
#######################################################
#                                                     #
#                        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 T0356AL333_1-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected    8 , name T0356_D2.pdb
# PARAMETERS: T0356AL333_1-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:     8       269 - 276         3.72     3.72
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       270 - 274         0.66     5.26
  LCS_AVERAGE:      2.21

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       270 - 274         0.66     5.26
  LCS_AVERAGE:      2.21

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     A     269     A     269      3    3    8     0    3    3    3    3    5    6    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     E     270     E     270      5    5    8     4    4    5    5    5    5    6    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     I     271     I     271      5    5    8     4    4    5    5    5    5    6    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     V     272     V     272      5    5    8     4    4    5    5    5    5    6    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     L     273     L     273      5    5    8     4    4    5    5    5    5    6    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     E     274     E     274      5    5    8     4    4    5    5    5    5    6    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     G     275     G     275      3    3    8     0    3    3    3    3    5    5    7    7    7    7    7    7    7    8    8    8    8    8    8 
LCS_GDT     Y     276     Y     276      3    3    8     0    3    3    3    3    4    4    4    4    5    5    5    6    6    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   2.86  (   2.21    2.21    4.17 )

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      5      5      5      5      6      7      7      7      7      7      7      7      8      8      8      8      8      8 
GDT PERCENT_CA   2.08   2.08   2.60   2.60   2.60   2.60   3.13   3.65   3.65   3.65   3.65   3.65   3.65   3.65   4.17   4.17   4.17   4.17   4.17   4.17
GDT RMS_LOCAL    0.29   0.29   0.66   0.66   0.66   0.66   2.07   2.66   2.66   2.66   2.66   2.66   2.66   2.66   3.72   3.72   3.72   3.72   3.72   3.72
GDT RMS_ALL_CA   5.31   5.31   5.26   5.26   5.26   5.26   4.78   3.96   3.96   3.96   3.96   3.96   3.96   3.96   3.72   3.72   3.72   3.72   3.72   3.72

#      Molecule1      Molecule2       DISTANCE
LGA    A     269      A     269          3.185
LGA    E     270      E     270          3.112
LGA    I     271      I     271          1.302
LGA    V     272      V     272          1.646
LGA    L     273      L     273          1.260
LGA    E     274      E     274          2.865
LGA    G     275      G     275          3.926
LGA    Y     276      Y     276          8.704

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    8  192    4.0      7    2.66     3.125     2.886     0.254

LGA_LOCAL      RMSD =  2.658  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.956  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  3.718  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.181434 * X  +   0.595179 * Y  +  -0.782843 * Z  +  77.524117
  Y_new =   0.143052 * X  +   0.803561 * Y  +   0.577776 * Z  + -105.238457
  Z_new =   0.972943 * X  +  -0.007159 * Y  +  -0.230935 * Z  + -26.504076 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.110604    0.030988  [ DEG:  -178.2245      1.7755 ]
  Theta =  -1.337644   -1.803949  [ DEG:   -76.6413   -103.3587 ]
  Phi   =   2.473935   -0.667658  [ DEG:   141.7460    -38.2540 ]
 
# 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: T0356AL333_1-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_1-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    8  192   4.0    7   2.66   2.886     3.72
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_1-D2
REMARK Aligment from pdb entry: 1lwh_A
ATOM    129  N   ALA   269      75.549  74.333  86.504  1.00  0.00              
ATOM    130  CA  ALA   269      76.864  74.238  87.162  1.00  0.00              
ATOM    131  C   ALA   269      77.328  72.774  87.168  1.00  0.00              
ATOM    132  O   ALA   269      76.617  71.884  87.628  1.00  0.00              
ATOM    133  N   GLU   270      78.528  72.545  86.641  1.00  0.00              
ATOM    134  CA  GLU   270      79.104  71.211  86.523  1.00  0.00              
ATOM    135  C   GLU   270      79.021  70.354  87.762  1.00  0.00              
ATOM    136  O   GLU   270      78.676  70.828  88.834  1.00  0.00              
ATOM    137  N   ILE   271      79.331  69.077  87.594  1.00  0.00              
ATOM    138  CA  ILE   271      79.304  68.114  88.680  1.00  0.00              
ATOM    139  C   ILE   271      79.907  66.853  88.085  1.00  0.00              
ATOM    140  O   ILE   271      79.526  66.450  86.994  1.00  0.00              
ATOM    141  N   VAL   272      80.849  66.231  88.786  1.00  0.00              
ATOM    142  CA  VAL   272      81.501  65.033  88.251  1.00  0.00              
ATOM    143  C   VAL   272      80.929  63.681  88.668  1.00  0.00              
ATOM    144  O   VAL   272      80.583  63.471  89.824  1.00  0.00              
ATOM    145  N   LEU   273      80.815  62.777  87.698  1.00  0.00              
ATOM    146  CA  LEU   273      80.356  61.412  87.956  1.00  0.00              
ATOM    147  C   LEU   273      81.289  60.509  87.161  1.00  0.00              
ATOM    148  O   LEU   273      81.545  60.757  85.981  1.00  0.00              
ATOM    149  N   GLU   274      81.792  59.469  87.825  1.00  0.00              
ATOM    150  CA  GLU   274      82.715  58.530  87.226  1.00  0.00              
ATOM    151  C   GLU   274      83.769  59.233  86.363  1.00  0.00              
ATOM    152  O   GLU   274      84.102  58.794  85.255  1.00  0.00              
ATOM    153  N   GLY   275      84.288  60.338  86.892  1.00  0.00              
ATOM    154  CA  GLY   275      85.325  61.085  86.209  1.00  0.00              
ATOM    155  C   GLY   275      84.862  61.974  85.085  1.00  0.00              
ATOM    156  O   GLY   275      85.667  62.714  84.505  1.00  0.00              
ATOM    157  N   TYR   276      83.565  61.919  84.784  1.00  0.00              
ATOM    158  CA  TYR   276      82.973  62.718  83.704  1.00  0.00              
ATOM    159  C   TYR   276      82.412  64.082  84.149  1.00  0.00              
ATOM    160  O   TYR   276      81.693  64.181  85.149  1.00  0.00              
END
