
#######################################################
#                                                     #
#                        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 T0378AL257_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   15 , name T0378_D1.pdb
# PARAMETERS: T0378AL257_3-D1.T0378_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:     8        33 - 40          1.05    13.70
  LCS_AVERAGE:      8.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        33 - 40          1.05    13.70
  LCS_AVERAGE:      7.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        33 - 39          0.89    12.95
  LCS_AVERAGE:      6.22

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:   89
LCS_GDT     R      14     R      14      4    4    7     3    5    5    5    5    6    6    6    7    9    9    9   10   11   11   12   12   12   14   14 
LCS_GDT     E      15     E      15      4    4    7     3    5    5    5    5    6    6    6    7    7    8    9   10   11   11   12   12   12   14   14 
LCS_GDT     R      16     R      16      4    5    7     3    5    5    5    5    6    6    6    7    7    8    9   10   11   11   12   12   12   14   14 
LCS_GDT     K      17     K      17      4    5    7     4    5    5    5    5    6    6    6    7    7    8    9   10   11   11   12   12   12   14   14 
LCS_GDT     Y      18     Y      18      4    5    7     4    4    4    4    4    5    6    6    7    7    8    9   10   11   11   12   12   12   14   14 
LCS_GDT     R      19     R      19      4    5    7     4    4    4    4    4    5    6    6    7    7    8    9   10   11   11   12   12   12   14   14 
LCS_GDT     L      20     L      20      4    5    7     4    5    5    5    5    6    6    6    7    7    8    9    9   10   10   12   12   12   12   12 
LCS_GDT     V      33     V      33      7    8    8     5    5    8    8    8    8    8    8    8    9    9    9   10   10   10   10   11   12   14   14 
LCS_GDT     G      34     G      34      7    8    8     5    5    8    8    8    8    8    8    8    9    9    9   10   10   10   10   11   12   14   14 
LCS_GDT     E      35     E      35      7    8    8     5    5    8    8    8    8    8    8    8    9    9    9   10   10   10   10   11   12   14   14 
LCS_GDT     M      36     M      36      7    8    8     5    5    8    8    8    8    8    8    8    9    9    9   10   11   11   12   12   12   14   14 
LCS_GDT     L      37     L      37      7    8    8     5    5    8    8    8    8    8    8    8    9    9    9   10   11   11   12   12   12   14   14 
LCS_GDT     P      38     P      38      7    8    8     4    5    8    8    8    8    8    8    8    9    9    9   10   11   11   12   12   12   14   14 
LCS_GDT     F      39     F      39      7    8    8     4    5    8    8    8    8    8    8    8    9    9    9   10   11   11   12   12   12   14   14 
LCS_GDT     Y      40     Y      40      6    8    8     3    5    8    8    8    8    8    8    8    9    9    9   10   11   11   12   12   12   14   14 
LCS_AVERAGE  LCS_A:   7.32  (   6.22    7.27    8.46 )

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      5      8      8      8      8      8      8      8      9      9      9     10     11     11     12     12     12     14     14 
GDT PERCENT_CA   5.62   5.62   8.99   8.99   8.99   8.99   8.99   8.99   8.99  10.11  10.11  10.11  11.24  12.36  12.36  13.48  13.48  13.48  15.73  15.73
GDT RMS_LOCAL    0.34   0.34   1.05   1.05   1.05   1.05   1.05   1.05   1.05   2.44   2.44   2.44   3.58   5.58   5.58   5.74   5.74   5.74   7.14   7.14
GDT RMS_ALL_CA  12.23  12.23  13.70  13.70  13.70  13.70  13.70  13.70  13.70  11.88  11.88  11.88  10.55   8.09   8.09   8.34   8.34   8.34   7.64   7.64

#      Molecule1      Molecule2       DISTANCE
LGA    R      14      R      14         13.807
LGA    E      15      E      15         15.211
LGA    R      16      R      16         16.991
LGA    K      17      K      17         23.207
LGA    Y      18      Y      18         22.525
LGA    R      19      R      19         22.599
LGA    L      20      L      20         23.185
LGA    V      33      V      33          1.003
LGA    G      34      G      34          0.990
LGA    E      35      E      35          1.210
LGA    M      36      M      36          0.908
LGA    L      37      L      37          0.929
LGA    P      38      P      38          1.011
LGA    F      39      F      39          0.886
LGA    Y      40      Y      40          1.372

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   89    4.0      8    1.05     9.270     8.864     0.695

LGA_LOCAL      RMSD =  1.050  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.696  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  7.560  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.937530 * X  +   0.082048 * Y  +   0.338092 * Z  +   8.691989
  Y_new =  -0.217979 * X  +  -0.895930 * Y  +  -0.387034 * Z  + 116.889679
  Z_new =   0.271151 * X  +  -0.436553 * Y  +   0.857845 * Z  +  51.471745 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.470738    2.670855  [ DEG:   -26.9713    153.0287 ]
  Theta =  -0.274589   -2.867004  [ DEG:   -15.7328   -164.2672 ]
  Phi   =  -2.913148    0.228445  [ DEG:  -166.9111     13.0889 ]
 
# 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: T0378AL257_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL257_3-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   89   4.0    8   1.05   8.864     7.56
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL257_3-D1
REMARK Aligment from pdb entry: 1gz0_A
ATOM      1  N   ARG    14      16.373  14.375  40.479  1.00  0.00              
ATOM      2  CA  ARG    14      14.944  14.073  40.368  1.00  0.00              
ATOM      3  C   ARG    14      14.114  15.347  40.471  1.00  0.00              
ATOM      4  O   ARG    14      14.077  15.983  41.523  1.00  0.00              
ATOM      5  N   GLU    15      13.457  15.732  39.385  1.00  0.00              
ATOM      6  CA  GLU    15      12.633  16.929  39.422  1.00  0.00              
ATOM      7  C   GLU    15      11.185  16.504  39.647  1.00  0.00              
ATOM      8  O   GLU    15      10.625  15.742  38.859  1.00  0.00              
ATOM      9  N   ARG    16      10.590  16.981  40.736  1.00  0.00              
ATOM     10  CA  ARG    16       9.214  16.624  41.053  1.00  0.00              
ATOM     11  C   ARG    16       8.222  17.508  40.332  1.00  0.00              
ATOM     12  O   ARG    16       8.383  18.724  40.300  1.00  0.00              
ATOM     13  N   LYS    17       7.199  16.892  39.750  1.00  0.00              
ATOM     14  CA  LYS    17       6.157  17.642  39.063  1.00  0.00              
ATOM     15  C   LYS    17       4.924  17.572  39.956  1.00  0.00              
ATOM     16  O   LYS    17       4.821  16.692  40.814  1.00  0.00              
ATOM     17  N   TYR    18       4.000  18.500  39.751  1.00  0.00              
ATOM     18  CA  TYR    18       2.771  18.575  40.527  1.00  0.00              
ATOM     19  C   TYR    18       2.131  17.219  40.720  1.00  0.00              
ATOM     20  O   TYR    18       1.603  16.911  41.787  1.00  0.00              
ATOM     21  N   ARG    19       2.197  16.407  39.673  1.00  0.00              
ATOM     22  CA  ARG    19       1.608  15.077  39.682  1.00  0.00              
ATOM     23  C   ARG    19       2.183  14.151  40.743  1.00  0.00              
ATOM     24  O   ARG    19       1.434  13.426  41.393  1.00  0.00              
ATOM     25  N   LEU    20       3.499  14.164  40.928  1.00  0.00              
ATOM     26  CA  LEU    20       4.087  13.266  41.918  1.00  0.00              
ATOM     27  C   LEU    20       4.176  13.821  43.338  1.00  0.00              
ATOM     28  O   LEU    20       4.905  13.288  44.176  1.00  0.00              
ATOM     29  N   VAL    33       3.409  14.868  43.617  1.00  0.00              
ATOM     30  CA  VAL    33       3.413  15.469  44.937  1.00  0.00              
ATOM     31  C   VAL    33       2.719  14.546  45.960  1.00  0.00              
ATOM     32  O   VAL    33       3.247  14.304  47.049  1.00  0.00              
ATOM     33  N   GLY    34       1.536  14.010  45.618  1.00  0.00              
ATOM     34  CA  GLY    34       0.815  13.118  46.531  1.00  0.00              
ATOM     35  C   GLY    34       1.608  11.903  47.000  1.00  0.00              
ATOM     36  O   GLY    34       1.414  11.426  48.120  1.00  0.00              
ATOM     37  N   GLU    35       2.501  11.406  46.152  1.00  0.00              
ATOM     38  CA  GLU    35       3.339  10.264  46.517  1.00  0.00              
ATOM     39  C   GLU    35       4.444  10.749  47.456  1.00  0.00              
ATOM     40  O   GLU    35       4.752  10.096  48.458  1.00  0.00              
ATOM     41  N   MET    36       5.046  11.892  47.119  1.00  0.00              
ATOM     42  CA  MET    36       6.113  12.471  47.932  1.00  0.00              
ATOM     43  C   MET    36       5.596  12.649  49.349  1.00  0.00              
ATOM     44  O   MET    36       6.258  12.294  50.327  1.00  0.00              
ATOM     45  N   LEU    37       4.401  13.209  49.446  1.00  0.00              
ATOM     46  CA  LEU    37       3.782  13.429  50.741  1.00  0.00              
ATOM     47  C   LEU    37       3.567  12.094  51.449  1.00  0.00              
ATOM     48  O   LEU    37       3.922  11.950  52.612  1.00  0.00              
ATOM     49  N   PRO    38       3.003  11.117  50.745  1.00  0.00              
ATOM     50  CA  PRO    38       2.766   9.802  51.336  1.00  0.00              
ATOM     51  C   PRO    38       4.044   9.173  51.908  1.00  0.00              
ATOM     52  O   PRO    38       3.979   8.399  52.865  1.00  0.00              
ATOM     53  N   PHE    39       5.200   9.502  51.338  1.00  0.00              
ATOM     54  CA  PHE    39       6.463   8.942  51.832  1.00  0.00              
ATOM     55  C   PHE    39       6.989   9.758  53.010  1.00  0.00              
ATOM     56  O   PHE    39       8.072   9.487  53.529  1.00  0.00              
ATOM     57  N   TYR    40       6.218  10.754  53.431  1.00  0.00              
ATOM     58  CA  TYR    40       6.636  11.616  54.529  1.00  0.00              
ATOM     59  C   TYR    40       5.984  11.271  55.855  1.00  0.00              
ATOM     60  O   TYR    40       4.737  11.219  55.984  1.00  0.00              
END
