
#######################################################
#                                                     #
#                        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 T0301TS464_3_2
# Molecule2: number of CA atoms  391 ( 2894),  selected   33 , name T0301.pdb
# PARAMETERS: T0301TS464_3_2.T0301.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:    15         6 - 33          4.83    25.43
  LCS_AVERAGE:      3.02

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        25 - 31          1.88    24.15
  LCS_AVERAGE:      1.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         6 - 10          0.47    25.80
  LONGEST_CONTINUOUS_SEGMENT:     5       141 - 145         0.22    31.83
  LCS_AVERAGE:      1.08

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:  391
LCS_GDT     Q       6     Q       6      5    5   15     4    5    5    5    6    7    7    9    9    9   11   12   14   14   14   14   15   15   15   15 
LCS_GDT     I       7     I       7      5    5   15     4    5    5    5    6    7    7    9    9   10   11   13   14   14   14   14   15   15   15   15 
LCS_GDT     R       8     R       8      5    5   15     4    5    5    5    6    7    7    9    9   10   11   13   14   14   14   14   15   15   15   15 
LCS_GDT     I       9     I       9      5    5   15     4    5    5    5    6    7    7    9    9   10   11   13   14   14   14   14   15   15   15   17 
LCS_GDT     P      10     P      10      5    5   15     4    5    5    5    6    7    7    9    9   10   11   13   14   14   14   14   15   15   15   16 
LCS_GDT     F      24     F      24      3    3   15     3    3    3    3    3    4    7    9    9   10   11   13   14   14   14   14   15   15   15   16 
LCS_GDT     R      25     R      25      5    7   15     5    5    5    6    7    7    7    9    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     L      26     L      26      5    7   15     5    5    5    6    7    7    7    9    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     E      27     E      27      5    7   15     5    5    5    6    7    7    7    8    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     D      28     D      28      5    7   15     5    5    5    6    7    7    7    8    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     L      29     L      29      5    7   15     5    5    5    6    7    7    7    9    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     P      30     P      30      4    7   15     4    4    4    6    6    7    7    8    9   10   11   13   14   14   14   14   16   16   16   17 
LCS_GDT     E      31     E      31      4    7   15     4    4    4    5    7    7    7    8    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     S      32     S      32      4    4   15     4    4    4    4    5    5    6    8    9   10   11   13   14   14   14   15   16   16   16   17 
LCS_GDT     C      33     C      33      4    4   15     4    4    4    5    7    7    7    8    8   10   10   11   13   14   14   15   16   16   16   17 
LCS_GDT     E     128     E     128      3    6    8     3    3    4    6    6    6    7    9    9    9    9    9    9   10   10   10   12   14   15   16 
LCS_GDT     D     129     D     129      3    6    8     3    3    4    6    7    7    7    9    9    9    9    9    9   10   10   10   12   14   15   16 
LCS_GDT     G     130     G     130      4    6    8     3    4    4    6    7    7    7    9    9    9    9    9    9   10   10   10   12   14   15   16 
LCS_GDT     I     131     I     131      4    6    8     3    4    4    6    7    7    7    9    9    9    9    9    9   10   10   10   12   14   15   16 
LCS_GDT     C     132     C     132      4    6    8     3    4    4    6    6    6    6    9    9    9    9    9    9   10   10   10   12   14   15   16 
LCS_GDT     E     133     E     133      4    6    8     3    4    4    6    7    7    7    9    9    9    9    9    9   10   10   10   12   14   15   16 
LCS_GDT     V     134     V     134      4    5   10     3    4    4    4    7    7    7    9    9    9   10   11   13   13   14   15   16   16   16   17 
LCS_GDT     R     135     R     135      4    5   10     3    4    4    4    7    7    7    9    9   10   10   11   13   13   14   15   16   16   16   17 
LCS_GDT     I     141     I     141      5    5   10     5    5    5    5    5    5    6    7    7    8    9    9   10   11   14   15   16   16   16   17 
LCS_GDT     G     142     G     142      5    5   10     5    5    5    5    5    5    7    7    9   10   10   11   13   13   14   15   16   16   16   17 
LCS_GDT     K     143     K     143      5    5   10     5    5    5    5    5    5    7    7    9   10   10   11   13   13   14   15   16   16   16   17 
LCS_GDT     T     144     T     144      5    5   10     5    5    5    5    5    5    7    7    9   10   10   11   13   13   14   15   16   16   16   17 
LCS_GDT     I     145     I     145      5    5   10     5    5    5    5    7    7    7    9    9   10   10   11   13   13   14   15   16   16   16   17 
LCS_GDT     T     319     T     319      3    5   10     3    3    3    4    5    5    5    6    6    8    9    9    9   11   11   11   12   14   15   16 
LCS_GDT     A     320     A     320      3    4   10     3    3    3    4    4    4    4    5    6    8    9    9    9   11   11   11   11   14   15   16 
LCS_GDT     A     321     A     321      3    4   10     3    3    3    4    4    4    4    5    6    6    9    9    9   11   11   11   11   14   15   16 
LCS_GDT     V     322     V     322      3    4   10     3    3    3    4    4    4    4    5    6    8    9    9    9   11   11   11   12   14   15   16 
LCS_GDT     A     323     A     323      3    3    7     3    3    3    3    3    3    4    5    6    6    6    6    7    8    8    8   10   10   10   12 
LCS_AVERAGE  LCS_A:   1.82  (   1.08    1.36    3.02 )

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      5      5      5      6      7      7      7      9      9     10     11     13     14     14     14     15     16     16     16     17 
GDT PERCENT_CA   1.28   1.28   1.28   1.53   1.79   1.79   1.79   2.30   2.30   2.56   2.81   3.32   3.58   3.58   3.58   3.84   4.09   4.09   4.09   4.35
GDT RMS_LOCAL    0.22   0.22   0.22   1.41   1.50   1.50   1.50   2.75   2.75   3.26   3.74   4.26   4.43   4.43   4.43   5.42   5.74   5.74   5.74   6.34
GDT RMS_ALL_CA  24.98  24.98  24.98  24.79  22.64  22.64  22.64  26.12  26.12  23.65  24.61  25.78  25.37  25.37  25.37  15.93  16.08  16.08  16.08  16.22

#      Molecule1      Molecule2       DISTANCE
LGA    Q       6      Q       6          2.231
LGA    I       7      I       7          0.737
LGA    R       8      R       8          0.262
LGA    I       9      I       9          2.063
LGA    P      10      P      10          3.548
LGA    F      24      F      24          3.989
LGA    R      25      R      25          3.550
LGA    L      26      L      26          3.999
LGA    E      27      E      27          8.568
LGA    D      28      D      28          6.808
LGA    L      29      L      29          1.163
LGA    P      30      P      30          6.753
LGA    E      31      E      31         11.063
LGA    S      32      S      32          7.805
LGA    C      33      C      33          9.081
LGA    E     128      E     128         25.978
LGA    D     129      D     129         26.608
LGA    G     130      G     130         28.908
LGA    I     131      I     131         26.188
LGA    C     132      C     132         27.143
LGA    E     133      E     133         27.545
LGA    V     134      V     134         22.525
LGA    R     135      R     135         25.955
LGA    I     141      I     141         33.765
LGA    G     142      G     142         36.876
LGA    K     143      K     143         35.364
LGA    T     144      T     144         35.946
LGA    I     145      I     145         33.988
LGA    T     319      T     319         46.448
LGA    A     320      A     320         48.023
LGA    A     321      A     321         44.094
LGA    V     322      V     322         42.505
LGA    A     323      A     323         44.999

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  391    4.0      9    2.75     2.238     2.005     0.315

LGA_LOCAL      RMSD =  2.755  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 26.122  Number of atoms =   33 
Std_ALL_ATOMS  RMSD = 14.417  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.739218 * X  +   0.294569 * Y  +   0.605628 * Z  + -31.250372
  Y_new =  -0.523250 * X  +  -0.314936 * Y  +   0.791849 * Z  +  11.891605
  Z_new =   0.423988 * X  +  -0.902244 * Y  +  -0.078673 * Z  +  62.769482 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.657774    1.483819  [ DEG:   -94.9834     85.0166 ]
  Theta =  -0.437845   -2.703748  [ DEG:   -25.0866   -154.9134 ]
  Phi   =  -0.615970    2.525623  [ DEG:   -35.2925    144.7075 ]
 
# 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: T0301TS464_3_2                                
REMARK     2: T0301.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_3_2.T0301.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  391   4.0    9   2.75   2.005    14.42
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  GLN     6      68.318  46.481   6.151  1.00  0.00
ATOM      2  CA  ILE     7      65.099  44.432   5.968  1.00  0.00
ATOM      3  CA  ARG     8      64.978  42.140   9.025  1.00  0.00
ATOM      4  CA  ILE     9      63.891  38.500   9.305  1.00  0.00
ATOM      5  CA  PRO    10      62.114  37.139  12.364  1.00  0.00
ATOM      6  CA  PHE    24      69.673  27.572   5.199  1.00  0.00
ATOM      7  CA  ARG    25      67.014  29.082   2.940  1.00  0.00
ATOM      8  CA  LEU    26      65.684  31.016   5.931  1.00  0.00
ATOM      9  CA  GLU    27      69.126  32.481   6.639  1.00  0.00
ATOM     10  CA  ASP    28      69.392  33.706   3.025  1.00  0.00
ATOM     11  CA  LEU    29      66.016  35.437   3.398  1.00  0.00
ATOM     12  CA  PRO    30      66.759  36.922   6.829  1.00  0.00
ATOM     13  CA  GLU    31      70.214  38.103   5.713  1.00  0.00
ATOM     14  CA  SER    32      68.893  39.626   2.499  1.00  0.00
ATOM     15  CA  CYS    33      65.865  40.929   4.401  1.00  0.00
ATOM     16  CA  GLU   128      73.222  32.330  13.316  1.00  0.00
ATOM     17  CA  ASP   129      71.861  31.694   9.837  1.00  0.00
ATOM     18  CA  GLY   130      70.219  35.062   9.140  1.00  0.00
ATOM     19  CA  ILE   131      67.396  35.572  11.662  1.00  0.00
ATOM     20  CA  CYS   132      67.377  38.958  13.416  1.00  0.00
ATOM     21  CA  GLU   133      64.681  37.900  15.838  1.00  0.00
ATOM     22  CA  VAL   134      62.851  34.800  17.045  1.00  0.00
ATOM     23  CA  ARG   135      59.079  34.615  17.301  1.00  0.00
ATOM     24  CA  ILE   141      71.708  40.636  22.011  1.00  0.00
ATOM     25  CA  GLY   142      70.055  43.689  20.473  1.00  0.00
ATOM     26  CA  LYS   143      67.083  41.691  19.176  1.00  0.00
ATOM     27  CA  THR   144      63.328  42.140  19.471  1.00  0.00
ATOM     28  CA  ILE   145      60.987  40.094  21.626  1.00  0.00
ATOM     29  CA  THR   319      58.576  46.858   5.411  1.00  0.00
ATOM     30  CA  ALA   320      60.671  46.719   8.559  1.00  0.00
ATOM     31  CA  ALA   321      60.717  43.043   9.497  1.00  0.00
ATOM     32  CA  VAL   322      59.179  39.926   7.942  1.00  0.00
ATOM     33  CA  ALA   323      58.129  37.360  10.537  1.00  0.00
TER
END
