
ATOM     28  CA  CYS    28      33.237  17.147  44.702  1.00  0.00
ATOM     29  CA  ALA    29      35.814  19.958  44.692  1.00  0.00
ATOM     30  CA  ALA   159      38.278  24.980  29.468  1.00  0.00
ATOM     31  CA  LYS   160      34.740  25.559  30.856  1.00  0.00
ATOM     32  CA  MET   161      33.743  24.865  34.473  1.00  0.00
ATOM     33  CA  ILE   162      37.318  24.488  35.758  1.00  0.00
ATOM     34  CA  ASN   163      38.428  27.605  33.843  1.00  0.00
TER
END
