
#######################################################
#                                                     #
#                        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    7 (   28),  selected    7 , name T0378AL333_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected    7 , name T0378_D1.pdb
# PARAMETERS: T0378AL333_1-D1.T0378_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:     7        16 - 89          3.23     3.23
  LCS_AVERAGE:      7.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        16 - 18          0.44     9.70
  LONGEST_CONTINUOUS_SEGMENT:     3        17 - 19          0.44     5.51
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.70     4.19
  LCS_AVERAGE:      3.37

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3        16 - 18          0.44     9.70
  LONGEST_CONTINUOUS_SEGMENT:     3        87 - 89          0.70     4.19
  LCS_AVERAGE:      3.37

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:   89
LCS_GDT     R      16     R      16      3    3    7     3    3    3    4    4    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K      17     K      17      3    3    7     3    3    3    3    3    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     Y      18     Y      18      3    3    7     3    3    3    3    3    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     R      19     R      19      3    3    7     3    3    3    3    3    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     V      87     V      87      3    3    7     2    3    3    4    4    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F      88     F      88      3    3    7     2    3    3    4    4    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     D      89     D      89      3    3    7     0    3    3    4    4    4    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   4.87  (   3.37    3.37    7.87 )

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      3      3      4      4      4      6      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   3.37   3.37   3.37   4.49   4.49   4.49   6.74   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87   7.87
GDT RMS_LOCAL    0.44   0.44   0.44   1.06   1.06   1.06   2.97   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23
GDT RMS_ALL_CA   5.51   5.51   5.51   4.45   4.45   4.45   3.60   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23

#      Molecule1      Molecule2       DISTANCE
LGA    R      16      R      16          3.417
LGA    K      17      K      17          2.710
LGA    Y      18      Y      18          3.154
LGA    R      19      R      19          3.988
LGA    V      87      V      87          3.495
LGA    F      88      F      88          2.421
LGA    D      89      D      89          3.313

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   89    4.0      7    3.23     5.899     5.322     0.210

LGA_LOCAL      RMSD =  3.230  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.250  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.230  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.773931 * X  +   0.435805 * Y  +   0.459461 * Z  + -23.361618
  Y_new =  -0.527124 * X  +  -0.845424 * Y  +  -0.086009 * Z  + 116.079338
  Z_new =   0.350956 * X  +  -0.308758 * Y  +   0.884024 * Z  +  49.869591 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.336020    2.805573  [ DEG:   -19.2525    160.7475 ]
  Theta =  -0.358592   -2.783001  [ DEG:   -20.5458   -159.4542 ]
  Phi   =  -2.543665    0.597928  [ DEG:  -145.7412     34.2588 ]
 
# 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: T0378AL333_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL333_1-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   89   4.0    7   3.23   5.322     3.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL333_1-D1
REMARK Aligment from pdb entry: 1gz0_A
ATOM      1  N   ARG    16      24.708  24.604  53.139  1.00  0.00              
ATOM      2  CA  ARG    16      23.519  23.747  53.151  1.00  0.00              
ATOM      3  C   ARG    16      22.248  24.589  53.118  1.00  0.00              
ATOM      4  O   ARG    16      21.954  25.311  54.070  1.00  0.00              
ATOM      5  N   LYS    17      21.499  24.511  52.027  1.00  0.00              
ATOM      6  CA  LYS    17      20.265  25.276  51.939  1.00  0.00              
ATOM      7  C   LYS    17      19.106  24.352  52.302  1.00  0.00              
ATOM      8  O   LYS    17      18.901  23.320  51.662  1.00  0.00              
ATOM      9  N   TYR    18      18.363  24.714  53.343  1.00  0.00              
ATOM     10  CA  TYR    18      17.243  23.895  53.784  1.00  0.00              
ATOM     11  C   TYR    18      15.985  24.193  53.000  1.00  0.00              
ATOM     12  O   TYR    18      15.647  25.354  52.787  1.00  0.00              
ATOM     13  N   ARG    19      15.296  23.141  52.569  1.00  0.00              
ATOM     14  CA  ARG    19      14.045  23.304  51.842  1.00  0.00              
ATOM     15  C   ARG    19      12.938  22.888  52.803  1.00  0.00              
ATOM     16  O   ARG    19      13.190  22.182  53.781  1.00  0.00              
ATOM     17  N   VAL    87      11.721  23.332  52.520  1.00  0.00              
ATOM     18  CA  VAL    87      10.560  23.032  53.344  1.00  0.00              
ATOM     19  C   VAL    87      10.514  21.580  53.763  1.00  0.00              
ATOM     20  O   VAL    87      10.147  21.255  54.890  1.00  0.00              
ATOM     21  N   PHE    88      10.905  20.711  52.840  1.00  0.00              
ATOM     22  CA  PHE    88      10.897  19.274  53.070  1.00  0.00              
ATOM     23  C   PHE    88      11.788  18.826  54.219  1.00  0.00              
ATOM     24  O   PHE    88      11.387  17.971  55.005  1.00  0.00              
ATOM     25  N   ASP    89      12.988  19.386  54.327  1.00  0.00              
ATOM     26  CA  ASP    89      13.879  18.956  55.400  1.00  0.00              
ATOM     27  C   ASP    89      13.731  19.710  56.720  1.00  0.00              
ATOM     28  O   ASP    89      14.607  19.644  57.583  1.00  0.00              
END
