
#######################################################
#                                                     #
#                        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 T0356AL044_3-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected    7 , name T0356_D2.pdb
# PARAMETERS: T0356AL044_3-D2.T0356_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:     7       305 - 313         3.87     3.87
  LCS_AVERAGE:      3.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       305 - 309         0.93     4.27
  LCS_AVERAGE:      1.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       305 - 309         0.93     4.27
  LCS_AVERAGE:      1.19

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:  192
LCS_GDT     T     305     T     305      4    4    7     2    3    4    5    5    5    5    5    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     V     306     V     306      4    4    7     0    3    4    5    5    5    5    5    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     H     308     H     308      4    4    7     0    3    4    5    5    5    5    5    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     I     309     I     309      4    4    7     2    3    4    5    5    5    5    5    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     T     310     T     310      0    0    7     0    0    0    0    0    2    4    5    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     R     312     R     312      0    0    7     1    1    2    5    5    5    5    5    6    6    6    6    7    7    7    7    7    7    7    7 
LCS_GDT     E     313     E     313      0    0    7     0    0    0    1    1    2    2    3    3    4    5    5    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   2.01  (   1.19    1.19    3.65 )

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      2      3      4      5      5      5      5      5      6      6      6      6      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   1.04   1.56   2.08   2.60   2.60   2.60   2.60   2.60   3.12   3.12   3.12   3.12   3.65   3.65   3.65   3.65   3.65   3.65   3.65   3.65
GDT RMS_LOCAL   22.37   0.50   0.93   1.47   1.47   1.47   1.47   1.47   2.42   2.42   2.42   2.42   3.87   3.87   3.87   3.87   3.87   3.87   3.87   3.87
GDT RMS_ALL_CA   5.31   5.31   4.27   4.62   4.62   4.62   4.62   4.62   4.74   4.74   4.74   4.74   3.87   3.87   3.87   3.87   3.87   3.87   3.87   3.87

#      Molecule1      Molecule2       DISTANCE
LGA    T     305      T     305          1.328
LGA    V     306      V     306          1.042
LGA    H     308      H     308          1.734
LGA    I     309      I     309          1.387
LGA    T     310      T     310          5.412
LGA    R     312      R     312          1.731
LGA    E     313      E     313         10.466

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7  192    4.0      5    1.47     2.604     2.344     0.319

LGA_LOCAL      RMSD =  1.468  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.623  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.869  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.086393 * X  +  -0.813310 * Y  +   0.575380 * Z  + 109.561165
  Y_new =   0.651625 * X  +   0.483000 * Y  +   0.584889 * Z  +  33.824085
  Z_new =  -0.753605 * X  +   0.324402 * Y  +   0.571701 * Z  +  73.105278 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.516129   -2.625463  [ DEG:    29.5720   -150.4280 ]
  Theta =   0.853530    2.288063  [ DEG:    48.9036    131.0964 ]
  Phi   =   1.438985   -1.702608  [ DEG:    82.4478    -97.5522 ]
 
# 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: T0356AL044_3-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_3-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7  192   4.0    5   1.47   2.344     3.87
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_3-D2
REMARK Aligment from pdb entry: 2bco_A
ATOM      1  N   THR   305      83.241  51.882  88.638  1.00  0.00              
ATOM      2  CA  THR   305      82.778  52.933  89.529  1.00  0.00              
ATOM      3  C   THR   305      83.368  54.249  89.060  1.00  0.00              
ATOM      4  O   THR   305      84.287  54.257  88.246  1.00  0.00              
ATOM      5  N   VAL   306      82.829  55.360  89.550  1.00  0.00              
ATOM      6  CA  VAL   306      83.304  56.666  89.129  1.00  0.00              
ATOM      7  C   VAL   306      83.450  57.620  90.296  1.00  0.00              
ATOM      8  O   VAL   306      82.878  57.410  91.371  1.00  0.00              
ATOM      9  N   HIS   308      84.217  58.676  90.067  1.00  0.00              
ATOM     10  CA  HIS   308      84.453  59.689  91.075  1.00  0.00              
ATOM     11  C   HIS   308      84.071  61.057  90.522  1.00  0.00              
ATOM     12  O   HIS   308      84.587  61.480  89.487  1.00  0.00              
ATOM     13  N   ILE   309      83.154  61.731  91.211  1.00  0.00              
ATOM     14  CA  ILE   309      82.696  63.057  90.807  1.00  0.00              
ATOM     15  C   ILE   309      83.435  64.117  91.633  1.00  0.00              
ATOM     16  O   ILE   309      83.301  64.158  92.858  1.00  0.00              
ATOM     17  N   THR   310      83.540  70.801  93.479  1.00  0.00              
ATOM     18  CA  THR   310      83.668  72.176  93.010  1.00  0.00              
ATOM     19  C   THR   310      82.376  72.903  93.355  1.00  0.00              
ATOM     20  O   THR   310      81.345  72.265  93.573  1.00  0.00              
ATOM     21  N   ARG   312      82.430  74.229  93.425  1.00  0.00              
ATOM     22  CA  ARG   312      81.248  75.027  93.743  1.00  0.00              
ATOM     23  C   ARG   312      80.305  75.049  92.537  1.00  0.00              
ATOM     24  O   ARG   312      79.123  75.370  92.659  1.00  0.00              
ATOM     25  N   GLU   313      78.228  70.438  88.715  1.00  0.00              
ATOM     26  CA  GLU   313      78.744  69.511  87.712  1.00  0.00              
ATOM     27  C   GLU   313      78.219  68.094  87.917  1.00  0.00              
ATOM     28  O   GLU   313      78.725  67.140  87.331  1.00  0.00              
END
