
#######################################################
#                                                     #
#                        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    8 (   32),  selected    8 , name T0295AL333_4-D2
# Molecule2: number of CA atoms   95 (  803),  selected    8 , name T0295_D2.pdb
# PARAMETERS: T0295AL333_4-D2.T0295_D2.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       217 - 268         4.45     4.45
  LCS_AVERAGE:      8.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       218 - 222         1.81     8.01
  LCS_AVERAGE:      3.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       219 - 222         0.40     9.79
  LCS_AVERAGE:      2.89

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:   95
LCS_GDT     N     217     N     217      3    4    8     0    3    3    4    4    5    5    6    6    6    6    7    7    8    8    8    8    8    8    8 
LCS_GDT     Y     218     Y     218      3    5    8     1    3    3    4    5    5    5    6    6    6    6    7    7    8    8    8    8    8    8    8 
LCS_GDT     K     219     K     219      4    5    8     4    4    4    4    5    5    5    6    6    6    6    7    7    8    8    8    8    8    8    8 
LCS_GDT     N     220     N     220      4    5    8     4    4    4    4    5    5    5    6    6    6    6    7    7    8    8    8    8    8    8    8 
LCS_GDT     W     221     W     221      4    5    8     4    4    4    4    5    5    5    6    6    6    6    7    7    8    8    8    8    8    8    8 
LCS_GDT     C     222     C     222      4    5    8     4    4    4    4    5    5    5    6    6    6    6    7    7    8    8    8    8    8    8    8 
LCS_GDT     F     267     F     267      0    0    8     0    0    0    0    0    3    3    3    3    3    4    7    7    8    8    8    8    8    8    8 
LCS_GDT     N     268     N     268      0    0    8     0    1    2    2    2    3    3    5    5    6    6    7    7    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   5.04  (   2.89    3.82    8.42 )

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      4      4      5      5      5      6      6      6      6      7      7      8      8      8      8      8      8      8 
GDT PERCENT_CA   4.21   4.21   4.21   4.21   5.26   5.26   5.26   6.32   6.32   6.32   6.32   7.37   7.37   8.42   8.42   8.42   8.42   8.42   8.42   8.42
GDT RMS_LOCAL    0.40   0.40   0.40   0.40   1.81   1.81   1.81   2.69   2.69   2.69   2.69   3.83   3.83   4.45   4.45   4.45   4.45   4.45   4.45   4.45
GDT RMS_ALL_CA   9.79   9.79   9.79   9.79   8.01   8.01   8.01   6.41   6.41   6.41   6.41   4.65   4.65   4.45   4.45   4.45   4.45   4.45   4.45   4.45

#      Molecule1      Molecule2       DISTANCE
LGA    N     217      N     217          3.220
LGA    Y     218      Y     218          1.802
LGA    K     219      K     219          1.417
LGA    N     220      N     220          3.035
LGA    W     221      W     221          2.304
LGA    C     222      C     222          3.629
LGA    F     267      F     267         10.343
LGA    N     268      N     268         13.348

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8   95    4.0      6    2.69     5.789     5.289     0.215

LGA_LOCAL      RMSD =  2.687  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.408  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  4.450  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.085183 * X  +  -0.335241 * Y  +   0.938274 * Z  +  19.478024
  Y_new =  -0.787232 * X  +  -0.554590 * Y  +  -0.269623 * Z  +  79.294479
  Z_new =   0.610746 * X  +  -0.761606 * Y  +  -0.216671 * Z  +  19.462723 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.847965    1.293627  [ DEG:  -105.8806     74.1194 ]
  Theta =  -0.657002   -2.484591  [ DEG:   -37.6434   -142.3566 ]
  Phi   =  -1.678583    1.463010  [ DEG:   -96.1757     83.8243 ]
 
# 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: T0295AL333_4-D2                               
REMARK     2: T0295_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0295AL333_4-D2.T0295_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8   95   4.0    6   2.69   5.289     4.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0295AL333_4-D2
REMARK Aligment from pdb entry: 1jg1_A
ATOM    585  N   ASN   217      23.718  26.638   0.298  1.00  0.00              
ATOM    586  CA  ASN   217      23.179  27.667   1.155  1.00  0.00              
ATOM    587  C   ASN   217      24.044  28.884   0.985  1.00  0.00              
ATOM    588  O   ASN   217      25.217  28.863   1.426  1.00  0.00              
ATOM    589  N   TYR   218      23.564  29.950   0.361  1.00  0.00              
ATOM    590  CA  TYR   218      24.365  31.112   0.004  1.00  0.00              
ATOM    591  C   TYR   218      23.973  32.245   0.939  1.00  0.00              
ATOM    592  O   TYR   218      22.777  32.626   0.951  1.00  0.00              
ATOM    593  N   LYS   219      24.921  32.743   1.719  1.00  0.00              
ATOM    594  CA  LYS   219      24.584  33.878   2.603  1.00  0.00              
ATOM    595  C   LYS   219      25.683  34.075   3.638  1.00  0.00              
ATOM    596  O   LYS   219      26.738  33.464   3.563  1.00  0.00              
ATOM    597  N   ASN   220      25.333  34.951   4.591  1.00  0.00              
ATOM    598  CA  ASN   220      26.333  35.448   5.519  1.00  0.00              
ATOM    599  C   ASN   220      26.941  34.352   6.365  1.00  0.00              
ATOM    600  O   ASN   220      28.140  34.424   6.651  1.00  0.00              
ATOM    601  N   TRP   221      26.144  33.369   6.739  1.00  0.00              
ATOM    602  CA  TRP   221      26.641  32.226   7.528  1.00  0.00              
ATOM    603  C   TRP   221      26.578  30.963   6.669  1.00  0.00              
ATOM    604  O   TRP   221      26.600  29.857   7.232  1.00  0.00              
ATOM    605  N   CYS   222      26.536  31.108   5.353  1.00  0.00              
ATOM    606  CA  CYS   222      26.687  29.996   4.445  1.00  0.00              
ATOM    607  C   CYS   222      27.884  30.242   3.524  1.00  0.00              
ATOM    608  O   CYS   222      28.933  30.763   3.938  1.00  0.00              
ATOM    609  N   PHE   267      27.735  29.869   2.264  1.00  0.00              
ATOM    610  CA  PHE   267      28.710  30.072   1.227  1.00  0.00              
ATOM    611  C   PHE   267      28.664  31.521   0.742  1.00  0.00              
ATOM    612  O   PHE   267      27.597  32.118   0.588  1.00  0.00              
ATOM    613  N   ASN   268      29.823  32.104   0.481  1.00  0.00              
ATOM    614  CA  ASN   268      29.773  33.431  -0.176  1.00  0.00              
ATOM    615  C   ASN   268      29.239  33.356  -1.601  1.00  0.00              
ATOM    616  O   ASN   268      29.300  32.310  -2.255  1.00  0.00              
END
