
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0353AL381_2
# Molecule2: number of CA atoms   85 ( 1334),  selected   15 , name T0353.pdb
# PARAMETERS: T0353AL381_2.T0353.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:    12        55 - 66          4.55     7.20
  LCS_AVERAGE:     13.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        62 - 66          1.39    16.71
  LCS_AVERAGE:      5.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        52 - 54          0.50    23.27
  LONGEST_CONTINUOUS_SEGMENT:     3        53 - 55          0.70    20.11
  LONGEST_CONTINUOUS_SEGMENT:     3        54 - 56          0.43     9.99
  LONGEST_CONTINUOUS_SEGMENT:     3        55 - 57          0.81    18.80
  LONGEST_CONTINUOUS_SEGMENT:     3        56 - 58          0.43     9.86
  LONGEST_CONTINUOUS_SEGMENT:     3        57 - 59          0.21    13.82
  LONGEST_CONTINUOUS_SEGMENT:     3        59 - 61          0.50    12.83
  LONGEST_CONTINUOUS_SEGMENT:     3        60 - 62          0.99    11.87
  LONGEST_CONTINUOUS_SEGMENT:     3        61 - 63          0.43    15.12
  LONGEST_CONTINUOUS_SEGMENT:     3        62 - 64          0.66    20.36
  LONGEST_CONTINUOUS_SEGMENT:     3        63 - 65          0.12    17.29
  LONGEST_CONTINUOUS_SEGMENT:     3        64 - 66          0.17    11.19
  LCS_AVERAGE:      3.53

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:   85
LCS_GDT     S      52     S      52      3    3   10     0    3    3    3    3    3    5    6    7    9    9    9   10   14   14   14   15   15   15   15 
LCS_GDT     E      53     E      53      3    4   10     1    3    3    3    4    4    5    6    7    9    9    9    9   11   11   12   15   15   15   15 
LCS_GDT     E      54     E      54      3    4   10     3    3    3    3    4    4    5    6    7    9    9    9   11   14   14   14   15   15   15   15 
LCS_GDT     C      55     C      55      3    4   12     3    3    3    3    4    4    5    6    7    9    9   12   12   14   14   14   15   15   15   15 
LCS_GDT     R      56     R      56      3    4   12     3    3    3    3    4    4    5    6    7   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     F      57     F      57      3    4   12     3    3    3    3    4    4    5    6    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     C      58     C      58      3    4   12     3    3    3    3    4    4    5    6    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     H      59     H      59      3    4   12     3    3    3    3    4    4    4    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     S      60     S      60      3    4   12     1    3    3    3    4    4    6    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     Q      61     Q      61      3    4   12     3    3    3    3    4    5    6    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     K      62     K      62      3    5   12     3    3    4    5    5    5    6    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     A      63     A      63      3    5   12     3    3    4    5    5    5    6    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     P      64     P      64      3    5   12     3    3    4    5    5    5    6    8    8   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     D      65     D      65      3    5   12     3    3    4    5    5    5    6    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_GDT     E      66     E      66      3    5   12     3    3    4    5    5    5    6    8    9   10   11   12   12   14   14   14   15   15   15   15 
LCS_AVERAGE  LCS_A:   7.40  (   3.53    5.02   13.65 )

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      3      3      4      5      5      5      6      8      9     10     11     12     12     14     14     14     15     15     15     15 
GDT PERCENT_CA   3.53   3.53   4.71   5.88   5.88   5.88   7.06   9.41  10.59  11.76  12.94  14.12  14.12  16.47  16.47  16.47  17.65  17.65  17.65  17.65
GDT RMS_LOCAL    0.12   0.12   1.09   1.39   1.39   1.39   2.53   3.20   3.80   3.93   4.12   4.55   4.55   5.65   5.65   5.65   5.96   5.96   5.96   5.96
GDT RMS_ALL_CA  17.29  17.29  19.31  16.71  16.71  16.71  11.51  10.68   7.89   8.00   7.79   7.20   7.20   6.02   6.02   6.02   5.96   5.96   5.96   5.96

#      Molecule1      Molecule2       DISTANCE
LGA    S      52      S      52         22.488
LGA    E      53      E      53         21.092
LGA    E      54      E      54         17.836
LGA    C      55      C      55         12.472
LGA    R      56      R      56          8.817
LGA    F      57      F      57          8.700
LGA    C      58      C      58          8.074
LGA    H      59      H      59          3.953
LGA    S      60      S      60          3.390
LGA    Q      61      Q      61          2.843
LGA    K      62      K      62          2.716
LGA    A      63      A      63          3.110
LGA    P      64      P      64          3.697
LGA    D      65      D      65          2.685
LGA    E      66      E      66          3.461

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   85    4.0      8    3.20     8.824     7.958     0.242

LGA_LOCAL      RMSD =  3.203  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.733  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  5.961  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.804173 * X  +   0.564754 * Y  +  -0.185361 * Z  +  -7.811792
  Y_new =  -0.472891 * X  +  -0.796813 * Y  +  -0.376116 * Z  +  44.214344
  Z_new =  -0.360111 * X  +  -0.214806 * Y  +   0.907843 * Z  +   8.586418 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.232339    2.909254  [ DEG:   -13.3120    166.6880 ]
  Theta =   0.368387    2.773206  [ DEG:    21.1070    158.8930 ]
  Phi   =  -2.610008    0.531584  [ DEG:  -149.5425     30.4575 ]
 
# 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: T0353AL381_2                                  
REMARK     2: T0353.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0353AL381_2.T0353.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   85   4.0    8   3.20   7.958     5.96
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL381_2
REMARK Aligment from pdb entry: 1mdvA
ATOM      1  N   SER    52      11.687  17.457  -8.537  1.00  0.00              
ATOM      2  CA  SER    52      12.190  17.209  -7.196  1.00  0.00              
ATOM      3  C   SER    52      11.470  15.939  -6.772  1.00  0.00              
ATOM      4  O   SER    52      10.333  15.718  -7.173  1.00  0.00              
ATOM      5  N   GLU    53      12.135  15.086  -6.003  1.00  0.00              
ATOM      6  CA  GLU    53      11.526  13.831  -5.562  1.00  0.00              
ATOM      7  C   GLU    53      10.367  14.023  -4.584  1.00  0.00              
ATOM      8  O   GLU    53      10.464  14.819  -3.647  1.00  0.00              
ATOM      9  N   GLU    54       9.273  13.296  -4.820  1.00  0.00              
ATOM     10  CA  GLU    54       8.077  13.362  -3.975  1.00  0.00              
ATOM     11  C   GLU    54       8.168  12.319  -2.863  1.00  0.00              
ATOM     12  O   GLU    54       9.111  11.534  -2.845  1.00  0.00              
ATOM     13  N   CYS    55       7.181  12.289  -1.964  1.00  0.00              
ATOM     14  CA  CYS    55       7.203  11.328  -0.860  1.00  0.00              
ATOM     15  C   CYS    55       7.250   9.898  -1.400  1.00  0.00              
ATOM     16  O   CYS    55       8.087   9.092  -0.986  1.00  0.00              
ATOM     17  N   ARG    56       6.365   9.605  -2.351  1.00  0.00              
ATOM     18  CA  ARG    56       6.284   8.284  -2.970  1.00  0.00              
ATOM     19  C   ARG    56       7.474   8.039  -3.896  1.00  0.00              
ATOM     20  O   ARG    56       8.032   6.937  -3.924  1.00  0.00              
ATOM     21  N   PHE    57       7.857   9.070  -4.645  1.00  0.00              
ATOM     22  CA  PHE    57       8.982   8.962  -5.563  1.00  0.00              
ATOM     23  C   PHE    57      10.287   8.455  -4.960  1.00  0.00              
ATOM     24  O   PHE    57      10.900   7.541  -5.504  1.00  0.00              
ATOM     25  N   CYS    58      10.703   9.032  -3.835  1.00  0.00              
ATOM     26  CA  CYS    58      11.945   8.630  -3.173  1.00  0.00              
ATOM     27  C   CYS    58      11.823   7.300  -2.415  1.00  0.00              
ATOM     28  O   CYS    58      12.784   6.531  -2.353  1.00  0.00              
ATOM     29  N   HIS    59      10.644   7.021  -1.858  1.00  0.00              
ATOM     30  CA  HIS    59      10.429   5.778  -1.107  1.00  0.00              
ATOM     31  C   HIS    59      10.569   4.500  -1.952  1.00  0.00              
ATOM     32  O   HIS    59      10.880   3.430  -1.427  1.00  0.00              
ATOM     33  N   SER    60      10.347   4.616  -3.259  1.00  0.00              
ATOM     34  CA  SER    60      10.458   3.472  -4.170  1.00  0.00              
ATOM     35  C   SER    60      11.921   3.029  -4.341  1.00  0.00              
ATOM     36  O   SER    60      12.227   1.831  -4.295  1.00  0.00              
ATOM     37  N   GLN    61      12.815   4.000  -4.520  1.00  0.00              
ATOM     38  CA  GLN    61      14.248   3.734  -4.689  1.00  0.00              
ATOM     39  C   GLN    61      14.860   3.189  -3.407  1.00  0.00              
ATOM     40  O   GLN    61      15.729   2.324  -3.447  1.00  0.00              
ATOM     41  N   LYS    62      14.392   3.707  -2.273  1.00  0.00              
ATOM     42  CA  LYS    62      14.859   3.305  -0.950  1.00  0.00              
ATOM     43  C   LYS    62      14.495   1.857  -0.601  1.00  0.00              
ATOM     44  O   LYS    62      15.251   1.185   0.097  1.00  0.00              
ATOM     45  N   ALA    63      13.341   1.384  -1.066  1.00  0.00              
ATOM     46  CA  ALA    63      12.910   0.017  -0.772  1.00  0.00              
ATOM     47  C   ALA    63      13.562  -1.022  -1.685  1.00  0.00              
ATOM     48  O   ALA    63      13.730  -2.183  -1.301  1.00  0.00              
ATOM     49  N   PRO    64      13.899  -0.599  -2.900  1.00  0.00              
ATOM     50  CA  PRO    64      14.541  -1.480  -3.864  1.00  0.00              
ATOM     51  C   PRO    64      13.893  -2.824  -4.158  1.00  0.00              
ATOM     52  O   PRO    64      12.778  -2.891  -4.682  1.00  0.00              
ATOM     53  N   ASP    65      14.597  -3.895  -3.803  1.00  0.00              
ATOM     54  CA  ASP    65      14.129  -5.253  -4.049  1.00  0.00              
ATOM     55  C   ASP    65      13.468  -5.924  -2.862  1.00  0.00              
ATOM     56  O   ASP    65      13.144  -7.109  -2.930  1.00  0.00              
ATOM     57  N   GLU    66      13.303  -5.195  -1.762  1.00  0.00              
ATOM     58  CA  GLU    66      12.651  -5.767  -0.589  1.00  0.00              
ATOM     59  C   GLU    66      11.151  -5.549  -0.761  1.00  0.00              
ATOM     60  O   GLU    66      10.656  -4.435  -0.594  1.00  0.00              
END
