
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0363AL044_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   13 , name T0363_D1.pdb
# PARAMETERS: T0363AL044_2-D1.T0363_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:    13        31 - 47          4.80     4.80
  LCS_AVERAGE:     28.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        38 - 47          1.61     6.99
  LCS_AVERAGE:     18.23

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        38 - 46          0.68     7.13
  LCS_AVERAGE:     14.05

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:   46
LCS_GDT     Q      31     Q      31      0    3   13     0    0    3    3    3    3    3    6    8    8    9    9   10   11   11   13   13   13   13   13 
LCS_GDT     V      32     V      32      0    3   13     0    1    3    3    3    6    6    6    8    8    9   10   11   11   12   13   13   13   13   13 
LCS_GDT     D      33     D      33      0    3   13     0    0    3    3    3    6    6    9   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     V      38     V      38      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     Q      39     Q      39      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     T      40     T      40      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     A      41     A      41      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     I      42     I      42      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     T      43     T      43      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     Q      44     Q      44      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     S      45     S      45      9   10   13     8    8    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     G      46     G      46      9   10   13     3    4    9    9    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_GDT     I      47     I      47      3   10   13     3    3    3    3    9    9   10   10   10   11   11   11   11   11   12   13   13   13   13   13 
LCS_AVERAGE  LCS_A:  20.18  (  14.05   18.23   28.26 )

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      8      8      9      9      9      9     10     10     10     11     11     11     11     11     12     13     13     13     13     13 
GDT PERCENT_CA  17.39  17.39  19.57  19.57  19.57  19.57  21.74  21.74  21.74  23.91  23.91  23.91  23.91  23.91  26.09  28.26  28.26  28.26  28.26  28.26
GDT RMS_LOCAL    0.24   0.24   0.68   0.68   0.68   0.68   1.61   1.61   1.61   2.89   2.89   2.89   2.89   2.89   3.97   4.80   4.80   4.80   4.80   4.80
GDT RMS_ALL_CA   7.01   7.01   7.13   7.13   7.13   7.13   6.99   6.99   6.99   5.89   5.89   5.89   5.89   5.89   5.21   4.80   4.80   4.80   4.80   4.80

#      Molecule1      Molecule2       DISTANCE
LGA    Q      31      Q      31         17.680
LGA    V      32      V      32         14.142
LGA    D      33      D      33          9.830
LGA    V      38      V      38          0.860
LGA    Q      39      Q      39          0.201
LGA    T      40      T      40          0.536
LGA    A      41      A      41          0.497
LGA    I      42      I      42          0.421
LGA    T      43      T      43          0.602
LGA    Q      44      Q      44          0.644
LGA    S      45      S      45          0.829
LGA    G      46      G      46          2.938
LGA    I      47      I      47          3.775

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   13   46    4.0     10    1.61    21.739    20.690     0.586

LGA_LOCAL      RMSD =  1.607  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.989  Number of atoms =   13 
Std_ALL_ATOMS  RMSD =  4.805  (standard rmsd on all 13 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.105650 * X  +   0.652238 * Y  +  -0.750615 * Z  +  44.501915
  Y_new =  -0.626685 * X  +  -0.542404 * Y  +  -0.559522 * Z  +  75.784660
  Z_new =  -0.772078 * X  +   0.529513 * Y  +   0.351442 * Z  +   1.002799 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.984844   -2.156749  [ DEG:    56.4274   -123.5726 ]
  Theta =   0.882104    2.259488  [ DEG:    50.5409    129.4591 ]
  Phi   =  -1.403781    1.737812  [ DEG:   -80.4307     99.5693 ]
 
# 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: T0363AL044_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL044_2-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   13   46   4.0   10   1.61  20.690     4.80
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL044_2-D1
REMARK Aligment from pdb entry: 1t6l_A
ATOM      1  N   GLN    31      27.169  12.049  18.698  1.00  0.00              
ATOM      2  CA  GLN    31      28.048  12.793  17.829  1.00  0.00              
ATOM      3  C   GLN    31      29.014  11.897  17.065  1.00  0.00              
ATOM      4  O   GLN    31      29.225  12.117  15.872  1.00  0.00              
ATOM      5  N   VAL    32      29.584  10.876  17.730  1.00  0.00              
ATOM      6  CA  VAL    32      30.418   9.885  17.032  1.00  0.00              
ATOM      7  C   VAL    32      29.761   9.179  15.838  1.00  0.00              
ATOM      8  O   VAL    32      30.422   8.811  14.841  1.00  0.00              
ATOM      9  N   ASP    33      28.448   8.993  15.915  1.00  0.00              
ATOM     10  CA  ASP    33      27.699   8.406  14.816  1.00  0.00              
ATOM     11  C   ASP    33      27.606   9.389  13.660  1.00  0.00              
ATOM     12  O   ASP    33      27.757   9.001  12.510  1.00  0.00              
ATOM     13  N   VAL    38      27.358  10.659  13.977  1.00  0.00              
ATOM     14  CA  VAL    38      27.318  11.712  12.970  1.00  0.00              
ATOM     15  C   VAL    38      28.674  11.819  12.261  1.00  0.00              
ATOM     16  O   VAL    38      28.752  11.902  11.022  1.00  0.00              
ATOM     17  N   GLN    39      29.743  11.811  13.055  1.00  0.00              
ATOM     18  CA  GLN    39      31.091  11.841  12.496  1.00  0.00              
ATOM     19  C   GLN    39      31.348  10.659  11.550  1.00  0.00              
ATOM     20  O   GLN    39      31.885  10.851  10.474  1.00  0.00              
ATOM     21  N   THR    40      30.971   9.456  11.957  1.00  0.00              
ATOM     22  CA  THR    40      31.109   8.270  11.111  1.00  0.00              
ATOM     23  C   THR    40      30.338   8.374   9.811  1.00  0.00              
ATOM     24  O   THR    40      30.833   7.949   8.754  1.00  0.00              
ATOM     25  N   ALA    41      29.119   8.909   9.878  1.00  0.00              
ATOM     26  CA  ALA    41      28.330   9.079   8.657  1.00  0.00              
ATOM     27  C   ALA    41      29.016  10.050   7.709  1.00  0.00              
ATOM     28  O   ALA    41      29.059   9.807   6.516  1.00  0.00              
ATOM     29  N   ILE    42      29.532  11.152   8.256  1.00  0.00              
ATOM     30  CA  ILE    42      30.208  12.208   7.478  1.00  0.00              
ATOM     31  C   ILE    42      31.479  11.692   6.791  1.00  0.00              
ATOM     32  O   ILE    42      31.763  12.044   5.646  1.00  0.00              
ATOM     33  N   THR    43      32.227  10.865   7.496  1.00  0.00              
ATOM     34  CA  THR    43      33.479  10.313   6.971  1.00  0.00              
ATOM     35  C   THR    43      33.197   9.299   5.878  1.00  0.00              
ATOM     36  O   THR    43      33.911   9.263   4.865  1.00  0.00              
ATOM     37  N   GLN    44      32.142   8.507   6.089  1.00  0.00              
ATOM     38  CA  GLN    44      31.624   7.533   5.119  1.00  0.00              
ATOM     39  C   GLN    44      31.137   8.238   3.867  1.00  0.00              
ATOM     40  O   GLN    44      31.591   7.920   2.762  1.00  0.00              
ATOM     41  N   SER    45      30.256   9.230   4.029  1.00  0.00              
ATOM     42  CA  SER    45      29.661   9.900   2.884  1.00  0.00              
ATOM     43  C   SER    45      30.628  10.878   2.213  1.00  0.00              
ATOM     44  O   SER    45      30.582  11.043   0.997  1.00  0.00              
ATOM     45  N   GLY    46      31.499  11.501   3.000  1.00  0.00              
ATOM     46  CA  GLY    46      32.520  12.387   2.472  1.00  0.00              
ATOM     47  C   GLY    46      33.591  11.574   1.751  1.00  0.00              
ATOM     48  O   GLY    46      34.406  10.891   2.395  1.00  0.00              
ATOM     49  N   ILE    47      33.579  11.615   0.420  1.00  0.00              
ATOM     50  CA  ILE    47      34.588  10.911  -0.375  1.00  0.00              
ATOM     51  C   ILE    47      35.745  11.852  -0.738  1.00  0.00              
ATOM     52  O   ILE    47      36.516  12.246   0.156  1.00  0.00              
END
