
#######################################################
#                                                     #
#                        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 T0352AL381_3
# Molecule2: number of CA atoms  109 ( 1766),  selected   15 , name T0352.pdb
# PARAMETERS: T0352AL381_3.T0352.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:    15        50 - 64          3.76     3.76
  LCS_AVERAGE:     13.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        53 - 61          1.88     4.83
  LONGEST_CONTINUOUS_SEGMENT:     9        54 - 62          1.91     4.89
  LCS_AVERAGE:      6.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        53 - 59          0.93     4.82
  LCS_AVERAGE:      5.26

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:  109
LCS_GDT     W      50     W      50      4    4   15     3    3    4    4    4    4    8    9   10   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     L      51     L      51      4    4   15     3    3    4    4    4    6    8    9   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q      52     Q      52      4    4   15     3    3    4    4    4    4    8    9   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     W      53     W      53      7    9   15     3    4    6    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     V      54     V      54      7    9   15     5    6    6    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     L      55     L      55      7    9   15     5    6    6    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     I      56     I      56      7    9   15     5    6    6    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     P      57     P      57      7    9   15     5    6    6    7    8   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     R      58     R      58      7    9   15     5    6    6    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     M      59     M      59      7    9   15     4    6    6    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     H      60     H      60      5    9   15     4    4    5    7    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     D      61     D      61      5    9   15     4    4    5    6    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     L      62     L      62      5    9   15     3    4    5    5    9   10   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     L      63     L      63      5    6   15     3    4    5    5    6    9   12   12   12   14   14   15   15   15   15   15   15   15   15   15 
LCS_GDT     D      64     D      64      5    6   15     3    4    5    7    8    8   12   12   12   12   14   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   8.66  (   5.26    6.97   13.76 )

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      5      6      6      7      9     10     12     12     12     14     14     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   4.59   5.50   5.50   6.42   8.26   9.17  11.01  11.01  11.01  12.84  12.84  13.76  13.76  13.76  13.76  13.76  13.76  13.76  13.76  13.76
GDT RMS_LOCAL    0.26   0.45   0.45   0.93   1.93   2.07   2.54   2.54   2.54   3.50   3.50   3.76   3.76   3.76   3.76   3.76   3.76   3.76   3.76   3.76
GDT RMS_ALL_CA   4.66   4.79   4.79   4.82   4.70   4.74   5.03   5.03   5.03   3.86   3.86   3.76   3.76   3.76   3.76   3.76   3.76   3.76   3.76   3.76

#      Molecule1      Molecule2       DISTANCE
LGA    W      50      W      50         10.536
LGA    L      51      L      51         10.743
LGA    Q      52      Q      52          8.751
LGA    W      53      W      53          2.209
LGA    V      54      V      54          2.367
LGA    L      55      L      55          1.545
LGA    I      56      I      56          2.175
LGA    P      57      P      57          3.027
LGA    R      58      R      58          1.798
LGA    M      59      M      59          0.558
LGA    H      60      H      60          1.641
LGA    D      61      D      61          2.560
LGA    L      62      L      62          3.614
LGA    L      63      L      63          3.466
LGA    D      64      D      64          3.541

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15  109    4.0     12    2.54     9.174     9.127     0.455

LGA_LOCAL      RMSD =  2.536  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.034  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  3.756  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.735742 * X  +   0.052106 * Y  +  -0.675254 * Z  + -33.674618
  Y_new =   0.578102 * X  +   0.471089 * Y  +   0.666238 * Z  + -154.444305
  Z_new =   0.352820 * X  +  -0.880545 * Y  +   0.316478 * Z  +   8.696323 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.225762    1.915830  [ DEG:   -70.2310    109.7690 ]
  Theta =  -0.360583   -2.781010  [ DEG:   -20.6599   -159.3401 ]
  Phi   =   0.665985   -2.475608  [ DEG:    38.1581   -141.8419 ]
 
# 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: T0352AL381_3                                  
REMARK     2: T0352.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0352AL381_3.T0352.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15  109   4.0   12   2.54   9.127     3.76
REMARK  ---------------------------------------------------------- 
MOLECULE T0352AL381_3
REMARK Aligment from pdb entry: 1jb0I
ATOM      1  N   TRP    50     -11.548  10.698   9.577  1.00  0.00              
ATOM      2  CA  TRP    50     -10.116  11.017   9.522  1.00  0.00              
ATOM      3  C   TRP    50      -9.357   9.968   8.669  1.00  0.00              
ATOM      4  O   TRP    50      -8.226  10.188   8.289  1.00  0.00              
ATOM      5  N   LEU    51      -9.986   8.839   8.372  1.00  0.00              
ATOM      6  CA  LEU    51      -9.328   7.792   7.594  1.00  0.00              
ATOM      7  C   LEU    51      -8.740   8.226   6.232  1.00  0.00              
ATOM      8  O   LEU    51      -7.592   7.896   5.917  1.00  0.00              
ATOM      9  N   GLN    52      -9.510   8.969   5.416  1.00  0.00              
ATOM     10  CA  GLN    52      -9.043   9.433   4.105  1.00  0.00              
ATOM     11  C   GLN    52      -7.785  10.288   4.191  1.00  0.00              
ATOM     12  O   GLN    52      -6.946  10.292   3.276  1.00  0.00              
ATOM     13  N   TRP    53      -7.695  11.042   5.283  1.00  0.00              
ATOM     14  CA  TRP    53      -6.576  11.933   5.566  1.00  0.00              
ATOM     15  C   TRP    53      -5.298  11.137   5.427  1.00  0.00              
ATOM     16  O   TRP    53      -4.291  11.611   4.895  1.00  0.00              
ATOM     17  N   VAL    54      -5.342   9.916   5.934  1.00  0.00              
ATOM     18  CA  VAL    54      -4.173   9.088   5.885  1.00  0.00              
ATOM     19  C   VAL    54      -4.150   8.083   4.725  1.00  0.00              
ATOM     20  O   VAL    54      -3.105   7.909   4.104  1.00  0.00              
ATOM     21  N   LEU    55      -5.286   7.462   4.410  1.00  0.00              
ATOM     22  CA  LEU    55      -5.321   6.491   3.326  1.00  0.00              
ATOM     23  C   LEU    55      -5.031   7.013   1.919  1.00  0.00              
ATOM     24  O   LEU    55      -4.553   6.258   1.068  1.00  0.00              
ATOM     25  N   ILE    56      -5.303   8.281   1.641  1.00  0.00              
ATOM     26  CA  ILE    56      -4.971   8.750   0.315  1.00  0.00              
ATOM     27  C   ILE    56      -3.438   8.846   0.198  1.00  0.00              
ATOM     28  O   ILE    56      -2.884   8.476  -0.829  1.00  0.00              
ATOM     29  N   PRO    57      -2.735   9.367   1.230  1.00  0.00              
ATOM     30  CA  PRO    57      -1.272   9.424   1.088  1.00  0.00              
ATOM     31  C   PRO    57      -0.694   8.002   1.042  1.00  0.00              
ATOM     32  O   PRO    57       0.252   7.733   0.312  1.00  0.00              
ATOM     33  N   ARG    58      -1.277   7.087   1.804  1.00  0.00              
ATOM     34  CA  ARG    58      -0.790   5.726   1.794  1.00  0.00              
ATOM     35  C   ARG    58      -1.007   5.047   0.440  1.00  0.00              
ATOM     36  O   ARG    58      -0.106   4.427  -0.086  1.00  0.00              
ATOM     37  N   MET    59      -2.192   5.183  -0.138  1.00  0.00              
ATOM     38  CA  MET    59      -2.479   4.536  -1.410  1.00  0.00              
ATOM     39  C   MET    59      -1.830   5.221  -2.601  1.00  0.00              
ATOM     40  O   MET    59      -1.485   4.566  -3.580  1.00  0.00              
ATOM     41  N   HIS    60      -1.630   6.527  -2.511  1.00  0.00              
ATOM     42  CA  HIS    60      -1.090   7.281  -3.635  1.00  0.00              
ATOM     43  C   HIS    60       0.385   7.595  -3.601  1.00  0.00              
ATOM     44  O   HIS    60       1.001   7.822  -4.647  1.00  0.00              
ATOM     45  N   ASP    61       0.960   7.634  -2.409  1.00  0.00              
ATOM     46  CA  ASP    61       2.359   7.966  -2.301  1.00  0.00              
ATOM     47  C   ASP    61       3.235   6.814  -1.796  1.00  0.00              
ATOM     48  O   ASP    61       4.136   6.355  -2.492  1.00  0.00              
ATOM     49  N   LEU    62       2.957   6.375  -0.575  1.00  0.00              
ATOM     50  CA  LEU    62       3.713   5.336   0.084  1.00  0.00              
ATOM     51  C   LEU    62       3.690   3.982  -0.618  1.00  0.00              
ATOM     52  O   LEU    62       4.724   3.449  -0.971  1.00  0.00              
ATOM     53  N   LEU    63       2.498   3.438  -0.812  1.00  0.00              
ATOM     54  CA  LEU    63       2.324   2.148  -1.454  1.00  0.00              
ATOM     55  C   LEU    63       2.969   2.112  -2.852  1.00  0.00              
ATOM     56  O   LEU    63       3.723   1.198  -3.157  1.00  0.00              
ATOM     57  N   ASP    64       2.704   3.116  -3.706  1.00  0.00              
ATOM     58  CA  ASP    64       3.347   3.023  -5.015  1.00  0.00              
ATOM     59  C   ASP    64       4.868   3.205  -4.991  1.00  0.00              
ATOM     60  O   ASP    64       5.561   2.729  -5.885  1.00  0.00              
END
