
#######################################################
#                                                     #
#                        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 T0386AL381_5-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   11 , name T0386_D1.pdb
# PARAMETERS: T0386AL381_5-D1.T0386_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:    11        13 - 23          2.99     2.99
  LCS_AVERAGE:      5.34

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        16 - 22          1.65     6.03
  LCS_AVERAGE:      3.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        16 - 21          0.82     7.30
  LCS_AVERAGE:      2.47

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:  206
LCS_GDT     I      13     I      13      4    5   11     3    4    4    5    5    6    7    9   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     I      14     I      14      4    5   11     3    4    4    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     S      15     S      15      4    5   11     3    4    4    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     P      16     P      16      6    7   11     4    5    6    6    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     H      17     H      17      6    7   11     4    5    6    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     H      18     H      18      6    7   11     4    5    6    6    7    7    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     Y      19     Y      19      6    7   11     4    5    6    6    7    7    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     V      20     V      20      6    7   11     4    5    6    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     Y      21     Y      21      6    7   11     3    4    6    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     P      22     P      22      4    7   11     3    4    4    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     N      23     N      23      4    5   11     3    4    4    7    8    8    9   10   10   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   3.62  (   2.47    3.05    5.34 )

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      5      6      7      8      8      9     10     10     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   1.94   2.43   2.91   3.40   3.88   3.88   4.37   4.85   4.85   5.34   5.34   5.34   5.34   5.34   5.34   5.34   5.34   5.34   5.34   5.34
GDT RMS_LOCAL    0.21   0.36   0.82   1.57   1.83   1.83   2.22   2.47   2.47   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_ALL_CA   7.64   7.91   7.30   3.13   3.12   3.12   3.22   3.31   3.31   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      I      13          7.696
LGA    I      14      I      14          2.110
LGA    S      15      S      15          2.468
LGA    P      16      P      16          2.454
LGA    H      17      H      17          1.639
LGA    H      18      H      18          3.834
LGA    Y      19      Y      19          3.474
LGA    V      20      V      20          1.714
LGA    Y      21      Y      21          2.358
LGA    P      22      P      22          1.841
LGA    N      23      N      23          1.775

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11  206    4.0     10    2.47     4.005     3.929     0.389

LGA_LOCAL      RMSD =  2.471  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.307  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  2.989  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.119738 * X  +  -0.041487 * Y  +   0.991938 * Z  +  -3.249140
  Y_new =   0.990442 * X  +  -0.073890 * Y  +   0.116467 * Z  +   9.876748
  Z_new =   0.068462 * X  +   0.996403 * Y  +   0.049938 * Z  +  26.288206 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.520720   -1.620873  [ DEG:    87.1308    -92.8692 ]
  Theta =  -0.068516   -3.073077  [ DEG:    -3.9257   -176.0743 ]
  Phi   =   1.691106   -1.450487  [ DEG:    96.8932    -83.1068 ]
 
# 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: T0386AL381_5-D1                               
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL381_5-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11  206   4.0   10   2.47   3.929     2.99
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL381_5-D1
REMARK Aligment from pdb entry: 1fdw
ATOM      5  N   ILE    13      15.015  55.675  32.299  1.00  0.00              
ATOM      6  CA  ILE    13      16.024  56.580  31.794  1.00  0.00              
ATOM      7  C   ILE    13      17.314  56.369  32.575  1.00  0.00              
ATOM      8  O   ILE    13      17.393  56.268  33.806  1.00  0.00              
ATOM      9  N   ILE    14      18.397  56.231  31.817  1.00  0.00              
ATOM     10  CA  ILE    14      19.711  56.030  32.405  1.00  0.00              
ATOM     11  C   ILE    14      20.236  57.354  32.940  1.00  0.00              
ATOM     12  O   ILE    14      20.670  58.208  32.164  1.00  0.00              
ATOM     13  N   SER    15      20.249  57.506  34.269  1.00  0.00              
ATOM     14  CA  SER    15      20.778  58.769  34.802  1.00  0.00              
ATOM     15  C   SER    15      22.250  58.618  35.110  1.00  0.00              
ATOM     16  O   SER    15      22.836  57.617  34.727  1.00  0.00              
ATOM     17  N   PRO    16      22.836  59.594  35.810  1.00  0.00              
ATOM     18  CA  PRO    16      24.237  59.530  36.199  1.00  0.00              
ATOM     19  C   PRO    16      24.522  60.455  37.369  1.00  0.00              
ATOM     20  O   PRO    16      23.843  61.434  37.627  1.00  0.00              
ATOM     21  N   HIS    17      25.622  60.200  38.077  1.00  0.00              
ATOM     22  CA  HIS    17      26.000  61.107  39.155  1.00  0.00              
ATOM     23  C   HIS    17      26.377  62.436  38.516  1.00  0.00              
ATOM     24  O   HIS    17      26.194  63.511  39.107  1.00  0.00              
ATOM     25  N   HIS    18      26.844  62.443  37.269  1.00  0.00              
ATOM     26  CA  HIS    18      27.170  63.715  36.627  1.00  0.00              
ATOM     27  C   HIS    18      25.936  64.542  36.300  1.00  0.00              
ATOM     28  O   HIS    18      26.058  65.705  35.879  1.00  0.00              
ATOM     29  N   TYR    19      24.742  64.007  36.444  1.00  0.00              
ATOM     30  CA  TYR    19      23.506  64.697  36.180  1.00  0.00              
ATOM     31  C   TYR    19      22.916  65.276  37.462  1.00  0.00              
ATOM     32  O   TYR    19      21.823  65.842  37.411  1.00  0.00              
ATOM     33  N   VAL    20      23.598  65.110  38.584  1.00  0.00              
ATOM     34  CA  VAL    20      23.257  65.630  39.873  1.00  0.00              
ATOM     35  C   VAL    20      24.364  66.518  40.478  1.00  0.00              
ATOM     36  O   VAL    20      24.075  67.096  41.537  1.00  0.00              
ATOM     37  N   TYR    21      25.550  66.596  39.892  1.00  0.00              
ATOM     38  CA  TYR    21      26.568  67.499  40.465  1.00  0.00              
ATOM     39  C   TYR    21      27.631  67.712  39.390  1.00  0.00              
ATOM     40  O   TYR    21      27.918  66.713  38.709  1.00  0.00              
ATOM     41  N   PRO    22      28.174  68.906  39.216  1.00  0.00              
ATOM     42  CA  PRO    22      29.130  69.128  38.139  1.00  0.00              
ATOM     43  C   PRO    22      30.526  68.616  38.377  1.00  0.00              
ATOM     44  O   PRO    22      31.115  68.764  39.448  1.00  0.00              
ATOM     45  N   ASN    23      31.147  67.999  37.392  1.00  0.00              
ATOM     46  CA  ASN    23      32.491  67.448  37.372  1.00  0.00              
ATOM     47  C   ASN    23      33.349  68.237  36.383  1.00  0.00              
ATOM     48  O   ASN    23      33.055  68.373  35.189  1.00  0.00              
END
