
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0316AL333_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected   11 , name T0316_D3.pdb
# PARAMETERS: T0316AL333_5-D3.T0316_D3.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       344 - 351         3.98    13.01
  LCS_AVERAGE:      7.37

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       344 - 349         1.72    10.57
  LCS_AVERAGE:      5.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       344 - 348         0.97    10.44
  LCS_AVERAGE:      4.34

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:   90
LCS_GDT     Q     344     Q     344      5    6    8     3    3    5    5    5    6    6    6    6    6    7    7    8    8    8    8    8    8    8    9 
LCS_GDT     A     345     A     345      5    6    8     4    4    5    5    5    6    6    6    6    6    7    7    8    8    8    8    8    8    8    9 
LCS_GDT     V     346     V     346      5    6    8     4    4    5    5    5    6    6    6    6    6    7    7    8    8    8    8    8    8    8    9 
LCS_GDT     V     347     V     347      5    6    8     4    4    5    5    5    6    6    6    6    6    7    7    8    8    8    8    8    8    8    9 
LCS_GDT     F     348     F     348      5    6    8     4    4    5    5    5    6    6    6    6    6    7    7    8    8    8    8    8    8    8    9 
LCS_GDT     Y     349     Y     349      3    6    8     3    3    3    5    5    6    6    6    6    6    7    7    8    8    8    8    8    8    8    9 
LCS_GDT     D     350     D     350      3    4    8     3    3    3    3    3    5    5    5    5    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     G     351     G     351      3    4    8     3    3    3    3    3    5    5    6    6    6    7    7    8    8    8    8    8    8    8    8 
LCS_GDT     Q     371     Q     371      3    3    3     3    3    3    3    3    3    3    3    3    3    3    5    6    6    6    7    7    8    8    9 
LCS_GDT     Y     372     Y     372      3    3    3     3    3    3    3    3    3    3    4    4    5    5    5    6    6    6    7    7    8    8    9 
LCS_GDT     I     373     I     373      3    3    3     3    3    3    3    3    3    3    4    4    5    5    5    6    6    6    7    7    8    8    9 
LCS_AVERAGE  LCS_A:   5.69  (   4.34    5.35    7.37 )

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      6      6      6      6      6      7      7      8      8      8      8      8      8      8      9 
GDT PERCENT_CA   4.44   4.44   5.56   5.56   5.56   6.67   6.67   6.67   6.67   6.67   7.78   7.78   8.89   8.89   8.89   8.89   8.89   8.89   8.89  10.00
GDT RMS_LOCAL    0.36   0.36   0.97   0.97   0.97   1.72   1.72   1.72   1.72   1.72   3.44   3.44   3.98   3.98   3.98   3.98   3.98   3.98   3.98   6.77
GDT RMS_ALL_CA  10.38  10.38  10.44  10.44  10.44  10.57  10.57  10.57  10.57  10.57  13.79  13.79  13.01  13.01  13.01  13.01  13.01  13.01  13.01  10.07

#      Molecule1      Molecule2       DISTANCE
LGA    Q     344      Q     344          2.501
LGA    A     345      A     345          0.989
LGA    V     346      V     346          0.797
LGA    V     347      V     347          1.120
LGA    F     348      F     348          0.669
LGA    Y     349      Y     349          2.875
LGA    D     350      D     350          9.447
LGA    G     351      G     351         11.126
LGA    Q     371      Q     371         17.838
LGA    Y     372      Y     372         15.591
LGA    I     373      I     373         20.881

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   90    4.0      6    1.72     6.389     6.285     0.329

LGA_LOCAL      RMSD =  1.724  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.566  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  9.272  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.396947 * X  +  -0.727804 * Y  +   0.559227 * Z  +  67.688240
  Y_new =  -0.731940 * X  +   0.618634 * Y  +   0.285579 * Z  + -21.700567
  Z_new =  -0.553802 * X  +  -0.295961 * Y  +  -0.778274 * Z  +  46.251518 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.778202    0.363390  [ DEG:  -159.1793     20.8207 ]
  Theta =   0.586924    2.554669  [ DEG:    33.6283    146.3717 ]
  Phi   =  -2.067725    1.073867  [ DEG:  -118.4719     61.5281 ]
 
# 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: T0316AL333_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_5-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   90   4.0    6   1.72   6.285     9.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_5-D3
REMARK Aligment from pdb entry: 1kqp_A
ATOM    861  N   GLN   344      28.162  18.614  -3.227  1.00  0.00              
ATOM    862  CA  GLN   344      28.843  18.840  -1.943  1.00  0.00              
ATOM    863  C   GLN   344      28.797  17.571  -1.130  1.00  0.00              
ATOM    864  O   GLN   344      28.068  16.628  -1.460  1.00  0.00              
ATOM    865  N   ALA   345      29.624  17.433  -0.092  1.00  0.00              
ATOM    866  CA  ALA   345      29.658  16.161   0.671  1.00  0.00              
ATOM    867  C   ALA   345      28.257  15.744   1.113  1.00  0.00              
ATOM    868  O   ALA   345      27.418  16.541   1.489  1.00  0.00              
ATOM    869  N   VAL   346      28.009  14.443   1.030  1.00  0.00              
ATOM    870  CA  VAL   346      26.694  13.914   1.309  1.00  0.00              
ATOM    871  C   VAL   346      26.313  13.978   2.777  1.00  0.00              
ATOM    872  O   VAL   346      27.106  13.682   3.654  1.00  0.00              
ATOM    873  N   VAL   347      25.064  14.329   3.032  1.00  0.00              
ATOM    874  CA  VAL   347      24.449  14.172   4.319  1.00  0.00              
ATOM    875  C   VAL   347      23.149  13.388   4.251  1.00  0.00              
ATOM    876  O   VAL   347      22.656  13.061   3.165  1.00  0.00              
ATOM    877  N   PHE   348      22.610  13.079   5.410  1.00  0.00              
ATOM    878  CA  PHE   348      21.382  12.285   5.497  1.00  0.00              
ATOM    879  C   PHE   348      20.188  13.042   4.968  1.00  0.00              
ATOM    880  O   PHE   348      19.130  12.464   4.728  1.00  0.00              
ATOM    881  N   TYR   349      20.269  14.302   4.792  1.00  0.00              
ATOM    882  CA  TYR   349      19.250  15.209   4.236  1.00  0.00              
ATOM    883  C   TYR   349      19.265  15.258   2.734  1.00  0.00              
ATOM    884  O   TYR   349      18.326  15.827   2.143  1.00  0.00              
ATOM    885  N   ASP   350      20.286  14.719   2.097  1.00  0.00              
ATOM    886  CA  ASP   350      20.355  14.700   0.630  1.00  0.00              
ATOM    887  C   ASP   350      19.656  13.439   0.134  1.00  0.00              
ATOM    888  O   ASP   350      19.685  12.430   0.857  1.00  0.00              
ATOM    889  N   GLY   351      19.019  13.509  -1.024  1.00  0.00              
ATOM    890  CA  GLY   351      18.390  12.326  -1.597  1.00  0.00              
ATOM    891  C   GLY   351      19.179  11.812  -2.775  1.00  0.00              
ATOM    892  O   GLY   351      18.915  10.672  -3.171  1.00  0.00              
ATOM    893  N   GLN   371      20.084  12.554  -3.380  1.00  0.00              
ATOM    894  CA  GLN   371      20.634  12.158  -4.680  1.00  0.00              
ATOM    895  C   GLN   371      21.343  10.812  -4.619  1.00  0.00              
ATOM    896  O   GLN   371      21.423  10.144  -5.660  1.00  0.00              
ATOM    897  N   TYR   372      21.884  10.453  -3.469  1.00  0.00              
ATOM    898  CA  TYR   372      22.761   9.288  -3.327  1.00  0.00              
ATOM    899  C   TYR   372      22.018   7.997  -3.054  1.00  0.00              
ATOM    900  O   TYR   372      22.610   6.898  -3.064  1.00  0.00              
ATOM    901  N   ILE   373      20.729   8.078  -2.766  1.00  0.00              
ATOM    902  CA  ILE   373      19.989   6.902  -2.306  1.00  0.00              
ATOM    903  C   ILE   373      19.683   5.874  -3.386  1.00  0.00              
ATOM    904  O   ILE   373      19.412   4.695  -3.008  1.00  0.00              
END
