
#######################################################
#                                                     #
#                        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   20 (   20),  selected   17 , name T0330TS464_3_2-D2
# Molecule2: number of CA atoms   72 (  556),  selected   17 , name T0330_D2.pdb
# PARAMETERS: T0330TS464_3_2-D2.T0330_D2.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:    10        37 - 50          5.00    13.62
  LCS_AVERAGE:     11.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        18 - 22          1.92    27.60
  LONGEST_CONTINUOUS_SEGMENT:     5        36 - 44          1.00    12.98
  LONGEST_CONTINUOUS_SEGMENT:     5        45 - 49          0.92    16.34
  LCS_AVERAGE:      6.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        45 - 49          0.92    16.34
  LCS_AVERAGE:      5.72

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:   72
LCS_GDT     V      17     V      17      4    4    6     3    4    4    5    5    5    7    7    7    7    9    9    9   12   13   13   14   14   15   15 
LCS_GDT     E      18     E      18      4    5    6     3    4    4    4    4    5    7    7    7    7    9    9    9   12   13   13   14   14   15   15 
LCS_GDT     S      19     S      19      4    5    6     3    4    4    5    5    5    7    7    7    7    9    9    9   12   13   13   14   14   15   15 
LCS_GDT     M      20     M      20      4    5    6     3    4    4    4    4    5    7    7    7    7    9    9    9   12   13   13   14   14   15   15 
LCS_GDT     N      21     N      21      3    5    6     3    3    4    4    4    5    5    6    6    6    9    9    9    9   10   10   10   11   14   14 
LCS_GDT     R      22     R      22      3    5    6     3    3    4    4    4    5    5    6    6    7    9    9    9    9   10   10   10   10   11   11 
LCS_GDT     E      36     E      36      4    5    8     3    3    5    5    5    5    5    6    7    7    9   10   10   12   13   13   14   14   15   15 
LCS_GDT     G      37     G      37      4    5   10     3    4    5    5    5    5    5    6    7    7    9   10   10   12   13   13   14   14   15   15 
LCS_GDT     S      38     S      38      4    5   10     3    4    5    5    5    5    5    6    7    7    9   10   10   12   13   13   14   14   15   15 
LCS_GDT     T      39     T      39      4    5   10     1    4    5    5    5    5    5    6    7    7    9   10   10   12   13   13   14   14   15   15 
LCS_GDT     F      44     F      44      4    5   10     3    4    5    5    5    5    7    7    7    7    9   10   10   11   11   12   12   14   15   15 
LCS_GDT     S      45     S      45      5    5   10     3    4    5    5    5    5    7    7    7    7    9   10   10   11   11   13   14   14   15   15 
LCS_GDT     G      46     G      46      5    5   10     3    4    5    5    5    5    7    7    7    7    9   10   10   11   13   13   14   14   15   15 
LCS_GDT     K      47     K      47      5    5   10     3    4    5    5    5    5    5    6    7    7    8   10   10   12   13   13   14   14   15   15 
LCS_GDT     M      48     M      48      5    5   10     3    4    5    5    5    5    5    6    6    7    7    8   10   12   13   13   14   14   15   15 
LCS_GDT     D      49     D      49      5    5   10     3    4    5    5    5    5    5    6    6    7    9   10   10   12   13   13   14   14   15   15 
LCS_GDT     G      50     G      50      3    3   10     3    3    4    4    4    4    4    6    7    7    9   10   10   12   13   13   14   14   15   15 
LCS_AVERAGE  LCS_A:   8.06  (   5.72    6.70   11.76 )

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      3      4      5      5      5      5      7      7      7      7      9     10     10     12     13     13     14     14     15     15 
GDT PERCENT_CA   4.17   5.56   6.94   6.94   6.94   6.94   9.72   9.72   9.72   9.72  12.50  13.89  13.89  16.67  18.06  18.06  19.44  19.44  20.83  20.83
GDT RMS_LOCAL    0.04   0.48   0.92   0.92   0.92   0.92   2.28   2.28   2.28   2.28   3.74   4.73   4.73   5.76   6.04   6.04   6.37   6.37   6.73   6.73
GDT RMS_ALL_CA  28.10  14.93  16.34  16.34  16.34  16.34  14.58  14.58  14.58  14.58  15.29  13.45  13.45   8.58   8.33   8.33   8.19   8.19   8.09   8.09

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17          1.716
LGA    E      18      E      18          3.272
LGA    S      19      S      19          2.865
LGA    M      20      M      20          3.162
LGA    N      21      N      21          8.411
LGA    R      22      R      22          7.549
LGA    E      36      E      36         28.669
LGA    G      37      G      37         27.962
LGA    S      38      S      38         25.286
LGA    T      39      T      39         18.888
LGA    F      44      F      44          1.641
LGA    S      45      S      45          0.719
LGA    G      46      G      46          1.207
LGA    K      47      K      47          8.076
LGA    M      48      M      48         13.691
LGA    D      49      D      49         17.642
LGA    G      50      G      50         16.863

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20   72    4.0      7    2.28    10.069     9.040     0.294

LGA_LOCAL      RMSD =  2.284  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.577  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  7.873  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.005429 * X  +  -0.791670 * Y  +   0.610925 * Z  +  42.102062
  Y_new =  -0.554036 * X  +  -0.510976 * Y  +  -0.657227 * Z  + 110.479446
  Z_new =   0.832475 * X  +  -0.334907 * Y  +  -0.441387 * Z  +  -3.977905 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.492509    0.649083  [ DEG:  -142.8103     37.1897 ]
  Theta =  -0.983560   -2.158033  [ DEG:   -56.3538   -123.6462 ]
  Phi   =  -1.560998    1.580594  [ DEG:   -89.4386     90.5614 ]
 
# 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: T0330TS464_3_2-D2                             
REMARK     2: T0330_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0330TS464_3_2-D2.T0330_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20   72   4.0    7   2.28   9.040     7.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS464_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0330
PARENT N/A
ATOM     13  CA  VAL    17      16.429  34.446  12.717  1.00  0.00
ATOM     14  CA  GLU    18      16.571  34.864   8.934  1.00  0.00
ATOM     15  CA  SER    19      14.477  33.010   6.361  1.00  0.00
ATOM     16  CA  MET    20      16.761  31.157   3.967  1.00  0.00
ATOM     17  CA  ASN    21      14.301  29.262   1.760  1.00  0.00
ATOM     18  CA  ARG    22      15.577  30.977  -1.398  1.00  0.00
ATOM     19  CA  GLU    36      33.837  33.651  20.706  1.00  0.00
ATOM     20  CA  GLY    37      30.652  35.115  22.095  1.00  0.00
ATOM     21  CA  SER    38      26.898  35.519  21.457  1.00  0.00
ATOM     22  CA  THR    39      25.653  35.657  17.877  1.00  0.00
ATOM     23  CA  GLY    40      23.406  38.691  18.274  1.00  0.00
ATOM     24  CA  SER    41      22.314  39.169  14.685  1.00  0.00
ATOM     25  CA  HIS    42      22.039  37.037  11.557  1.00  0.00
ATOM     26  CA  PHE    44      26.365  37.403   7.839  1.00  0.00
ATOM     27  CA  SER    45      26.677  37.363  11.624  1.00  0.00
ATOM     28  CA  GLY    46      27.188  40.117  14.191  1.00  0.00
ATOM     29  CA  LYS    47      28.611  39.069  17.544  1.00  0.00
ATOM     30  CA  MET    48      29.351  40.152  21.078  1.00  0.00
ATOM     31  CA  ASP    49      32.924  39.204  20.294  1.00  0.00
ATOM     32  CA  GLY    50      33.100  42.511  18.362  1.00  0.00
TER
END
