
#######################################################
#                                                     #
#                        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   67 (   67),  selected   64 , name T0379TS677_2-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS677_2-D2.T0379_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:    35        49 - 83          4.98     5.59
  LCS_AVERAGE:     48.02

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        54 - 67          1.69    12.61
  LONGEST_CONTINUOUS_SEGMENT:    14        55 - 68          1.76    12.59
  LCS_AVERAGE:     17.65

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        55 - 67          0.29    14.06
  LCS_AVERAGE:     14.92

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:   64
LCS_GDT     N      17     N      17     12   12   26     9   11   11   11   12   12   13   21   26   36   43   50   53   56   59   61   62   62   63   63 
LCS_GDT     R      18     R      18     12   12   26     9   11   11   11   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      19     E      19     12   12   26     9   11   11   11   12   12   12   18   29   36   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      20     E      20     12   12   26     9   11   11   11   12   12   12   21   26   36   43   50   53   56   59   61   62   62   63   63 
LCS_GDT     S      21     S      21     12   12   26     9   11   11   11   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     I      22     I      22     12   12   26     9   11   11   11   12   17   23   28   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     R      23     R      23     12   12   26     9   11   11   11   12   12   12   20   32   38   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     R      24     R      24     12   12   26     9   11   11   11   12   17   24   29   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     F      25     F      25     12   12   26     9   11   11   11   12   15   24   30   35   39   43   50   53   56   59   61   62   62   63   63 
LCS_GDT     K      26     K      26     12   12   26     9   11   11   11   12   14   23   28   34   39   43   50   53   56   59   61   62   62   63   63 
LCS_GDT     A      27     A      27     12   12   26     5   11   11   11   12   12   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     I      28     I      28     12   12   26     3    4    7   10   12   12   18   25   32   38   43   50   53   56   59   61   62   62   63   63 
LCS_GDT     G      29     G      29      5   10   26     3    3    5    7   10   11   15   17   26   35   40   48   53   56   59   61   62   62   63   63 
LCS_GDT     V      30     V      30      5   10   26     4    4    5    8   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     A      31     A      31      5   10   26     4    4    5    7   10   17   22   28   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     D      32     D      32      7   10   26     7    7    7    7   10   17   22   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     I      33     I      33      7   10   26     7    7    7    7   12   17   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      34     E      34      7   10   26     7    7    7    7   10   11   12   13   21   33   41   49   53   56   59   61   62   62   63   63 
LCS_GDT     E      35     E      35      7   10   26     7    7    7    7   10   11   12   14   18   31   43   50   53   56   59   61   62   62   63   63 
LCS_GDT     M      36     M      36      7   10   26     7    7    7    9   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     L      37     L      37      7   10   26     7    7    7    7   10   11   12   14   27   33   42   50   53   56   59   61   62   62   63   63 
LCS_GDT     D      38     D      38      7   10   26     7    7    7    7   10   10   12   14   18   23   28   31   41   52   57   60   62   62   63   63 
LCS_GDT     P      39     P      39      3    9   26     0    3    3    7    8    8   11   14   19   29   41   47   52   56   59   61   62   62   63   63 
LCS_GDT     K      43     K      43      3    8   26     0    3    3    6    7    8    8   27   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     G      44     G      44      7    8   26     5    7    7    7    7   10   17   24   33   38   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     L      45     L      45      7    8   26     5    7    7    7    7    8    9   15   26   37   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     F      46     F      46      7    8   22     5    7    7    7    7    8    9   10   12   15   18   20   35   51   57   61   62   62   63   63 
LCS_GDT     L      47     L      47      7    8   22     5    7    7    7    7    8    8   10   12   17   26   41   48   55   59   61   62   62   63   63 
LCS_GDT     D      48     D      48      7    8   22     5    7    7    7    7    8    8   10   11   14   21   38   49   55   59   61   62   62   63   63 
LCS_GDT     L      49     L      49      7    8   35     5    7    7    7    7    8    8    9   11   14   18   20   22   25   34   53   58   61   63   63 
LCS_GDT     E      50     E      50      7    8   35     5    7    7    7    7    8    8    9   11   14   18   20   22   23   26   29   57   61   62   63 
LCS_GDT     S      51     S      51      3    5   35     3    3    3    6    7   10   23   28   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     G      52     G      52      4    5   35     3    4    5    8   11   13   15   21   32   39   43   48   53   56   59   61   62   62   63   63 
LCS_GDT     R      53     R      53      4    5   35     3    4    5    6    7    8    9   10   11   26   31   46   51   56   59   61   62   62   63   63 
LCS_GDT     K      54     K      54      4   14   35     3    4    5    7    9   17   23   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     S      55     S      55     13   14   35    13   13   13   13   13   15   24   29   35   39   43   47   52   56   59   61   62   62   63   63 
LCS_GDT     E      56     E      56     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      57     E      57     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      58     E      58     13   14   35    13   13   13   13   13   15   24   30   35   39   43   47   52   56   59   61   62   62   63   63 
LCS_GDT     F      59     F      59     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     R      60     R      60     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     T      61     T      61     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      62     E      62     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     L      63     L      63     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     S      64     S      64     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     R      65     R      65     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     Y      66     Y      66     13   14   35    13   13   13   13   13   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     I      67     I      67     13   14   35    13   13   13   13   13   16   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     G      68     G      68      5   14   35     3    4    5    6   12   17   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     K      69     K      69      5    6   35     4    4    5    9   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     E      70     E      70      5    6   35     4    4    5    6   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     L      71     L      71      5   13   35     4    4    5    6    9   15   23   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     T      72     T      72     12   13   35     9   10   12   12   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     Y      73     Y      73     12   13   35     9   10   12   12   12   12   23   28   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     Q      74     Q      74     12   13   35     9   10   12   12   12   17   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     Q      75     Q      75     12   13   35     9   10   12   12   12   17   23   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     V      76     V      76     12   13   35     9   10   12   12   12   12   17   26   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     Y      77     Y      77     12   13   35     9   10   12   12   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     D      78     D      78     12   13   35     9   10   12   12   12   12   18   27   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     A      79     A      79     12   13   35     9   10   12   12   12   13   16   20   28   37   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     L      80     L      80     12   13   35     9   10   12   12   12   12   19   28   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     L      81     L      81     12   13   35     7   10   12   12   12   19   24   30   35   39   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     G      82     G      82     12   13   35     3    9   12   12   12   13   16   20   28   37   44   50   53   56   59   61   62   62   63   63 
LCS_GDT     F      83     F      83     12   13   35     3    9   12   12   12   13   16   21   28   37   44   50   53   56   59   61   62   62   63   63 
LCS_AVERAGE  LCS_A:  26.86  (  14.92   17.65   48.02 )

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     13     13     13     13     13     19     24     30     35     39     44     50     53     56     59     61     62     62     63     63 
GDT PERCENT_CA  20.31  20.31  20.31  20.31  20.31  29.69  37.50  46.88  54.69  60.94  68.75  78.12  82.81  87.50  92.19  95.31  96.88  96.88  98.44  98.44
GDT RMS_LOCAL    0.29   0.29   0.29   0.29   0.29   2.49   2.70   3.05   3.28   3.51   4.05   4.33   4.48   4.62   4.85   5.00   5.09   5.09   5.22   5.22
GDT RMS_ALL_CA  14.06  14.06  14.06  14.06  14.06   6.38   6.27   6.29   6.25   6.16   5.45   5.42   5.42   5.50   5.40   5.40   5.40   5.40   5.38   5.38

#      Molecule1      Molecule2       DISTANCE
LGA    N      17      N      17          6.913
LGA    R      18      R      18          2.257
LGA    E      19      E      19          7.962
LGA    E      20      E      20          7.639
LGA    S      21      S      21          2.714
LGA    I      22      I      22          4.466
LGA    R      23      R      23          6.375
LGA    R      24      R      24          4.430
LGA    F      25      F      25          3.994
LGA    K      26      K      26          5.081
LGA    A      27      A      27          3.679
LGA    I      28      I      28          5.739
LGA    G      29      G      29          6.465
LGA    V      30      V      30          3.180
LGA    A      31      A      31          4.339
LGA    D      32      D      32          3.667
LGA    I      33      I      33          3.779
LGA    E      34      E      34          7.918
LGA    E      35      E      35          7.194
LGA    M      36      M      36          1.926
LGA    L      37      L      37          8.077
LGA    D      38      D      38         11.254
LGA    P      39      P      39          9.916
LGA    K      43      K      43          7.727
LGA    G      44      G      44          8.040
LGA    L      45      L      45          8.639
LGA    F      46      F      46         11.630
LGA    L      47      L      47         10.777
LGA    D      48      D      48          9.759
LGA    L      49      L      49         12.474
LGA    E      50      E      50         14.306
LGA    S      51      S      51          7.285
LGA    G      52      G      52          7.610
LGA    R      53      R      53          9.758
LGA    K      54      K      54          3.774
LGA    S      55      S      55          4.290
LGA    E      56      E      56          1.715
LGA    E      57      E      57          2.694
LGA    E      58      E      58          3.996
LGA    F      59      F      59          2.886
LGA    R      60      R      60          1.929
LGA    T      61      T      61          3.016
LGA    E      62      E      62          2.996
LGA    L      63      L      63          2.669
LGA    S      64      S      64          2.997
LGA    R      65      R      65          2.327
LGA    Y      66      Y      66          2.014
LGA    I      67      I      67          3.886
LGA    G      68      G      68          3.325
LGA    K      69      K      69          2.472
LGA    E      70      E      70          2.910
LGA    L      71      L      71          3.977
LGA    T      72      T      72          2.768
LGA    Y      73      Y      73          5.285
LGA    Q      74      Q      74          3.651
LGA    Q      75      Q      75          3.788
LGA    V      76      V      76          4.992
LGA    Y      77      Y      77          2.210
LGA    D      78      D      78          4.391
LGA    A      79      A      79          7.161
LGA    L      80      L      80          5.282
LGA    L      81      L      81          2.331
LGA    G      82      G      82          8.507
LGA    F      83      F      83          7.980

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   67   64    4.0     30    3.05    45.703    38.582     0.951

LGA_LOCAL      RMSD =  3.054  Number of atoms =   30  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.217  Number of atoms =   64 
Std_ALL_ATOMS  RMSD =  5.376  (standard rmsd on all 64 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.715514 * X  +   0.693449 * Y  +  -0.084666 * Z  +  56.791790
  Y_new =  -0.690045 * X  +  -0.682638 * Y  +   0.240506 * Z  +  31.129423
  Z_new =   0.108983 * X  +   0.230509 * Y  +   0.966948 * Z  +  -6.594794 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.234020   -2.907573  [ DEG:    13.4084   -166.5916 ]
  Theta =  -0.109200   -3.032393  [ DEG:    -6.2567   -173.7433 ]
  Phi   =  -2.374312    0.767280  [ DEG:  -136.0381     43.9619 ]
 
# 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: T0379TS677_2-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0379TS677_2-D2.T0379_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   67   64   4.0   30   3.05  38.582     5.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS677_2-D2
PFRMAT TS
TARGET T0379
MODEL  2  REFINED
PARENT 1qh9_A
ATOM     19  CA  ASN    17      62.626   3.886  15.318  1.00 99.00
ATOM     20  CA  ARG    18      64.966   6.731  16.260  1.00 99.00
ATOM     21  CA  GLU    19      62.805   7.559  19.295  1.00 99.00
ATOM     22  CA  GLU    20      63.109   3.975  20.552  1.00 91.00
ATOM     23  CA  SER    21      66.865   4.337  20.842  1.00 99.00
ATOM     24  CA  ILE    22      66.643   7.720  22.512  1.00 90.00
ATOM     25  CA  ARG    23      64.256   6.167  25.073  1.00 99.00
ATOM     26  CA  ARG    24      66.607   3.269  25.806  1.00 99.00
ATOM     27  CA  PHE    25      69.421   5.717  26.445  1.00 99.00
ATOM     28  CA  LYS    26      67.253   7.448  29.038  1.00 99.00
ATOM     29  CA  ALA    27      66.020   4.214  30.636  1.00 99.00
ATOM     30  CA  ILE    28      68.520   1.431  29.689  1.00 99.00
ATOM     31  CA  GLY    29      66.871  -1.846  28.715  1.00 94.00
ATOM     32  CA  VAL    30      63.329  -0.377  28.666  1.00 84.00
ATOM     33  CA  ALA    31      63.386   1.481  25.318  1.00 84.00
ATOM     34  CA  ASP    32      61.104  -0.847  23.328  1.00 99.00
ATOM     35  CA  ILE    33      58.554  -0.945  26.174  1.00 99.00
ATOM     36  CA  GLU    34      58.463   2.807  26.696  1.00 99.00
ATOM     37  CA  GLU    35      58.140   3.717  23.024  1.00 99.00
ATOM     38  CA  MET    36      55.547   1.008  22.392  1.00 99.00
ATOM     39  CA  LEU    37      53.137   2.124  25.135  1.00 99.00
ATOM     40  CA  ASP    38      53.906   5.833  24.601  1.00 99.00
ATOM     41  CA  PRO    39      52.723   5.619  20.972  1.00 99.00
ATOM     42  CA  TYR    40      49.467   3.848  21.856  1.00 82.00
ATOM     43  CA  LEU    41      48.640   6.372  24.579  1.00 80.00
ATOM     44  CA  GLN    42      49.292   9.214  22.104  1.00 66.00
ATOM     45  CA  LYS    43      46.712   7.639  19.776  1.00 52.00
ATOM     46  CA  GLY    44      44.199   6.890  22.525  1.00 37.00
ATOM     47  CA  LEU    45      44.432  10.356  24.039  1.00 56.00
ATOM     48  CA  PHE    46      43.787  12.118  20.734  1.00 60.00
ATOM     49  CA  LEU    47      40.776   9.870  20.082  1.00 99.00
ATOM     50  CA  ASP    48      39.384   9.983  23.635  1.00 99.00
ATOM     51  CA  LEU    49      39.743  13.753  24.007  1.00 99.00
ATOM     52  CA  GLU    50      38.015  14.218  20.634  1.00 79.00
ATOM     60  CA  SER    51      49.540  17.359  20.337  1.00 92.00
ATOM     61  CA  GLY    52      52.556  18.569  22.302  1.00 99.00
ATOM     62  CA  ARG    53      50.590  18.394  25.551  1.00 99.00
ATOM     63  CA  LYS    54      49.055  15.080  24.470  1.00 99.00
ATOM     64  CA  SER    55      52.566  13.709  23.830  1.00 99.00
ATOM     65  CA  GLU    56      53.852  14.751  27.271  1.00 99.00
ATOM     66  CA  GLU    57      50.785  13.319  29.049  1.00 94.00
ATOM     67  CA  GLU    58      51.179  10.059  27.159  1.00 99.00
ATOM     68  CA  PHE    59      54.819   9.844  28.293  1.00 99.00
ATOM     69  CA  ARG    60      54.019  10.771  31.909  1.00 99.00
ATOM     70  CA  THR    61      51.451   7.945  32.094  1.00 99.00
ATOM     71  CA  GLU    62      53.862   5.532  30.375  1.00 99.00
ATOM     72  CA  LEU    63      56.633   6.060  32.918  1.00 99.00
ATOM     73  CA  SER    64      54.264   6.101  35.888  1.00 99.00
ATOM     74  CA  ARG    65      52.774   2.825  34.621  1.00 99.00
ATOM     75  CA  TYR    66      56.241   1.271  34.259  1.00 99.00
ATOM     76  CA  ILE    67      57.567   2.411  37.630  1.00 99.00
ATOM     77  CA  GLY    68      60.008   4.784  35.941  1.00 99.00
ATOM     78  CA  LYS    69      60.862   8.180  37.395  1.00 99.00
ATOM     79  CA  GLU    70      60.536  10.904  34.752  1.00 99.00
ATOM     80  CA  LEU    71      62.057  14.312  35.455  1.00 99.00
ATOM     81  CA  THR    72      61.381  17.427  33.347  1.00 99.00
ATOM     82  CA  TYR    73      64.795  17.411  31.695  1.00 99.00
ATOM     83  CA  GLN    74      64.487  13.835  30.420  1.00 99.00
ATOM     84  CA  GLN    75      60.873  14.443  29.382  1.00 99.00
ATOM     85  CA  VAL    76      61.832  17.275  27.049  1.00 99.00
ATOM     86  CA  TYR    77      64.690  15.278  25.484  1.00 99.00
ATOM     87  CA  ASP    78      62.478  12.327  24.546  1.00 99.00
ATOM     88  CA  ALA    79      59.879  14.716  23.171  1.00 99.00
ATOM     89  CA  LEU    80      62.491  16.569  21.094  1.00 99.00
ATOM     90  CA  LEU    81      63.393  13.207  19.544  1.00 53.00
ATOM     91  CA  GLY    82      60.391  13.509  17.204  1.00 78.00
ATOM     92  CA  PHE    83      61.792  16.682  15.619  1.00 87.00
TER
END
