
#######################################################
#                                                     #
#                        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   76 (   76),  selected   62 , name T0309TS599_4
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS599_4.T0309.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:    27        30 - 56          4.98    17.95
  LCS_AVERAGE:     33.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        26 - 40          1.99    19.57
  LCS_AVERAGE:     16.39

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        34 - 43          0.77    20.92
  LCS_AVERAGE:     10.07

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:   62
LCS_GDT     A       2     A       2      3    3   14     3    3    3    3    3    4    5    6    8   10   13   14   14   15   15   16   16   16   16   16 
LCS_GDT     S       3     S       3      3    3   14     3    3    3    3    3    4    5    6    8   10   13   14   14   15   15   16   16   16   16   17 
LCS_GDT     K       4     K       4      3    3   14     3    3    3    3    3    4    5    6    8   10   13   14   14   15   15   16   16   16   16   18 
LCS_GDT     K       5     K       5      3    3   14     3    3    3    3    3    4    5    5    7   10   13   14   14   15   15   16   16   16   16   17 
LCS_GDT     V       6     V       6      3    3   14     3    3    3    3    4    6    7    8    9   10   13   14   14   15   15   16   18   18   23   23 
LCS_GDT     H       7     H       7      3    8   14     3    3    4    6    6    8    9    9    9   10   13   14   14   16   18   19   20   21   24   24 
LCS_GDT     Q       8     Q       8      6    8   14     3    5    6    7    7    8    9    9    9   10   13   14   14   16   18   19   20   21   24   25 
LCS_GDT     I       9     I       9      6    8   14     3    5    6    7    7    8    9    9    9   10   13   14   14   16   18   19   20   21   24   28 
LCS_GDT     N      10     N      10      6    8   14     3    5    6    7    7    8    9    9    9   10   13   14   14   17   25   27   31   32   34   35 
LCS_GDT     V      11     V      11      6    8   14     3    5    6    7    7    8    9    9    9   11   13   15   17   20   21   23   25   32   34   35 
LCS_GDT     K      12     K      12      6    8   14     3    5    6    7    7    8    9    9    9   10   13   15   16   20   21   23   25   30   34   35 
LCS_GDT     G      13     G      13      6    8   14     3    5    6    7    7    8    9    9    9   10   13   14   14   15   17   19   21   22   25   27 
LCS_GDT     F      14     F      14      5    8   14     3    5    5    7    7    8    9    9    9   10   11   12   13   15   18   19   21   23   24   26 
LCS_GDT     F      15     F      15      5    8   14     3    5    5    6    6    8    9   11   14   16   18   20   20   22   23   24   24   27   27   29 
LCS_GDT     D      16     D      16      5    5   13     3    5    5    6    6    6    7    8   11   13   16   18   19   20   23   24   24   26   27   27 
LCS_GDT     M      17     M      17      5    5   13     3    5    5    6    6    6    7    7   10   11   12   15   18   20   23   24   24   26   27   27 
LCS_GDT     D      18     D      18      5    5   13     3    5    5    6    6    6    7    7    9   10   12   13   15   17   19   22   24   26   26   27 
LCS_GDT     V      19     V      19      3    4   13     3    3    3    4    4    6    7    7    9   10   11   12   14   17   19   20   21   22   25   27 
LCS_GDT     M      20     M      20      3    4   13     3    3    3    3    4    4    5    6    9   10   11   13   13   16   17   20   21   22   25   27 
LCS_GDT     E      21     E      21      3    4   13     3    3    3    4    4    5    6    7    9   10   12   13   16   20   20   22   24   26   26   27 
LCS_GDT     V      22     V      22      3    4   13     1    3    3    4    5    5    6    7    9   10   12   15   17   20   23   24   24   28   31   34 
LCS_GDT     T      23     T      23      3    3   23     1    3    3    4    5    5    6    7    9   10   12   13   15   20   23   24   25   28   32   35 
LCS_GDT     E      24     E      24      3    3   25     3    4    4   10   13   13   14   14   15   16   17   20   23   27   30   30   31   32   34   35 
LCS_GDT     Q      25     Q      25      3    4   26     3    4    4    4    5   11   14   16   18   19   21   21   26   29   30   30   31   32   34   35 
LCS_GDT     T      26     T      26      4   15   26     4    4    5   11   13   14   15   17   18   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     K      27     K      27      4   15   26     4    5    5   11   13   14   15   17   18   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     E      28     E      28      4   15   26     4    4    6   11   13   14   15   17   18   20   21   23   27   29   30   30   31   32   34   35 
LCS_GDT     A      29     A      29      5   15   26     4    5    8   11   13   14   15   17   18   20   21   21   23   26   30   30   31   32   34   35 
LCS_GDT     E      30     E      30      5   15   27     3    5    6    8   10   14   15   17   18   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     Y      31     Y      31      6   15   27     4    5    8   11   13   14   15   17   18   20   21   21   24   29   30   30   31   32   34   35 
LCS_GDT     T      32     T      32      6   15   27     4    5    8   11   13   14   15   17   18   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     Y      33     Y      33      8   15   27     4    5    8   11   13   14   15   17   18   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     D      34     D      34     10   15   27     4    8   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     F      35     F      35     10   15   27     6    9   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     K      36     K      36     10   15   27     6    9   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     E      37     E      37     10   15   27     6    9   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     I      38     I      38     10   15   27     6    9   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     L      39     L      39     10   15   27     6    9   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     S      40     S      40     10   15   27     6    9   10   10   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     E      41     E      41     10   14   27     5    9   10   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     F      42     F      42     10   14   27     5    9   10   11   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     N      43     N      43     10   14   27     5    9   10   10   11   12   14   16   18   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     G      44     G      44      6   14   27     3    5    8   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     K      45     K      45      8   14   27     3    5    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     N      46     N      46      9   14   27     4    8    9   12   13   14   14   15   18   19   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     V      47     V      47      9   14   27     5    8    9   12   13   14   14   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     S      48     S      48      9   14   27     5    8    9   12   13   14   14   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     I      49     I      49      9   14   27     5    8    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     T      50     T      50      9   14   27     5    8    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     V      51     V      51      9   14   27     4    8    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     K      52     K      52      9   14   27     5    8    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     E      53     E      53      9   14   27     4    8    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     E      54     E      54      9   14   27     4    8    9   12   13   14   15   17   19   20   21   24   27   29   30   30   31   32   34   35 
LCS_GDT     N      55     N      55      4    9   27     3    3    5    6    8    9    9   11   14   17   20   22   23   24   28   30   31   32   34   35 
LCS_GDT     E      56     E      56      6    9   27     4    5    6    7    8    9    9    9   10   12   19   22   23   24   24   26   30   31   32   33 
LCS_GDT     L      57     L      57      6    9   25     4    5    6    7    8    9    9    9   10   10   10   10   10   12   13   16   19   22   24   25 
LCS_GDT     P      58     P      58      6    9   11     4    5    6    7    8    9    9    9   10   10   10   10   10   12   14   16   19   21   24   24 
LCS_GDT     V      59     V      59      6    9   11     4    5    6    7    8    9    9    9   10   10   10   10   10   11   14   16   19   19   20   25 
LCS_GDT     K      60     K      60      6    9   11     3    5    6    7    8    9    9    9   10   10   10   10   10   10   10   16   19   19   19   25 
LCS_GDT     G      61     G      61      6    9   11     3    4    6    7    8    9    9    9   10   10   10   10   10   10   11   11   12   14   16   21 
LCS_GDT     V      62     V      62      5    9   11     3    4    5    7    8    9    9    9   10   10   10   10   10   10   11   11   12   13   16   17 
LCS_GDT     E      63     E      63      5    9   11     3    4    5    7    8    9    9    9   10   10   10   10   10   10   10   10   11   11   11   11 
LCS_AVERAGE  LCS_A:  19.96  (  10.07   16.39   33.43 )

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      6      9     10     12     13     14     15     17     19     20     21     24     27     29     30     30     31     32     34     35 
GDT PERCENT_CA   9.68  14.52  16.13  19.35  20.97  22.58  24.19  27.42  30.65  32.26  33.87  38.71  43.55  46.77  48.39  48.39  50.00  51.61  54.84  56.45
GDT RMS_LOCAL    0.26   0.60   0.77   1.39   1.50   1.80   1.99   2.51   3.02   3.17   3.33   4.36   4.92   5.21   5.32   5.32   5.54   5.66   6.24   6.44
GDT RMS_ALL_CA  21.68  21.20  20.92  18.06  17.95  19.66  19.57  19.19  18.42  18.39  18.38  17.84  17.72  17.74  17.77  17.77  17.75  17.77  17.76  17.67

#      Molecule1      Molecule2       DISTANCE
LGA    A       2      A       2         37.890
LGA    S       3      S       3         37.996
LGA    K       4      K       4         37.190
LGA    K       5      K       5         32.178
LGA    V       6      V       6         28.026
LGA    H       7      H       7         28.804
LGA    Q       8      Q       8         24.108
LGA    I       9      I       9         18.945
LGA    N      10      N      10         13.707
LGA    V      11      V      11         12.124
LGA    K      12      K      12          8.795
LGA    G      13      G      13         13.841
LGA    F      14      F      14         14.744
LGA    F      15      F      15         14.636
LGA    D      16      D      16         21.556
LGA    M      17      M      17         22.654
LGA    D      18      D      18         29.385
LGA    V      19      V      19         29.283
LGA    M      20      M      20         27.176
LGA    E      21      E      21         20.318
LGA    V      22      V      22         15.273
LGA    T      23      T      23         14.950
LGA    E      24      E      24         11.073
LGA    Q      25      Q      25          7.358
LGA    T      26      T      26          1.630
LGA    K      27      K      27          1.956
LGA    E      28      E      28          2.911
LGA    A      29      A      29          2.574
LGA    E      30      E      30          3.850
LGA    Y      31      Y      31          2.631
LGA    T      32      T      32          1.405
LGA    Y      33      Y      33          2.310
LGA    D      34      D      34          2.397
LGA    F      35      F      35          3.657
LGA    K      36      K      36          2.293
LGA    E      37      E      37          0.800
LGA    I      38      I      38          2.111
LGA    L      39      L      39          1.100
LGA    S      40      S      40          2.059
LGA    E      41      E      41          3.533
LGA    F      42      F      42          3.956
LGA    N      43      N      43          4.530
LGA    G      44      G      44          5.324
LGA    K      45      K      45          7.033
LGA    N      46      N      46         10.380
LGA    V      47      V      47          9.788
LGA    S      48      S      48         11.055
LGA    I      49      I      49         11.207
LGA    T      50      T      50         11.530
LGA    V      51      V      51         12.358
LGA    K      52      K      52         13.297
LGA    E      53      E      53         13.249
LGA    E      54      E      54         14.081
LGA    N      55      N      55         14.981
LGA    E      56      E      56         18.282
LGA    L      57      L      57         22.479
LGA    P      58      P      58         27.313
LGA    V      59      V      59         29.418
LGA    K      60      K      60         35.594
LGA    G      61      G      61         35.862
LGA    V      62      V      62         30.760
LGA    E      63      E      63         33.093

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   76   62    4.0     17    2.51    27.419    24.810     0.651

LGA_LOCAL      RMSD =  2.510  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 18.898  Number of atoms =   62 
Std_ALL_ATOMS  RMSD = 15.335  (standard rmsd on all 62 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.355045 * X  +  -0.656644 * Y  +  -0.665403 * Z  +   0.608720
  Y_new =  -0.914370 * X  +  -0.095756 * Y  +  -0.393393 * Z  + -18.150095
  Z_new =   0.194603 * X  +   0.748097 * Y  +  -0.634413 * Z  +  -8.988368 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.274149   -0.867444  [ DEG:   130.2991    -49.7009 ]
  Theta =  -0.195853   -2.945740  [ DEG:   -11.2215   -168.7785 ]
  Phi   =  -1.200421    1.941171  [ DEG:   -68.7791    111.2209 ]
 
# 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: T0309TS599_4                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309TS599_4.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   76   62   4.0   17   2.51  24.810    15.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS599_4
PFRMAT TS                                                                       
TARGET T0309                                                                    
MODEL  4                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1      -2.636 -30.554 -20.799  1.00  0.00              
ATOM      2  CA  ALA     2       0.112 -31.753 -23.758  1.00  0.00              
ATOM      3  CA  SER     3       3.337 -34.308 -22.822  1.00  0.00              
ATOM      4  CA  LYS     4       6.250 -31.410 -21.848  1.00  0.00              
ATOM      5  CA  LYS     5       3.347 -29.583 -20.176  1.00  0.00              
ATOM      6  CA  VAL     6       2.493 -32.712 -18.094  1.00  0.00              
ATOM      7  CA  HIS     7       6.037 -33.227 -16.906  1.00  0.00              
ATOM      8  CA  GLN     8       6.812 -29.561 -16.242  1.00  0.00              
ATOM      9  CA  ILE     9       4.076 -28.659 -13.840  1.00  0.00              
ATOM     10  CA  ASN    10       5.587 -26.491 -11.196  1.00  0.00              
ATOM     11  CA  VAL    11       3.854 -26.483  -7.769  1.00  0.00              
ATOM     12  CA  LYS    12       5.295 -23.533  -5.952  1.00  0.00              
ATOM     13  CA  GLY    13       4.642 -24.270  -2.269  1.00  0.00              
ATOM     14  CA  PHE    14       1.996 -21.544  -1.762  1.00  0.00              
ATOM     15  CA  PHE    15       0.148 -22.427  -4.983  1.00  0.00              
ATOM     16  CA  ASP    16       0.131 -26.113  -5.824  1.00  0.00              
ATOM     17  CA  MET    17       0.189 -25.765  -9.613  1.00  0.00              
ATOM     18  CA  ASP    18      -0.899 -28.698 -11.559  1.00  0.00              
ATOM     19  CA  VAL    19       0.093 -29.024 -15.100  1.00  0.00              
ATOM     20  CA  MET    20      -3.124 -28.202 -16.963  1.00  0.00              
ATOM     21  CA  GLU    21      -3.582 -25.003 -14.893  1.00  0.00              
ATOM     22  CA  VAL    22      -0.042 -23.746 -15.438  1.00  0.00              
ATOM     23  CA  THR    23      -0.152 -24.250 -19.230  1.00  0.00              
ATOM     24  CA  GLU    24      -3.435 -22.516 -19.770  1.00  0.00              
ATOM     25  CA  GLN    25      -2.542 -19.439 -17.803  1.00  0.00              
ATOM     26  CA  THR    26       0.886 -19.210 -19.523  1.00  0.00              
ATOM     27  CA  LYS    27      -0.399 -19.527 -23.037  1.00  0.00              
ATOM     28  CA  GLU    28      -2.874 -16.763 -22.652  1.00  0.00              
ATOM     29  CA  ALA    29      -0.560 -14.315 -20.790  1.00  0.00              
ATOM     30  CA  GLU    30      -3.072 -12.819 -18.462  1.00  0.00              
ATOM     31  CA  TYR    31      -1.812 -11.653 -15.123  1.00  0.00              
ATOM     32  CA  THR    32      -2.775  -8.215 -13.704  1.00  0.00              
ATOM     33  CA  TYR    33      -3.182  -7.500 -10.020  1.00  0.00              
ATOM     34  CA  ASP    34      -3.201  -4.057  -8.309  1.00  0.00              
ATOM     35  CA  PHE    35      -2.363  -4.225  -4.549  1.00  0.00              
ATOM     36  CA  LYS    36      -5.678  -2.818  -3.246  1.00  0.00              
ATOM     37  CA  GLU    37      -7.511  -5.256  -5.532  1.00  0.00              
ATOM     38  CA  ILE    38      -5.533  -8.280  -4.427  1.00  0.00              
ATOM     39  CA  LEU    39      -6.117  -7.400  -0.745  1.00  0.00              
ATOM     40  CA  SER    40      -9.815  -6.928  -1.490  1.00  0.00              
ATOM     41  CA  GLU    41     -10.065 -10.267  -3.318  1.00  0.00              
ATOM     42  CA  PHE    42      -8.419 -12.103  -0.473  1.00  0.00              
ATOM     43  CA  ASN    43     -10.593 -10.506   2.277  1.00  0.00              
ATOM     44  CA  GLY    44      -7.584  -9.082   4.118  1.00  0.00              
ATOM     45  CA  LYS    45      -5.378 -12.181   3.643  1.00  0.00              
ATOM     46  CA  ASN    46      -2.007 -11.636   2.085  1.00  0.00              
ATOM     47  CA  VAL    47      -1.746 -13.032  -1.379  1.00  0.00              
ATOM     48  CA  SER    48       1.351 -13.815  -3.335  1.00  0.00              
ATOM     49  CA  ILE    49       1.334 -13.186  -7.120  1.00  0.00              
ATOM     50  CA  THR    50       3.964 -14.730  -9.339  1.00  0.00              
ATOM     51  CA  VAL    51       4.937 -12.964 -12.610  1.00  0.00              
ATOM     52  CA  LYS    52       6.274 -15.170 -15.353  1.00  0.00              
ATOM     53  CA  GLU    53       9.010 -13.789 -17.533  1.00  0.00              
ATOM     54  CA  GLU    54       9.383 -16.675 -19.935  1.00  0.00              
ATOM     55  CA  ASN    55       5.669 -17.421 -20.315  1.00  0.00              
ATOM     56  CA  GLU    56       4.917 -13.725 -20.939  1.00  0.00              
ATOM     57  CA  LEU    57       3.098 -12.441 -17.915  1.00  0.00              
ATOM     58  CA  PRO    58       1.198  -9.213 -18.202  1.00  0.00              
ATOM     59  CA  VAL    59       2.524  -6.638 -15.655  1.00  0.00              
ATOM     60  CA  LYS    60      -0.097  -5.048 -13.462  1.00  0.00              
ATOM     61  CA  GLY    61       1.436  -4.979  -9.973  1.00  0.00              
ATOM     62  CA  VAL    62       3.416  -8.193 -10.003  1.00  0.00              
ATOM     63  CA  GLU    63       4.400  -9.736  -6.637  1.00  0.00              
ATOM     64  CA  MET    64       6.975 -12.351  -6.554  1.00  0.00              
ATOM     65  CA  ALA    65       6.768 -14.854  -3.879  1.00  0.00              
ATOM     66  CA  GLY    66       9.829 -16.818  -2.981  1.00  0.00              
ATOM     67  CA  ASP    67       8.460 -17.840   0.467  1.00  0.00              
ATOM     68  CA  PRO    68       5.727 -20.258  -0.361  1.00  0.00              
ATOM     69  CA  LEU    69       6.213 -22.971   2.339  1.00  0.00              
ATOM     70  CA  GLU    70       2.757 -24.039   3.499  1.00  0.00              
ATOM     71  CA  HIS    71       3.206 -26.023   6.739  1.00  0.00              
ATOM     72  CA  HIS    72       0.031 -28.041   6.754  1.00  0.00              
ATOM     73  CA  HIS    73      -1.409 -28.879  10.032  1.00  0.00              
ATOM     74  CA  HIS    74       0.837 -25.964  10.854  1.00  0.00              
ATOM     75  CA  HIS    75      -0.251 -23.879  13.892  1.00  0.00              
ATOM     76  CA  HIS    76      -3.888 -22.727  13.675  1.00  0.00              
TER                                                                             
END
