
#######################################################
#                                                     #
#                        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   10 (   40),  selected   10 , name T0372AL257_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   10 , name T0372_D1.pdb
# PARAMETERS: T0372AL257_3-D1.T0372_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       290 - 298         2.00    17.81
  LCS_AVERAGE:      6.03

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 298         2.00    17.81
  LCS_AVERAGE:      5.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       290 - 293         0.75    19.71
  LONGEST_CONTINUOUS_SEGMENT:     4       291 - 294         0.60    20.58
  LONGEST_CONTINUOUS_SEGMENT:     4       293 - 296         0.70    12.01
  LCS_AVERAGE:      2.70

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:  126
LCS_GDT     F       4     F       4      3    4    6     0    3    3    4    4    4    4    4    4    5    5    6    6    6    7    7    8    9    9    9 
LCS_GDT     K       5     K       5      3    4    6     1    3    3    4    4    4    4    4    4    5    5    6    6    6    7    7    8    9    9    9 
LCS_GDT     K     290     K     290      4    8    8     3    4    5    6    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     Y     291     Y     291      4    8    8     3    4    5    6    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     M     292     M     292      4    8    8     3    4    5    6    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     A     293     A     293      4    8    8     3    4    5    6    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     C     294     C     294      4    8    8     3    4    5    5    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     L     295     L     295      4    8    8     3    4    5    6    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     K     296     K     296      4    8    8     3    4    5    5    6    8    8    8    8    8    8    8    8    8    8    8    8    9    9    9 
LCS_GDT     H     298     H     298      0    8    8     3    4    5    6    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   4.81  (   2.70    5.71    6.03 )

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      3      4      5      6      6      8      8      8      8      8      8      8      8      8      8      8      8      9      9      9 
GDT PERCENT_CA   2.38   3.17   3.97   4.76   4.76   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   6.35   7.14   7.14   7.14
GDT RMS_LOCAL    0.03   0.60   0.89   1.12   1.12   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   6.84   6.84   6.84
GDT RMS_ALL_CA  20.22  20.58  18.87  20.12  20.12  17.81  17.81  17.81  17.81  17.81  17.81  17.81  17.81  17.81  17.81  17.81  17.81   8.16   8.16   8.16

#      Molecule1      Molecule2       DISTANCE
LGA    F       4      F       4         39.120
LGA    K       5      K       5         40.105
LGA    K     290      K     290          0.976
LGA    Y     291      Y     291          2.207
LGA    M     292      M     292          2.715
LGA    A     293      A     293          1.986
LGA    C     294      C     294          2.776
LGA    L     295      L     295          1.408
LGA    K     296      K     296          2.084
LGA    H     298      H     298          0.897

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  126    4.0      8    2.00     5.159     5.557     0.381

LGA_LOCAL      RMSD =  1.999  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.807  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  7.833  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.850681 * X  +   0.136896 * Y  +  -0.507545 * Z  +  45.033928
  Y_new =  -0.505584 * X  +  -0.477482 * Y  +   0.718607 * Z  +  39.216240
  Z_new =  -0.143969 * X  +   0.867912 * Y  +   0.475397 * Z  + -11.438144 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.069684   -2.071909  [ DEG:    61.2884   -118.7116 ]
  Theta =   0.144471    2.997122  [ DEG:     8.2776    171.7224 ]
  Phi   =  -2.605354    0.536239  [ DEG:  -149.2758     30.7242 ]
 
# 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: T0372AL257_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL257_3-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  126   4.0    8   2.00   5.557     7.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL257_3-D1
REMARK Aligment from pdb entry: 1ne9_A
ATOM      1  N   PHE     4      27.941  31.247  22.675  1.00  0.00              
ATOM      2  CA  PHE     4      26.862  32.027  23.247  1.00  0.00              
ATOM      3  C   PHE     4      26.759  32.239  24.740  1.00  0.00              
ATOM      4  O   PHE     4      27.325  31.488  25.535  1.00  0.00              
ATOM      5  N   LYS     5      26.025  33.290  25.134  1.00  0.00              
ATOM      6  CA  LYS     5      25.839  33.587  26.553  1.00  0.00              
ATOM      7  C   LYS     5      24.874  32.524  27.064  1.00  0.00              
ATOM      8  O   LYS     5      24.177  31.880  26.276  1.00  0.00              
ATOM    581  N   LYS   290      26.562  45.631   7.220  1.00  0.00              
ATOM    582  CA  LYS   290      25.855  46.421   6.220  1.00  0.00              
ATOM    583  C   LYS   290      26.777  46.515   5.017  1.00  0.00              
ATOM    584  O   LYS   290      27.852  47.100   5.095  1.00  0.00              
ATOM    585  N   TYR   291      26.347  45.941   3.903  1.00  0.00              
ATOM    586  CA  TYR   291      27.156  45.937   2.700  1.00  0.00              
ATOM    587  C   TYR   291      26.992  47.177   1.832  1.00  0.00              
ATOM    588  O   TYR   291      26.028  47.936   1.965  1.00  0.00              
ATOM    589  N   MET   292      27.955  47.360   0.938  1.00  0.00              
ATOM    590  CA  MET   292      27.992  48.491   0.022  1.00  0.00              
ATOM    591  C   MET   292      26.758  48.546  -0.874  1.00  0.00              
ATOM    592  O   MET   292      26.406  49.603  -1.394  1.00  0.00              
ATOM    593  N   ALA   293      26.097  47.408  -1.049  1.00  0.00              
ATOM    594  CA  ALA   293      24.908  47.384  -1.880  1.00  0.00              
ATOM    595  C   ALA   293      25.191  47.059  -3.329  1.00  0.00              
ATOM    596  O   ALA   293      26.121  46.316  -3.641  1.00  0.00              
ATOM    597  N   CYS   294      24.395  47.622  -4.228  1.00  0.00              
ATOM    598  CA  CYS   294      24.586  47.347  -5.643  1.00  0.00              
ATOM    599  C   CYS   294      25.479  48.376  -6.311  1.00  0.00              
ATOM    600  O   CYS   294      25.286  49.583  -6.160  1.00  0.00              
ATOM    601  N   LEU   295      26.480  47.877  -7.026  1.00  0.00              
ATOM    602  CA  LEU   295      27.404  48.723  -7.757  1.00  0.00              
ATOM    603  C   LEU   295      27.032  48.500  -9.211  1.00  0.00              
ATOM    604  O   LEU   295      27.195  47.400  -9.749  1.00  0.00              
ATOM    605  N   LYS   296      26.508  49.545  -9.840  1.00  0.00              
ATOM    606  CA  LYS   296      26.073  49.448 -11.222  1.00  0.00              
ATOM    607  C   LYS   296      26.991  50.128 -12.218  1.00  0.00              
ATOM    608  O   LYS   296      27.328  51.300 -12.061  1.00  0.00              
ATOM    609  N   HIS   298      27.403  49.379 -13.233  1.00  0.00              
ATOM    610  CA  HIS   298      28.213  49.941 -14.306  1.00  0.00              
ATOM    611  C   HIS   298      27.135  50.186 -15.358  1.00  0.00              
ATOM    612  O   HIS   298      26.638  49.248 -15.983  1.00  0.00              
END
