
#######################################################
#                                                     #
#                        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   38 (   38),  selected   38 , name T0304TS464_4_2-D1
# Molecule2: number of CA atoms  101 (  799),  selected   38 , name T0304_D1.pdb
# PARAMETERS: T0304TS464_4_2-D1.T0304_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        69 - 87          4.77    17.53
  LCS_AVERAGE:     16.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        59 - 73          1.11    15.91
  LCS_AVERAGE:      6.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        66 - 73          0.34    16.44
  LCS_AVERAGE:      5.18

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:  101
LCS_GDT     A      45     A      45      5    5   12     4    4    4    5    5    5    7    9   11   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     D      46     D      46      5    5   12     4    4    4    5    5    5    6    8   11   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     R      47     R      47      5    5   14     4    4    4    5    5    5    6   10   10   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     A      48     A      48      5    5   14     4    4    4    5    7    9    9   10   11   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     G      49     G      49      5    5   14     0    4    4    5    5    5    7    9   11   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     I      50     I      50      3    4   14     1    3    3    4    4    4    6    7    9   10   11   14   17   18   20   21   22   23   24   25 
LCS_GDT     R      51     R      51      3    4   14     1    3    3    4    4    4    5    9    9   10   11   12   14   17   20   21   21   23   24   24 
LCS_GDT     G      52     G      52      3    4   14     1    3    3    4    4    5    7    9    9   10   10   13   15   17   20   21   22   23   24   25 
LCS_GDT     L      53     L      53      3    4   14     1    3    3    4    4    5    7    9    9   10   11   12   14   17   20   21   22   23   24   24 
LCS_GDT     F      54     F      54      3    4   14     3    3    3    4    4    5    7    9    9   10   11   12   15   17   20   21   22   23   24   24 
LCS_GDT     S      55     S      55      6    6   14     5    5    6    6    6    6    6    7    9   10   11   11   14   16   20   21   22   23   24   25 
LCS_GDT     D      56     D      56      6    6   16     5    5    6    6    6    6    6    9    9   10   11   14   17   18   20   21   22   23   24   25 
LCS_GDT     A      57     A      57      6    6   16     5    5    6    6    6    6    7    9    9   11   12   15   17   18   20   21   22   23   24   25 
LCS_GDT     D      58     D      58      6    6   16     5    5    6    6    6    6    7    9   10   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     A      59     A      59      7   10   16     5    5   10   10   10   10   10   12   13   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     Y      60     Y      60      7   10   16     3    4   10   10   10   10   10   12   13   13   13   15   17   18   20   21   22   23   24   25 
LCS_GDT     F      66     F      66      8   10   16     7    8   10   10   10   10   11   12   13   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     P      67     P      67      8   10   16     7    8   10   10   10   10   11   12   13   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     L      68     L      68      8   10   16     7    8   10   10   10   10   11   12   13   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     L      69     L      69      8   10   19     7    8   10   10   10   10   11   12   13   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     M      70     M      70      8   10   19     7    8   10   10   10   10   11   12   13   13   14   16   17   18   20   21   22   23   24   25 
LCS_GDT     K      71     K      71      8   10   19     7    8   10   10   10   10   11   12   13   13   14   15   17   18   20   21   22   23   24   25 
LCS_GDT     Q      72     Q      72      8   10   19     7    8   10   10   10   10   11   12   13   13   14   16   17   18   20   21   22   23   24   25 
LCS_GDT     L      73     L      73      8   10   19     7    8   10   10   10   10   11   12   13   13   14   16   17   18   19   19   22   23   24   25 
LCS_GDT     E      74     E      74      4    9   19     3    4    4    5    8   10   11   12   13   13   14   16   16   18   19   19   20   21   22   25 
LCS_GDT     L      75     L      75      4    5   19     3    4    4    5    8   10   11   12   13   13   14   16   17   18   19   19   20   21   22   25 
LCS_GDT     M      76     M      76      3    5   19     3    3    3    5    7    9   11   12   13   13   14   16   17   18   19   19   20   21   23   25 
LCS_GDT     L      77     L      77      3    3   19     3    3    3    3    5    8   10   11   12   13   14   16   17   18   19   19   20   21   23   25 
LCS_GDT     T      78     T      78      3    3   19     3    3    3    4    7    8   10   11   12   13   14   16   17   18   19   19   20   21   22   23 
LCS_GDT     S      79     S      79      3    5   19     3    3    3    4    5    5    8    9   11   13   14   16   17   18   19   19   20   21   22   23 
LCS_GDT     G      80     G      80      4    5   19     3    4    4    4    7    8   10   11   12   13   14   16   17   18   19   19   20   21   22   24 
LCS_GDT     E      81     E      81      4    5   19     3    4    4    5    7    8   10   11   12   13   14   16   17   18   19   19   20   21   23   24 
LCS_GDT     L      82     L      82      4    5   19     3    4    4    5    7    8   10   11   12   13   14   16   17   18   19   19   20   21   22   24 
LCS_GDT     N      83     N      83      5    5   19     5    5    5    5    7    8   10   11   12   13   14   16   17   18   19   19   20   21   22   22 
LCS_GDT     P      84     P      84      5    5   19     5    5    5    5    6    6    8    9   10   12   14   16   17   18   19   19   20   21   22   22 
LCS_GDT     R      85     R      85      5    5   19     5    5    5    5    6    6    7    8   12   13   14   16   16   18   19   19   20   21   22   22 
LCS_GDT     H      86     H      86      5    5   19     5    5    5    5    6    6   10   11   12   13   14   16   17   18   19   19   20   21   22   22 
LCS_GDT     Q      87     Q      87      5    5   19     5    5    5    5    6    8   10   11   12   13   14   15   17   18   19   19   20   21   22   22 
LCS_AVERAGE  LCS_A:   9.35  (   5.18    6.23   16.65 )

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      7      8     10     10     10     10     11     12     13     13     14     16     17     18     20     21     22     23     24     25 
GDT PERCENT_CA   6.93   7.92   9.90   9.90   9.90   9.90  10.89  11.88  12.87  12.87  13.86  15.84  16.83  17.82  19.80  20.79  21.78  22.77  23.76  24.75
GDT RMS_LOCAL    0.25   0.34   1.11   1.11   1.11   1.11   2.35   2.54   2.89   2.89   3.36   4.25   4.33   4.55   5.77   5.75   5.86   6.05   6.26   6.84
GDT RMS_ALL_CA  16.36  16.44  15.91  15.91  15.91  15.91  15.76  15.79  15.32  15.32  17.09  18.28  17.24  18.28  13.35  12.71  12.80  12.92  12.96  12.41

#      Molecule1      Molecule2       DISTANCE
LGA    A      45      A      45         16.419
LGA    D      46      D      46         17.671
LGA    R      47      R      47         11.321
LGA    A      48      A      48          9.593
LGA    G      49      G      49         14.097
LGA    I      50      I      50         15.784
LGA    R      51      R      51         15.363
LGA    G      52      G      52         15.408
LGA    L      53      L      53         17.086
LGA    F      54      F      54         14.583
LGA    S      55      S      55         14.399
LGA    D      56      D      56         12.902
LGA    A      57      A      57          9.981
LGA    D      58      D      58          6.887
LGA    A      59      A      59          2.677
LGA    Y      60      Y      60          3.010
LGA    F      66      F      66          1.760
LGA    P      67      P      67          1.421
LGA    L      68      L      68          1.721
LGA    L      69      L      69          1.941
LGA    M      70      M      70          1.511
LGA    K      71      K      71          2.574
LGA    Q      72      Q      72          3.334
LGA    L      73      L      73          2.753
LGA    E      74      E      74          3.750
LGA    L      75      L      75          3.756
LGA    M      76      M      76          4.987
LGA    L      77      L      77         11.171
LGA    T      78      T      78         15.455
LGA    S      79      S      79         17.390
LGA    G      80      G      80         19.381
LGA    E      81      E      81         15.571
LGA    L      82      L      82         18.243
LGA    N      83      N      83         25.437
LGA    P      84      P      84         28.225
LGA    R      85      R      85         30.208
LGA    H      86      H      86         30.885
LGA    Q      87      Q      87         33.750

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   38  101    4.0     12    2.54    12.624    10.785     0.455

LGA_LOCAL      RMSD =  2.539  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.324  Number of atoms =   38 
Std_ALL_ATOMS  RMSD = 10.073  (standard rmsd on all 38 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.377374 * X  +   0.924070 * Y  +  -0.060693 * Z  +  11.527105
  Y_new =   0.422602 * X  +  -0.113525 * Y  +   0.899177 * Z  + -50.337700
  Z_new =   0.824012 * X  +  -0.364975 * Y  +  -0.433355 * Z  +  67.741806 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.441640    0.699952  [ DEG:  -139.8957     40.1043 ]
  Theta =  -0.968457   -2.173136  [ DEG:   -55.4885   -124.5115 ]
  Phi   =   0.841876   -2.299717  [ DEG:    48.2359   -131.7641 ]
 
# 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: T0304TS464_4_2-D1                             
REMARK     2: T0304_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0304TS464_4_2-D1.T0304_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   38  101   4.0   12   2.54  10.785    10.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0304TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0304
PARENT N/A
ATOM      1  CA  ALA    45      46.247  30.179  50.808  1.00  0.00
ATOM      2  CA  ASP    46      49.522  30.212  48.754  1.00  0.00
ATOM      3  CA  ARG    47      49.400  26.510  48.384  1.00  0.00
ATOM      4  CA  ALA    48      45.880  26.740  46.885  1.00  0.00
ATOM      5  CA  GLY    49      47.107  29.134  44.211  1.00  0.00
ATOM      6  CA  ILE    50      50.349  27.472  43.218  1.00  0.00
ATOM      7  CA  ARG    51      48.595  24.162  43.437  1.00  0.00
ATOM      8  CA  GLY    52      45.893  25.539  41.192  1.00  0.00
ATOM      9  CA  LEU    53      48.532  26.641  38.679  1.00  0.00
ATOM     10  CA  PHE    54      50.635  23.512  38.676  1.00  0.00
ATOM     11  CA  SER    55      47.638  21.236  38.529  1.00  0.00
ATOM     12  CA  ASP    56      46.306  23.080  35.513  1.00  0.00
ATOM     13  CA  ALA    57      49.306  22.359  33.332  1.00  0.00
ATOM     14  CA  ASP    58      49.038  18.696  34.254  1.00  0.00
ATOM     15  CA  ALA    59      45.622  18.413  32.572  1.00  0.00
ATOM     16  CA  TYR    60      47.325  17.653  29.299  1.00  0.00
ATOM     17  CA  PHE    66      54.057  20.994  37.305  1.00  0.00
ATOM     18  CA  PRO    67      57.127  19.823  39.204  1.00  0.00
ATOM     19  CA  LEU    68      58.852  23.130  38.656  1.00  0.00
ATOM     20  CA  LEU    69      55.812  25.091  39.866  1.00  0.00
ATOM     21  CA  MET    70      55.421  22.829  42.906  1.00  0.00
ATOM     22  CA  LYS    71      59.137  22.999  43.735  1.00  0.00
ATOM     23  CA  GLN    72      58.564  26.747  43.735  1.00  0.00
ATOM     24  CA  LEU    73      55.079  26.714  45.208  1.00  0.00
ATOM     25  CA  GLU    74      53.513  30.004  46.228  1.00  0.00
ATOM     26  CA  LEU    75      56.012  31.940  44.096  1.00  0.00
ATOM     27  CA  MET    76      55.050  33.248  40.688  1.00  0.00
ATOM     28  CA  LEU    77      57.222  31.772  37.971  1.00  0.00
ATOM     29  CA  THR    78      57.537  33.596  34.600  1.00  0.00
ATOM     30  CA  SER    79      57.466  32.056  31.119  1.00  0.00
ATOM     31  CA  GLY    80      61.061  33.219  30.920  1.00  0.00
ATOM     32  CA  GLU    81      62.080  31.284  34.042  1.00  0.00
ATOM     33  CA  LEU    82      60.232  28.191  32.782  1.00  0.00
ATOM     34  CA  ASN    83      61.785  28.446  29.336  1.00  0.00
ATOM     35  CA  PRO    84      65.238  28.674  30.891  1.00  0.00
ATOM     36  CA  ARG    85      64.628  25.562  32.969  1.00  0.00
ATOM     37  CA  HIS    86      62.702  23.343  30.552  1.00  0.00
ATOM     38  CA  GLN    87      64.222  21.601  27.545  1.00  0.00
TER
END
