
#######################################################
#                                                     #
#                        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   58 (   58),  selected   58 , name T0356TS464_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected   58 , name T0356_D1.pdb
# PARAMETERS: T0356TS464_4-D1.T0356_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:    23        34 - 65          4.52    24.36
  LCS_AVERAGE:     16.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        34 - 52          1.22    27.07
  LCS_AVERAGE:     10.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        35 - 46          0.93    25.50
  LONGEST_CONTINUOUS_SEGMENT:    12        36 - 47          1.00    26.84
  LCS_AVERAGE:      6.72

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:  124
LCS_GDT     R      10     R      10     10   10   20    10   10   10   11   11   11   11   13   14   14   15   16   18   20   24   24   24   25   26   29 
LCS_GDT     D      11     D      11     10   10   21    10   10   10   11   11   11   11   13   14   14   16   17   21   22   24   24   24   26   27   30 
LCS_GDT     F      12     F      12     10   10   21    10   10   10   11   11   11   11   13   14   15   17   18   21   22   24   24   24   26   27   30 
LCS_GDT     L      13     L      13     10   10   21    10   10   10   11   11   11   11   13   14   15   17   18   21   22   24   24   24   26   27   30 
LCS_GDT     T      14     T      14     10   10   21    10   10   10   11   11   11   11   13   14   15   17   18   21   22   24   24   24   26   27   30 
LCS_GDT     L      15     L      15     10   10   21    10   10   10   11   11   11   11   13   15   16   17   18   21   22   24   24   24   26   27   30 
LCS_GDT     L      16     L      16     10   10   21    10   10   10   11   11   11   11   14   15   16   17   18   21   22   24   24   24   26   27   30 
LCS_GDT     E      17     E      17     10   10   21    10   10   10   11   11   11   11   13   14   14   16   18   21   22   24   24   24   26   27   30 
LCS_GDT     Q      18     Q      18     10   10   21    10   10   10   11   11   11   11   14   15   16   17   18   21   22   24   24   24   26   27   30 
LCS_GDT     Q      19     Q      19     10   10   21    10   10   10   11   11   11   11   13   15   16   16   17   21   22   24   24   24   26   28   31 
LCS_GDT     E      34     E      34      9   19   23     5   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   26   27   28 
LCS_GDT     I      35     I      35     12   19   23     5   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   27   29   31 
LCS_GDT     T      36     T      36     12   19   23     5   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   27   29   31 
LCS_GDT     E      37     E      37     12   19   23     6   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   26   27   30 
LCS_GDT     I      38     I      38     12   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   27   29   31 
LCS_GDT     A      39     A      39     12   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   26   28   30   32 
LCS_GDT     D      40     D      40     12   19   23     6   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   27   29   32 
LCS_GDT     R      41     R      41     12   19   23     4    9   17   18   19   19   19   19   19   19   19   20   21   22   24   24   24   27   29   31 
LCS_GDT     T      42     T      42     12   19   23     4    5   16   18   19   19   19   19   19   19   19   20   21   22   24   24   26   28   30   32 
LCS_GDT     L      43     L      43     12   19   23     4    9   17   18   19   19   19   19   19   19   19   20   21   22   24   24   26   28   30   32 
LCS_GDT     R      44     R      44     12   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   22   24   24   26   28   30   32 
LCS_GDT     A      45     A      45     12   19   23     4   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     G      46     G      46     12   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     G      47     G      47     12   19   23     6   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     P      48     P      48      5   19   23     3    8   12   14   19   19   19   19   19   19   19   20   21   21   21   21   24   26   29   31 
LCS_GDT     A      49     A      49      5   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     L      50     L      50      5   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     L      51     L      51      5   19   23     5   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     F      52     F      52      5   19   23     7   13   17   18   19   19   19   19   19   19   19   20   21   21   21   23   26   28   30   32 
LCS_GDT     V      62     V      62      3    5   23     3    3    3    4    6    8    8   11   12   14   16   17   21   22   24   24   24   26   27   28 
LCS_GDT     L      63     L      63      3    5   23     3    3    3    4    6    8    8   11   15   17   18   20   21   22   24   24   26   28   30   32 
LCS_GDT     C      64     C      64      3    5   23     3    3    4    6    8   12   14   14   15   17   18   20   21   22   24   24   26   28   30   32 
LCS_GDT     N      65     N      65      3    5   23     0    3    3    4    5    6    7    9   10   13   16   19   19   20   20   23   26   28   30   32 
LCS_GDT     L      66     L      66      3    5   20     2    3    3    4    7    8   11   12   13   15   17   19   19   19   19   23   26   28   30   32 
LCS_GDT     M      77     M      77      3    4   20     2    2    3    4    7    7    8   10   13   14   17   19   19   19   20   23   26   27   30   32 
LCS_GDT     G      78     G      78      3    4   20     3    3    3    4    7    7    8    9   13   13   16   19   19   19   20   23   26   28   30   32 
LCS_GDT     Q      79     Q      79      3    4   20     3    3    3    4    7    7   11   12   14   14   17   19   19   19   19   22   26   28   30   32 
LCS_GDT     E      80     E      80      3   14   20     3    3    3   11   11   11   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     D      81     D      81      6   14   20     4    5   10   13   13   13   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     V      82     V      82      6   14   20     4    5   10   13   13   13   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     S      83     S      83     11   14   20     4    5   10   13   13   13   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     A      84     A      84     11   14   20     4    5   10   13   13   13   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     L      85     L      85     11   14   20     7    9   10   13   13   13   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     R      86     R      86     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   22   24   27   30   32 
LCS_GDT     E      87     E      87     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   22   25   28   30   32 
LCS_GDT     V      88     V      88     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   20   23   26   28   30   32 
LCS_GDT     G      89     G      89     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   22   25   28   30   32 
LCS_GDT     K      90     K      90     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   22   22   24   27   30 
LCS_GDT     L      91     L      91     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   22   24   28   30   32 
LCS_GDT     L      92     L      92     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   22   26   28   30   32 
LCS_GDT     A      93     A      93     11   14   20     8    9   10   13   13   13   14   14   14   15   17   19   19   19   19   20   24   27   30   32 
LCS_GDT     A     315     A     315      5    7   15     4    5    5    5    9   10   11   13   13   14   15   16   17   18   18   18   18   20   26   30 
LCS_GDT     I     316     I     316      5    7    7     4    5    5    5    8   10   11   13   13   14   15   16   17   18   18   18   18   20   26   30 
LCS_GDT     Y     317     Y     317      5    7    7     4    5    5    5    9   10   11   12   12   13   15   16   17   18   18   18   24   24   26   30 
LCS_GDT     H     318     H     318      5    7    7     4    5    5    5    9   10   11   12   12   14   15   16   17   18   18   22   24   24   27   30 
LCS_GDT     S     319     S     319      5    7    7     3    5    5    5    9   10   11   12   12   13   13   14   14   16   17   20   21   23   27   30 
LCS_GDT     T     320     T     320      4    7    7     3    4    4    5    9   10   11   12   12   13   13   13   14   16   19   22   22   24   27   30 
LCS_GDT     Y     321     Y     321      4    7    7     2    4    4    5    9   10   11   12   12   13   13   13   14   16   17   20   22   23   27   30 
LCS_AVERAGE  LCS_A:  11.04  (   6.72   10.33   16.06 )

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     10     13     17     18     19     19     19     19     19     19     19     20     21     22     24     24     26     28     30     32 
GDT PERCENT_CA   8.06  10.48  13.71  14.52  15.32  15.32  15.32  15.32  15.32  15.32  15.32  16.13  16.94  17.74  19.35  19.35  20.97  22.58  24.19  25.81
GDT RMS_LOCAL    0.29   0.66   0.91   0.99   1.22   1.22   1.22   1.22   1.22   1.22   1.22   2.45   3.11   4.95   5.24   5.24   6.75   7.05   7.23   7.43
GDT RMS_ALL_CA  17.66  27.17  26.68  26.60  27.07  27.07  27.07  27.07  27.07  27.07  27.07  26.06  25.40  14.25  14.53  14.53  15.77  15.53  15.73  15.62

#      Molecule1      Molecule2       DISTANCE
LGA    R      10      R      10         38.122
LGA    D      11      D      11         39.130
LGA    F      12      F      12         33.839
LGA    L      13      L      13         31.299
LGA    T      14      T      14         34.856
LGA    L      15      L      15         34.347
LGA    L      16      L      16         29.246
LGA    E      17      E      17         29.545
LGA    Q      18      Q      18         33.469
LGA    Q      19      Q      19         31.576
LGA    E      34      E      34          0.994
LGA    I      35      I      35          0.719
LGA    T      36      T      36          0.637
LGA    E      37      E      37          0.817
LGA    I      38      I      38          1.003
LGA    A      39      A      39          0.904
LGA    D      40      D      40          0.670
LGA    R      41      R      41          1.401
LGA    T      42      T      42          1.959
LGA    L      43      L      43          1.622
LGA    R      44      R      44          0.929
LGA    A      45      A      45          1.049
LGA    G      46      G      46          1.048
LGA    G      47      G      47          0.982
LGA    P      48      P      48          2.941
LGA    A      49      A      49          0.759
LGA    L      50      L      50          0.629
LGA    L      51      L      51          1.043
LGA    F      52      F      52          0.305
LGA    V      62      V      62         15.424
LGA    L      63      L      63         10.414
LGA    C      64      C      64         10.655
LGA    N      65      N      65         12.585
LGA    L      66      L      66         15.819
LGA    M      77      M      77         36.422
LGA    G      78      G      78         35.986
LGA    Q      79      Q      79         33.136
LGA    E      80      E      80         31.422
LGA    D      81      D      81         31.796
LGA    V      82      V      82         27.881
LGA    S      83      S      83         29.506
LGA    A      84      A      84         34.204
LGA    L      85      L      85         33.562
LGA    R      86      R      86         32.936
LGA    E      87      E      87         35.882
LGA    V      88      V      88         38.576
LGA    G      89      G      89         38.345
LGA    K      90      K      90         38.502
LGA    L      91      L      91         42.320
LGA    L      92      L      92         44.955
LGA    A      93      A      93         44.725
LGA    A     315      A     315         40.984
LGA    I     316      I     316         35.349
LGA    Y     317      Y     317         34.240
LGA    H     318      H     318         32.493
LGA    S     319      S     319         30.176
LGA    T     320      T     320         31.461
LGA    Y     321      Y     321         30.306

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   58  124    4.0     19    1.22    14.919    13.993     1.444

LGA_LOCAL      RMSD =  1.216  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 27.073  Number of atoms =   58 
Std_ALL_ATOMS  RMSD = 11.782  (standard rmsd on all 58 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.825510 * X  +  -0.343813 * Y  +  -0.447578 * Z  +  70.201019
  Y_new =  -0.310349 * X  +  -0.385844 * Y  +   0.868797 * Z  +  96.211090
  Z_new =  -0.471399 * X  +   0.856106 * Y  +   0.211816 * Z  +  63.024242 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.328249   -1.813343  [ DEG:    76.1031   -103.8969 ]
  Theta =   0.490876    2.650716  [ DEG:    28.1251    151.8748 ]
  Phi   =  -2.781991    0.359602  [ DEG:  -159.3963     20.6036 ]
 
# 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: T0356TS464_4-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_4-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   58  124   4.0   19   1.22  13.993    11.78
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_4-D1
PFRMAT TS
TARGET T0356
MODEL 4
PARENT N/A
ATOM      1  CA  ARG    10      37.915  88.143 100.515  1.00  0.00
ATOM      2  CA  ASP    11      35.973  85.216  99.120  1.00  0.00
ATOM      3  CA  PHE    12      39.054  83.094  98.500  1.00  0.00
ATOM      4  CA  LEU    13      40.383  83.983 101.947  1.00  0.00
ATOM      5  CA  THR    14      36.954  83.185 103.368  1.00  0.00
ATOM      6  CA  LEU    15      37.231  79.806 101.646  1.00  0.00
ATOM      7  CA  LEU    16      40.714  79.075 103.017  1.00  0.00
ATOM      8  CA  GLU    17      39.736  80.319 106.483  1.00  0.00
ATOM      9  CA  GLN    18      36.786  77.949 106.364  1.00  0.00
ATOM     10  CA  GLN    19      39.254  75.129 105.751  1.00  0.00
ATOM     11  CA  GLU    34      56.860  64.289  97.541  1.00  0.00
ATOM     12  CA  ILE    35      59.144  66.225  95.185  1.00  0.00
ATOM     13  CA  THR    36      58.586  63.887  92.225  1.00  0.00
ATOM     14  CA  GLU    37      54.763  64.224  92.495  1.00  0.00
ATOM     15  CA  ILE    38      55.422  67.935  92.993  1.00  0.00
ATOM     16  CA  ALA    39      56.933  68.673  89.578  1.00  0.00
ATOM     17  CA  ASP    40      54.268  66.368  88.107  1.00  0.00
ATOM     18  CA  ARG    41      51.505  67.571  90.449  1.00  0.00
ATOM     19  CA  THR    42      53.394  70.862  90.893  1.00  0.00
ATOM     20  CA  LEU    43      53.491  71.321  87.102  1.00  0.00
ATOM     21  CA  ARG    44      50.613  70.527  84.665  1.00  0.00
ATOM     22  CA  ALA    45      49.659  73.718  86.497  1.00  0.00
ATOM     23  CA  GLY    46      51.672  76.203  84.439  1.00  0.00
ATOM     24  CA  GLY    47      54.933  76.120  86.395  1.00  0.00
ATOM     25  CA  PRO    48      58.329  76.483  84.765  1.00  0.00
ATOM     26  CA  ALA    49      60.670  76.279  87.767  1.00  0.00
ATOM     27  CA  LEU    50      60.930  74.848  91.266  1.00  0.00
ATOM     28  CA  LEU    51      63.331  74.910  94.195  1.00  0.00
ATOM     29  CA  PHE    52      63.908  72.269  96.873  1.00  0.00
ATOM     30  CA  VAL    62      55.914  80.131  93.919  1.00  0.00
ATOM     31  CA  LEU    63      58.292  77.210  94.551  1.00  0.00
ATOM     32  CA  CYS    64      57.322  74.083  96.449  1.00  0.00
ATOM     33  CA  ASN    65      60.260  73.229  98.710  1.00  0.00
ATOM     34  CA  LEU    66      60.687  69.639  99.902  1.00  0.00
ATOM     35  CA  MET    77      48.622  72.043 104.088  1.00  0.00
ATOM     36  CA  GLY    78      47.458  70.529 100.769  1.00  0.00
ATOM     37  CA  GLN    79      46.872  71.012  97.021  1.00  0.00
ATOM     38  CA  GLU    80      43.934  73.304  97.719  1.00  0.00
ATOM     39  CA  ASP    81      46.099  75.517  99.978  1.00  0.00
ATOM     40  CA  VAL    82      48.976  75.681  97.515  1.00  0.00
ATOM     41  CA  SER    83      46.522  76.736  94.794  1.00  0.00
ATOM     42  CA  ALA    84      44.738  79.192  97.146  1.00  0.00
ATOM     43  CA  LEU    85      48.089  80.782  97.931  1.00  0.00
ATOM     44  CA  ARG    86      48.922  81.105  94.197  1.00  0.00
ATOM     45  CA  GLU    87      45.596  82.843  93.549  1.00  0.00
ATOM     46  CA  VAL    88      45.863  85.146  96.584  1.00  0.00
ATOM     47  CA  GLY    89      49.291  86.391  95.521  1.00  0.00
ATOM     48  CA  LYS    90      48.047  87.082  92.006  1.00  0.00
ATOM     49  CA  LEU    91      44.816  88.785  93.191  1.00  0.00
ATOM     50  CA  LEU    92      46.691  90.850  95.780  1.00  0.00
ATOM     51  CA  ALA    93      49.076  91.954  93.037  1.00  0.00
ATOM    114  CA  ALA   315      43.589  92.633 109.330  1.00  0.00
ATOM    115  CA  ILE   316      46.751  90.558 109.104  1.00  0.00
ATOM    116  CA  TYR   317      46.906  87.191 107.352  1.00  0.00
ATOM    117  CA  HIS   318      48.803  84.206 108.708  1.00  0.00
ATOM    118  CA  SER   319      49.009  80.509 107.900  1.00  0.00
ATOM    119  CA  THR   320      47.721  78.075 110.513  1.00  0.00
ATOM    120  CA  TYR   321      49.991  75.104 111.145  1.00  0.00
TER
END
