
#######################################################
#                                                     #
#                        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   14 (   56),  selected   14 , name T0335AL333_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   14 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_1-D1.T0335_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:    10         5 - 19          4.68     9.16
  LCS_AVERAGE:     26.98

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        18 - 23          1.94    16.18
  LCS_AVERAGE:     12.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        19 - 23          0.80    15.39
  LCS_AVERAGE:     10.32

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:   36
LCS_GDT     A       5     A       5      3    3   10     0    3    3    4    4    5    5    6    7    7    8    9    9    9   10   10   11   11   11   11 
LCS_GDT     K       6     K       6      3    3   10     1    3    3    4    4    5    5    7    7    7    8    9    9    9   10   10   11   11   11   11 
LCS_GDT     I       7     I       7      3    4   10     3    3    3    4    4    5    5    7    7    7    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     A       8     A       8      3    4   10     3    3    3    4    4    5    5    7    7    7    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     R       9     R       9      3    4   10     3    3    3    4    4    5    5    7    7    7    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     I      10     I      10      3    4   10     3    3    3    4    4    4    5    7    7    7    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     N      11     N      11      3    3   10     3    3    3    3    3    4    5    7    7    7    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     E      12     E      12      3    3   10     0    3    3    3    3    4    6    6    7    7    8    8    9    9   10   10   11   11   11   12 
LCS_GDT     K      18     K      18      3    6   10     3    3    3    4    4    5    5    7    7    7    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     A      19     A      19      5    6   10     3    4    5    5    5    5    6    6    6    6    8    9    9    9   10   10   11   11   11   12 
LCS_GDT     G      20     G      20      5    6    9     4    4    5    5    5    5    6    6    6    6    7    7    9    9   10   10   11   11   11   12 
LCS_GDT     V      21     V      21      5    6    9     4    4    5    5    5    5    6    6    6    6    7    7    9    9   10   10   10   11   11   12 
LCS_GDT     I      22     I      22      5    6    9     4    4    5    5    5    5    6    6    6    6    7    7    9    9   10   10   11   11   11   12 
LCS_GDT     T      23     T      23      5    6    9     4    4    5    5    5    5    6    6    6    6    7    7    9    9   10   10   10   11   11   12 
LCS_AVERAGE  LCS_A:  16.67  (  10.32   12.70   26.98 )

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      4      4      5      5      5      5      6      7      7      7      8      9      9      9     10     10     11     11     11     12 
GDT PERCENT_CA  11.11  11.11  13.89  13.89  13.89  13.89  16.67  19.44  19.44  19.44  22.22  25.00  25.00  25.00  27.78  27.78  30.56  30.56  30.56  33.33
GDT RMS_LOCAL    0.16   0.16   0.80   0.80   0.80   0.80   1.93   3.12   3.10   3.10   3.58   4.21   4.11   4.11   4.68   4.68   5.24   5.24   5.24   6.94
GDT RMS_ALL_CA  15.68  15.68  15.39  15.39  15.39  15.39  14.27   9.02   9.25   9.25   9.28   9.16   9.47   9.47   9.16   9.16   8.89   8.89   8.89   8.74

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          9.117
LGA    K       6      K       6          3.783
LGA    I       7      I       7          2.691
LGA    A       8      A       8          2.882
LGA    R       9      R       9          2.832
LGA    I      10      I      10          3.883
LGA    N      11      N      11          3.780
LGA    E      12      E      12          5.323
LGA    K      18      K      18          2.662
LGA    A      19      A      19          8.783
LGA    G      20      G      20         12.578
LGA    V      21      V      21         16.053
LGA    I      22      I      22         14.154
LGA    T      23      T      23         18.097

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14   36    4.0      7    3.12    18.056    16.674     0.217

LGA_LOCAL      RMSD =  3.123  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.284  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  7.746  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.427717 * X  +  -0.458533 * Y  +   0.778977 * Z  + -13.524271
  Y_new =  -0.357249 * X  +   0.877373 * Y  +   0.320296 * Z  +  12.307010
  Z_new =  -0.830320 * X  +  -0.141293 * Y  +  -0.539078 * Z  +  18.362625 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.885258    0.256335  [ DEG:  -165.3131     14.6869 ]
  Theta =   0.979682    2.161910  [ DEG:    56.1317    123.8683 ]
  Phi   =  -2.445726    0.695866  [ DEG:  -140.1298     39.8702 ]
 
# 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: T0335AL333_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_1-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14   36   4.0    7   3.12  16.674     7.75
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_1-D1
REMARK Aligment from pdb entry: 1uwv_A
ATOM     17  N   ALA     5       8.677  -6.358  -6.672  1.00  0.00              
ATOM     18  CA  ALA     5       7.416  -6.951  -6.217  1.00  0.00              
ATOM     19  C   ALA     5       6.187  -6.682  -7.074  1.00  0.00              
ATOM     20  O   ALA     5       6.126  -5.712  -7.835  1.00  0.00              
ATOM     21  N   LYS     6       5.181  -7.527  -6.864  1.00  0.00              
ATOM     22  CA  LYS     6       3.870  -7.402  -7.474  1.00  0.00              
ATOM     23  C   LYS     6       2.802  -7.278  -6.414  1.00  0.00              
ATOM     24  O   LYS     6       2.731  -8.102  -5.493  1.00  0.00              
ATOM     25  N   ILE     7       1.924  -6.299  -6.585  1.00  0.00              
ATOM     26  CA  ILE     7       0.815  -6.075  -5.668  1.00  0.00              
ATOM     27  C   ILE     7      -0.358  -6.997  -5.970  1.00  0.00              
ATOM     28  O   ILE     7      -0.800  -7.101  -7.089  1.00  0.00              
ATOM     29  N   ALA     8      -0.845  -7.669  -4.938  1.00  0.00              
ATOM     30  CA  ALA     8      -1.899  -8.666  -5.096  1.00  0.00              
ATOM     31  C   ALA     8      -3.263  -7.997  -4.936  1.00  0.00              
ATOM     32  O   ALA     8      -4.222  -8.319  -5.643  1.00  0.00              
ATOM     33  N   ARG     9      -3.322  -7.063  -3.992  1.00  0.00              
ATOM     34  CA  ARG     9      -4.575  -6.567  -3.445  1.00  0.00              
ATOM     35  C   ARG     9      -4.472  -5.102  -3.069  1.00  0.00              
ATOM     36  O   ARG     9      -3.411  -4.594  -2.778  1.00  0.00              
ATOM     37  N   ILE    10      -5.613  -4.439  -3.039  1.00  0.00              
ATOM     38  CA  ILE    10      -5.720  -3.070  -2.575  1.00  0.00              
ATOM     39  C   ILE    10      -6.495  -3.126  -1.313  1.00  0.00              
ATOM     40  O   ILE    10      -7.647  -3.558  -1.343  1.00  0.00              
ATOM     41  N   ASN    11      -5.891  -2.724  -0.199  1.00  0.00              
ATOM     42  CA  ASN    11      -6.534  -2.909   1.092  1.00  0.00              
ATOM     43  C   ASN    11      -7.606  -1.806   1.353  1.00  0.00              
ATOM     44  O   ASN    11      -7.728  -0.834   0.574  1.00  0.00              
ATOM     45  N   GLU    12      -8.415  -1.973   2.395  1.00  0.00              
ATOM     46  CA  GLU    12      -9.385  -0.928   2.749  1.00  0.00              
ATOM     47  C   GLU    12      -8.736   0.474   2.705  1.00  0.00              
ATOM     48  O   GLU    12      -9.320   1.402   2.141  1.00  0.00              
ATOM     49  N   LYS    18      -7.509   0.574   3.247  1.00  0.00              
ATOM     50  CA  LYS    18      -6.810   1.844   3.549  1.00  0.00              
ATOM     51  C   LYS    18      -5.937   2.403   2.386  1.00  0.00              
ATOM     52  O   LYS    18      -5.245   3.425   2.517  1.00  0.00              
ATOM     53  N   ALA    19      -5.970   1.733   1.249  1.00  0.00              
ATOM     54  CA  ALA    19      -5.456   2.323   0.033  1.00  0.00              
ATOM     55  C   ALA    19      -3.995   2.056  -0.314  1.00  0.00              
ATOM     56  O   ALA    19      -3.523   2.575  -1.320  1.00  0.00              
ATOM     57  N   GLY    20      -3.291   1.316   0.536  1.00  0.00              
ATOM     58  CA  GLY    20      -1.954   0.816   0.262  1.00  0.00              
ATOM     59  C   GLY    20      -2.113  -0.501  -0.471  1.00  0.00              
ATOM     60  O   GLY    20      -3.003  -1.294  -0.168  1.00  0.00              
ATOM     61  N   VAL    21      -1.227  -0.740  -1.412  1.00  0.00              
ATOM     62  CA  VAL    21      -1.176  -2.015  -2.115  1.00  0.00              
ATOM     63  C   VAL    21      -0.610  -3.079  -1.183  1.00  0.00              
ATOM     64  O   VAL    21       0.214  -2.782  -0.325  1.00  0.00              
ATOM     65  N   ILE    22      -1.092  -4.306  -1.328  1.00  0.00              
ATOM     66  CA  ILE    22      -0.713  -5.426  -0.466  1.00  0.00              
ATOM     67  C   ILE    22       0.003  -6.396  -1.371  1.00  0.00              
ATOM     68  O   ILE    22      -0.536  -6.778  -2.381  1.00  0.00              
ATOM     69  N   THR    23       1.254  -6.687  -1.054  1.00  0.00              
ATOM     70  CA  THR    23       2.094  -7.588  -1.834  1.00  0.00              
ATOM     71  C   THR    23       2.752  -8.564  -0.885  1.00  0.00              
ATOM     72  O   THR    23       2.637  -8.430   0.321  1.00  0.00              
END
