
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0283AL044_4-D1
# Molecule2: number of CA atoms   97 (  768),  selected   16 , name T0283_D1.pdb
# PARAMETERS: T0283AL044_4-D1.T0283_D1.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:     9        40 - 59          4.18    21.86
  LCS_AVERAGE:      6.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        54 - 58          1.20    20.56
  LCS_AVERAGE:      2.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        54 - 57          0.43    20.66
  LCS_AVERAGE:      2.00

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:   97
LCS_GDT     H      32     H      32      0    0    6     0    0    0    0    2    2    2    4    4    7    7    7    9   11   11   11   11   11   11   11 
LCS_GDT     H      33     H      33      0    0    6     0    0    0    0    2    2    2    4    4    7    7    7    9   11   11   11   11   11   11   11 
LCS_GDT     K      40     K      40      3    3    9     3    3    3    4    5    5    6    6    6    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     Y      41     Y      41      3    3    9     3    3    3    4    5    5    6    6    6    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     M      42     M      42      3    3    9     3    3    3    4    4    5    6    6    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     T      54     T      54      4    5    9     3    4    4    5    5    5    5    5    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     K      55     K      55      4    5    9     3    4    4    5    5    5    5    5    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     R      56     R      56      4    5    9     3    4    4    5    5    5    5    5    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     I      57     I      57      4    5    9     3    4    4    5    5    5    6    6    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     F      58     F      58      3    5    9     0    3    3    5    5    5    6    6    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     G      59     G      59      3    3    9     2    3    3    4    5    5    6    6    7    7    7    9    9   11   11   11   11   11   11   11 
LCS_GDT     G      60     G      60      0    0    8     0    0    0    0    0    0    0    0    0    0    2    7    7    8    8    9   10   10   10   10 
LCS_GDT     I      61     I      61      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     L      62     L      62      0    0    0     0    0    0    0    1    1    1    1    1    1    1    1    2    2    2    2    3    3    3    3 
LCS_GDT     D      63     D      63      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    2    2    2    2    3    3    3    3 
LCS_GDT     A      84     A      84      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    3    3    3    3 
LCS_AVERAGE  LCS_A:   3.63  (   2.00    2.38    6.51 )

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      4      4      5      5      5      6      6      7      7      7      9      9     11     11     11     11     11     11     11 
GDT PERCENT_CA   3.09   4.12   4.12   5.15   5.15   5.15   6.19   6.19   7.22   7.22   7.22   9.28   9.28  11.34  11.34  11.34  11.34  11.34  11.34  11.34
GDT RMS_LOCAL    0.05   0.43   0.43   1.20   1.20   1.20   2.25   2.25   3.44   3.44   3.12   4.18   4.18   5.48   5.48   5.48   5.48   5.48   5.48   5.48
GDT RMS_ALL_CA  20.59  20.66  20.66  20.56  20.56  20.56  21.60  21.60  21.04  21.04  21.64  21.86  21.86  23.35  23.35  23.35  23.35  23.35  23.35  23.35

#      Molecule1      Molecule2       DISTANCE
LGA    H      32      H      32         13.309
LGA    H      33      H      33         12.225
LGA    K      40      K      40          1.116
LGA    Y      41      Y      41          2.820
LGA    M      42      M      42          3.162
LGA    T      54      T      54          7.964
LGA    K      55      K      55          8.918
LGA    R      56      R      56          6.969
LGA    I      57      I      57          1.662
LGA    F      58      F      58          2.491
LGA    G      59      G      59          1.527
LGA    G      60      G      60         13.771
LGA    I      61      I      61         21.757
LGA    L      62      L      62         38.766
LGA    D      63      D      63         39.677
LGA    A      84      A      84         56.373

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   97    4.0      6    2.25     6.701     5.529     0.255

LGA_LOCAL      RMSD =  2.254  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 21.602  Number of atoms =   16 
Std_ALL_ATOMS  RMSD = 18.970  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.418707 * X  +  -0.011848 * Y  +  -0.908044 * Z  +  68.224800
  Y_new =  -0.030367 * X  +  -0.999173 * Y  +   0.027039 * Z  +  60.548431
  Z_new =  -0.907613 * X  +   0.038896 * Y  +   0.418001 * Z  +  -9.365305 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.092786   -3.048806  [ DEG:     5.3163   -174.6837 ]
  Theta =   1.137563    2.004029  [ DEG:    65.1776    114.8224 ]
  Phi   =  -3.069193    0.072400  [ DEG:  -175.8518      4.1482 ]
 
# 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: T0283AL044_4-D1                               
REMARK     2: T0283_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0283AL044_4-D1.T0283_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   97   4.0    6   2.25   5.529    18.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0283AL044_4-D1
REMARK Aligment from pdb entry: 1kzy_C
ATOM      1  N   HIS    32      27.607  36.418  -4.631  1.00  0.00              
ATOM      2  CA  HIS    32      28.934  36.777  -4.168  1.00  0.00              
ATOM      3  C   HIS    32      29.091  36.433  -2.665  1.00  0.00              
ATOM      4  O   HIS    32      30.137  35.941  -2.230  1.00  0.00              
ATOM      5  N   HIS    33      28.033  36.656  -1.901  1.00  0.00              
ATOM      6  CA  HIS    33      27.993  36.321  -0.474  1.00  0.00              
ATOM      7  C   HIS    33      27.927  34.795  -0.403  1.00  0.00              
ATOM      8  O   HIS    33      26.881  34.221  -0.676  1.00  0.00              
ATOM      9  N   LYS    40      29.028  34.147  -0.039  1.00  0.00              
ATOM     10  CA  LYS    40      29.085  32.692  -0.005  1.00  0.00              
ATOM     11  C   LYS    40      28.104  32.014   0.935  1.00  0.00              
ATOM     12  O   LYS    40      27.875  30.808   0.811  1.00  0.00              
ATOM     13  N   TYR    41      27.544  32.747   1.891  1.00  0.00              
ATOM     14  CA  TYR    41      26.565  32.135   2.806  1.00  0.00              
ATOM     15  C   TYR    41      25.163  32.720   2.631  1.00  0.00              
ATOM     16  O   TYR    41      24.424  32.847   3.586  1.00  0.00              
ATOM     17  N   MET    42      24.803  33.058   1.411  1.00  0.00              
ATOM     18  CA  MET    42      23.501  33.641   1.138  1.00  0.00              
ATOM     19  C   MET    42      22.334  32.730   1.470  1.00  0.00              
ATOM     20  O   MET    42      21.339  33.185   2.038  1.00  0.00              
ATOM     21  N   THR    54      22.442  31.452   1.128  1.00  0.00              
ATOM     22  CA  THR    54      21.337  30.540   1.390  1.00  0.00              
ATOM     23  C   THR    54      21.522  29.638   2.596  1.00  0.00              
ATOM     24  O   THR    54      20.737  28.702   2.793  1.00  0.00              
ATOM     25  N   LYS    55      22.541  29.936   3.409  1.00  0.00              
ATOM     26  CA  LYS    55      22.853  29.143   4.597  1.00  0.00              
ATOM     27  C   LYS    55      21.648  29.003   5.551  1.00  0.00              
ATOM     28  O   LYS    55      21.008  29.998   5.938  1.00  0.00              
ATOM     29  N   ARG    56      21.353  27.761   5.932  1.00  0.00              
ATOM     30  CA  ARG    56      20.217  27.520   6.798  1.00  0.00              
ATOM     31  C   ARG    56      18.978  27.147   5.994  1.00  0.00              
ATOM     32  O   ARG    56      17.883  27.027   6.552  1.00  0.00              
ATOM     33  N   ILE    57      19.150  26.959   4.686  1.00  0.00              
ATOM     34  CA  ILE    57      18.057  26.567   3.818  1.00  0.00              
ATOM     35  C   ILE    57      18.378  25.273   3.111  1.00  0.00              
ATOM     36  O   ILE    57      19.548  24.986   2.811  1.00  0.00              
ATOM     37  N   PHE    58      17.332  24.498   2.837  1.00  0.00              
ATOM     38  CA  PHE    58      17.486  23.242   2.104  1.00  0.00              
ATOM     39  C   PHE    58      16.562  23.402   0.923  1.00  0.00              
ATOM     40  O   PHE    58      15.487  24.008   1.053  1.00  0.00              
ATOM     41  N   GLY    59      16.956  22.866  -0.224  1.00  0.00              
ATOM     42  CA  GLY    59      16.100  23.001  -1.371  1.00  0.00              
ATOM     43  C   GLY    59      15.833  21.692  -2.087  1.00  0.00              
ATOM     44  O   GLY    59      16.680  20.811  -2.176  1.00  0.00              
ATOM     45  N   GLY    60      13.616  20.364  11.513  1.00  0.00              
ATOM     46  CA  GLY    60      14.513  20.884  12.512  1.00  0.00              
ATOM     47  C   GLY    60      15.689  21.690  11.990  1.00  0.00              
ATOM     48  O   GLY    60      15.847  22.846  12.334  1.00  0.00              
ATOM     49  N   ILE    61      -3.307  26.534   4.737  1.00  0.00              
ATOM     50  CA  ILE    61      -4.362  25.511   4.883  1.00  0.00              
ATOM     51  C   ILE    61      -4.063  24.537   6.013  1.00  0.00              
ATOM     52  O   ILE    61      -2.912  24.373   6.407  1.00  0.00              
ATOM     53  N   LEU    62      -2.552 -10.146  -2.308  1.00  0.00              
ATOM     54  CA  LEU    62      -2.767  -9.874  -0.882  1.00  0.00              
ATOM     55  C   LEU    62      -4.098 -10.533  -0.515  1.00  0.00              
ATOM     56  O   LEU    62      -5.062 -10.459  -1.276  1.00  0.00              
ATOM     57  N   ASP    63      -4.136 -11.196   0.638  1.00  0.00              
ATOM     58  CA  ASP    63      -5.345 -11.865   1.116  1.00  0.00              
ATOM     59  C   ASP    63      -6.097 -10.990   2.126  1.00  0.00              
ATOM     60  O   ASP    63      -5.605 -10.702   3.226  1.00  0.00              
ATOM     61  N   ALA    84      -7.301 -10.589   1.720  1.00  0.00              
ATOM     62  CA  ALA    84      -8.187  -9.701   2.478  1.00  0.00              
ATOM     63  C   ALA    84      -8.502 -10.025   3.946  1.00  0.00              
ATOM     64  O   ALA    84      -9.653 -10.327   4.288  1.00  0.00              
END
