
#######################################################
#                                                     #
#                        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   24 (   24),  selected   24 , name T0356TS464_3-D3
# Molecule2: number of CA atoms  120 (  972),  selected   24 , name T0356_D3.pdb
# PARAMETERS: T0356TS464_3-D3.T0356_D3.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:    11       396 - 429         4.79    12.84
  LCS_AVERAGE:      7.88

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       396 - 402         1.14    15.60
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       396 - 400         0.56    16.98
  LONGEST_CONTINUOUS_SEGMENT:     5       398 - 402         0.78    15.08
  LONGEST_CONTINUOUS_SEGMENT:     5       426 - 430         0.46    21.20
  LCS_AVERAGE:      3.47

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:  120
LCS_GDT     A     375     A     375      4    4    9     3    3    4    4    5    6    7    8    9   10   10   10   11   11   13   13   13   14   15   15 
LCS_GDT     G     376     G     376      4    4    9     3    3    4    4    4    5    5    6    9   10   10   10   11   11   13   13   13   14   15   16 
LCS_GDT     H     377     H     377      4    4    9     3    3    4    4    5    6    7    8    9   10   10   10   11   11   13   13   13   14   15   16 
LCS_GDT     A     378     A     378      4    4    9     3    3    4    4    4    5    7    8    9   10   10   10   11   11   13   13   13   13   15   15 
LCS_GDT     K     379     K     379      3    4    9     3    3    4    4    5    6    7    8    9   10   10   10   11   11   13   13   13   14   15   16 
LCS_GDT     R     380     R     380      3    4    9     1    3    4    4    4    4    5    8    9   10   10   10   11   11   13   13   13   14   15   16 
LCS_GDT     V     381     V     381      3    3    9     0    3    3    3    4    4    5    6    8    9   10   10   11   11   11   12   12   12   14   14 
LCS_GDT     K     396     K     396      5    7   11     4    5    7    7    8    8    8    9    9   10   10   10   10   11   13   13   13   14   15   16 
LCS_GDT     F     397     F     397      5    7   11     4    5    7    7    8    8    8    9    9   10   10   10   10   11   13   13   13   14   15   16 
LCS_GDT     V     398     V     398      5    7   11     4    5    7    7    8    8    8    9    9    9    9    9    9   11   13   13   13   14   15   16 
LCS_GDT     I     399     I     399      5    7   11     4    5    7    7    8    8    8    9    9    9    9    9    9   10   13   13   13   14   15   16 
LCS_GDT     V     400     V     400      5    7   11     3    5    7    7    8    8    8    9    9    9    9    9    9   10   11   11   13   14   15   16 
LCS_GDT     C     401     C     401      5    7   11     3    4    7    7    8    8    8    9    9    9    9    9    9   10   11   11   13   14   15   16 
LCS_GDT     D     402     D     402      5    7   11     3    4    7    7    8    8    8    9    9    9    9    9    9   10   10   11   11   12   14   14 
LCS_GDT     D     426     D     426      5    5   11     4    5    5    5    5    6    7    7    7    7   10   10   11   11   11   12   13   13   15   15 
LCS_GDT     T     427     T     427      5    5   11     4    5    5    5    5    6    7    9    9    9   10   10   11   11   13   13   13   14   15   15 
LCS_GDT     V     428     V     428      5    5   11     4    5    6    7    8    8    8    9    9   10   10   10   11   11   13   13   13   14   15   16 
LCS_GDT     L     429     L     429      5    5   11     4    5    5    5    5    6    7    8    9   10   10   10   11   11   13   13   13   14   14   16 
LCS_GDT     V     430     V     430      5    5    8     4    5    5    5    5    6    7    7    8   10   10   10   11   11   11   12   12   12   14   16 
LCS_GDT     L     453     L     453      3    3    7     3    3    3    3    4    5    5    5    5    6    6    6    6    6    7    7    7    7    7    8 
LCS_GDT     D     454     D     454      3    4    7     3    3    3    4    4    5    5    5    5    6    6    6    6    6    7    7    7   11   13   14 
LCS_GDT     A     455     A     455      3    4    7     3    3    3    4    4    5    5    5    5    6    6    6    6    7    9    9   11   12   13   16 
LCS_GDT     T     456     T     456      3    4    7     3    3    3    4    4    5    5    5    5    6    6    6    6    7    9   11   11   12   13   16 
LCS_GDT     N     457     N     457      3    4    7     3    3    3    4    4    5    5    5    5    6    7    8    8   10   10   11   11   12   13   16 
LCS_AVERAGE  LCS_A:   5.17  (   3.47    4.17    7.88 )

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      5      7      7      8      8      8      9      9     10     10     10     11     11     13     13     13     14     15     16 
GDT PERCENT_CA   3.33   4.17   5.83   5.83   6.67   6.67   6.67   7.50   7.50   8.33   8.33   8.33   9.17   9.17  10.83  10.83  10.83  11.67  12.50  13.33
GDT RMS_LOCAL    0.28   0.46   1.14   1.11   1.37   1.37   1.37   2.44   2.44   3.39   3.39   3.39   4.02   4.02   5.49   5.49   5.49   6.29   6.54   7.74
GDT RMS_ALL_CA  21.21  21.20  15.60  12.92  12.93  12.93  12.93  12.87  12.87  13.22  13.22  13.22  20.13  20.13  11.26  11.26  11.26  11.01  12.17  10.29

#      Molecule1      Molecule2       DISTANCE
LGA    A     375      A     375         14.105
LGA    G     376      G     376         13.787
LGA    H     377      H     377         14.699
LGA    A     378      A     378         16.640
LGA    K     379      K     379         12.662
LGA    R     380      R     380         17.629
LGA    V     381      V     381         19.177
LGA    K     396      K     396          2.880
LGA    F     397      F     397          3.774
LGA    V     398      V     398          1.628
LGA    I     399      I     399          1.500
LGA    V     400      V     400          2.699
LGA    C     401      C     401          2.691
LGA    D     402      D     402          3.720
LGA    D     426      D     426          9.475
LGA    T     427      T     427          3.533
LGA    V     428      V     428          3.164
LGA    L     429      L     429         10.185
LGA    V     430      V     430         16.012
LGA    L     453      L     453         24.150
LGA    D     454      D     454         17.504
LGA    A     455      A     455         18.046
LGA    T     456      T     456         16.247
LGA    N     457      N     457         16.568

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  120    4.0      9    2.44     7.083     6.436     0.355

LGA_LOCAL      RMSD =  2.437  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.914  Number of atoms =   24 
Std_ALL_ATOMS  RMSD = 10.151  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.031763 * X  +  -0.791634 * Y  +   0.610170 * Z  +  97.422119
  Y_new =   0.442822 * X  +   0.536147 * Y  +   0.718648 * Z  +  -1.264219
  Z_new =  -0.896047 * X  +   0.293023 * Y  +   0.333524 * Z  + 109.276299 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.720847   -2.420746  [ DEG:    41.3015   -138.6985 ]
  Theta =   1.110783    2.030810  [ DEG:    63.6432    116.3568 ]
  Phi   =   1.642402   -1.499191  [ DEG:    94.1027    -85.8973 ]
 
# 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: T0356TS464_3-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS464_3-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  120   4.0    9   2.44   6.436    10.15
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS464_3-D3
PFRMAT TS
TARGET T0356
MODEL 3
PARENT N/A
ATOM    142  CA  ALA   375      41.275  51.676  38.707  1.00  0.00
ATOM    143  CA  GLY   376      44.806  51.581  37.298  1.00  0.00
ATOM    144  CA  HIS   377      46.141  51.717  40.848  1.00  0.00
ATOM    145  CA  ALA   378      46.837  48.843  43.225  1.00  0.00
ATOM    146  CA  LYS   379      44.503  49.536  46.145  1.00  0.00
ATOM    147  CA  ARG   380      40.705  49.653  46.320  1.00  0.00
ATOM    148  CA  VAL   381      38.978  53.016  46.337  1.00  0.00
ATOM    149  CA  LYS   396      50.818  55.017  62.311  1.00  0.00
ATOM    150  CA  PHE   397      48.368  57.348  60.524  1.00  0.00
ATOM    151  CA  VAL   398      48.365  60.948  61.699  1.00  0.00
ATOM    152  CA  ILE   399      45.558  63.156  60.403  1.00  0.00
ATOM    153  CA  VAL   400      46.877  66.544  59.199  1.00  0.00
ATOM    154  CA  CYS   401      46.338  69.459  56.854  1.00  0.00
ATOM    155  CA  ASP   402      46.280  73.269  57.098  1.00  0.00
ATOM    156  CA  ASP   426      44.943  49.432  57.879  1.00  0.00
ATOM    157  CA  THR   427      43.661  51.463  54.918  1.00  0.00
ATOM    158  CA  VAL   428      43.903  55.278  54.847  1.00  0.00
ATOM    159  CA  LEU   429      40.828  56.999  53.426  1.00  0.00
ATOM    160  CA  VAL   430      40.826  60.329  51.561  1.00  0.00
ATOM    161  CA  LEU   453      53.212  72.203  40.421  1.00  0.00
ATOM    162  CA  ASP   454      52.531  70.870  43.910  1.00  0.00
ATOM    163  CA  ALA   455      50.161  73.721  44.718  1.00  0.00
ATOM    164  CA  THR   456      48.064  76.418  43.124  1.00  0.00
ATOM    165  CA  ASN   457      47.950  79.556  45.255  1.00  0.00
TER
END
