
#######################################################
#                                                     #
#                        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   31 (   31),  selected   31 , name T0385TS464_4_2
# Molecule2: number of CA atoms  142 ( 1050),  selected   31 , name T0385.pdb
# PARAMETERS: T0385TS464_4_2.T0385.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        54 - 145         4.94    13.51
  LCS_AVERAGE:     11.02

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        54 - 69          0.53    16.86
  LCS_AVERAGE:      8.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        54 - 69          0.53    16.86
  LCS_AVERAGE:      7.70

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:  142
LCS_GDT     A      25     A      25      5    5    6     5    5    5    5    5    5    5    5    5    5   12   14   16   19   20   20   20   21   21   21 
LCS_GDT     L      26     L      26      5    5    6     5    5    5    5    5    5    5    5    5    5    5   13   16   19   20   20   20   21   21   21 
LCS_GDT     C      27     C      27      5    5    6     5    5    5    5    5    5    5    5    5    5    5    5    5    5   17   19   20   21   21   21 
LCS_GDT     D      28     D      28      5    5   18     5    5    5    5    5    5    5    5    5    5   12   14   16   19   20   20   20   21   21   21 
LCS_GDT     A      29     A      29      5    5   18     5    5    5    5    5    5    5    5    5    9   12   14   16   19   20   20   20   21   21   21 
LCS_GDT     L      54     L      54     16   16   19     5   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     V      55     V      55     16   16   19     9   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     A      56     A      56     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     D      57     D      57     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     A      58     A      58     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     L      59     L      59     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     K      60     K      60     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     Q      61     Q      61     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     H      62     H      62     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     R      63     R      63     16   16   19    11   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     H      64     H      64     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     R      65     R      65     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     R      66     R      66     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     D      67     D      67     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     D      68     D      68     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   19   20   20   20   21   21   21 
LCS_GDT     V      69     V      69     16   16   19    12   16   16   16   16   16   16   16   16   16   18   18   18   18   20   20   20   21   21   21 
LCS_GDT     R     143     R     143      7    8   19     6    7    7    7    7    7    8    8   11   15   18   18   18   18   18   19   20   21   21   21 
LCS_GDT     W     144     W     144      7    8   19     6    7    7    7    7    7    8    8   11   15   18   18   18   18   18   19   20   21   21   21 
LCS_GDT     N     145     N     145      7    8   19     6    7    7    7    7    7    8    8    9    9   10   11   13   14   15   17   20   21   21   21 
LCS_GDT     R     146     R     146      7    8   10     6    7    7    7    7    7    8    8    9    9   10   11   13   16   16   19   20   21   21   21 
LCS_GDT     V     147     V     147      7    8   10     6    7    7    7    7    7    8    8    8    8   10   11   13   16   17   19   20   21   21   21 
LCS_GDT     L     148     L     148      7    8   10     6    7    7    7    7    7    8    8    8    8    9   10   13   14   14   14   16   17   18   21 
LCS_GDT     G     149     G     149      7    8   10     4    7    7    7    7    7    8    8    9    9   10   11   13   14   14   14   15   15   17   18 
LCS_GDT     A     150     A     150      3    8   10     3    3    3    3    4    7    8    8    9    9   10   11   13   14   14   14   15   15   15   16 
LCS_GDT     W     151     W     151      3    4   10     0    3    3    3    4    5    7    7    9    9   10   11   13   14   14   14   15   15   15   16 
LCS_GDT     P     152     P     152      3    4   10     0    3    3    3    4    4    7    7    9    9   10   11   12   12   14   14   14   14   15   16 
LCS_AVERAGE  LCS_A:   8.91  (   7.70    8.02   11.02 )

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     12     16     16     16     16     16     16     16     16     16     18     18     18     19     20     20     20     21     21     21 
GDT PERCENT_CA   8.45  11.27  11.27  11.27  11.27  11.27  11.27  11.27  11.27  11.27  12.68  12.68  12.68  13.38  14.08  14.08  14.08  14.79  14.79  14.79
GDT RMS_LOCAL    0.33   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   0.53   4.46   4.46   4.46   5.01   5.06   5.06   5.06   5.42   5.42   5.42
GDT RMS_ALL_CA  16.83  16.86  16.86  16.86  16.86  16.86  16.86  16.86  16.86  16.86  13.67  13.67  13.67  15.77  15.65  15.65  15.65  15.87  15.87  15.87

#      Molecule1      Molecule2       DISTANCE
LGA    A      25      A      25         18.432
LGA    L      26      L      26         16.524
LGA    C      27      C      27         16.560
LGA    D      28      D      28         17.995
LGA    A      29      A      29         16.772
LGA    L      54      L      54          0.984
LGA    V      55      V      55          0.738
LGA    A      56      A      56          0.630
LGA    D      57      D      57          0.354
LGA    A      58      A      58          0.377
LGA    L      59      L      59          0.596
LGA    K      60      K      60          0.504
LGA    Q      61      Q      61          0.165
LGA    H      62      H      62          0.315
LGA    R      63      R      63          0.667
LGA    H      64      H      64          0.404
LGA    R      65      R      65          0.349
LGA    R      66      R      66          0.343
LGA    D      67      D      67          0.495
LGA    D      68      D      68          0.491
LGA    V      69      V      69          0.478
LGA    R     143      R     143         22.490
LGA    W     144      W     144         19.270
LGA    N     145      N     145         22.090
LGA    R     146      R     146         26.523
LGA    V     147      V     147         25.281
LGA    L     148      L     148         26.766
LGA    G     149      G     149         32.215
LGA    A     150      A     150         30.061
LGA    W     151      W     151         31.312
LGA    P     152      P     152         31.153

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31  142    4.0     16    0.53    11.972    10.854     2.544

LGA_LOCAL      RMSD =  0.529  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 16.861  Number of atoms =   31 
Std_ALL_ATOMS  RMSD = 11.164  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.263529 * X  +   0.158794 * Y  +  -0.951492 * Z  +  16.213049
  Y_new =   0.818565 * X  +  -0.558692 * Y  +   0.133473 * Z  + -27.122364
  Z_new =  -0.510396 * X  +  -0.814032 * Y  +  -0.277214 * Z  +  85.459335 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.899023    1.242570  [ DEG:  -108.8060     71.1940 ]
  Theta =   0.535646    2.605947  [ DEG:    30.6902    149.3098 ]
  Phi   =   1.259335   -1.882258  [ DEG:    72.1546   -107.8454 ]
 
# 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: T0385TS464_4_2                                
REMARK     2: T0385.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0385TS464_4_2.T0385.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31  142   4.0   16   0.53  10.854    11.16
REMARK  ---------------------------------------------------------- 
MOLECULE T0385TS464_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0385
PARENT N/A
ATOM      1  CA  ALA    25      26.143   5.773  20.923  1.00  0.00
ATOM      2  CA  LEU    26      25.573   9.359  19.830  1.00  0.00
ATOM      3  CA  CYS    27      29.243   9.531  18.809  1.00  0.00
ATOM      4  CA  ASP    28      28.745   6.373  16.712  1.00  0.00
ATOM      5  CA  ALA    29      25.752   8.000  15.019  1.00  0.00
ATOM      6  CA  LEU    54      31.556  18.890  10.144  1.00  0.00
ATOM      7  CA  VAL    55      30.045  15.697  11.458  1.00  0.00
ATOM      8  CA  ALA    56      33.530  14.415  12.339  1.00  0.00
ATOM      9  CA  ASP    57      33.913  17.625  14.307  1.00  0.00
ATOM     10  CA  ALA    58      30.808  16.483  16.244  1.00  0.00
ATOM     11  CA  LEU    59      32.012  12.996  17.172  1.00  0.00
ATOM     12  CA  LYS    60      35.454  14.347  18.092  1.00  0.00
ATOM     13  CA  GLN    61      33.966  17.139  20.142  1.00  0.00
ATOM     14  CA  HIS    62      31.989  14.575  22.109  1.00  0.00
ATOM     15  CA  ARG    63      35.063  12.304  22.109  1.00  0.00
ATOM     16  CA  HIS    64      36.952  14.874  24.148  1.00  0.00
ATOM     17  CA  ARG    65      33.758  15.510  26.070  1.00  0.00
ATOM     18  CA  ARG    66      33.389  11.868  27.145  1.00  0.00
ATOM     19  CA  ASP    67      37.064  11.722  28.134  1.00  0.00
ATOM     20  CA  ASP    68      36.439  14.849  30.165  1.00  0.00
ATOM     21  CA  VAL    69      33.509  13.105  31.907  1.00  0.00
ATOM     22  CA  ARG   143      37.857   5.793  11.315  1.00  0.00
ATOM     23  CA  TRP   144      38.115   9.549  11.818  1.00  0.00
ATOM     24  CA  ASN   145      36.366   9.356  15.172  1.00  0.00
ATOM     25  CA  ARG   146      38.585   6.525  16.430  1.00  0.00
ATOM     26  CA  VAL   147      41.668   8.299  15.098  1.00  0.00
ATOM     27  CA  LEU   148      40.993  11.157  17.534  1.00  0.00
ATOM     28  CA  GLY   149      41.317   8.730  20.456  1.00  0.00
ATOM     29  CA  ALA   150      37.564   8.659  20.935  1.00  0.00
ATOM     30  CA  TRP   151      35.856   5.483  22.222  1.00  0.00
ATOM     31  CA  PRO   152      32.406   6.932  21.721  1.00  0.00
TER
END
