
#######################################################
#                                                     #
#                        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   29 (   29),  selected   29 , name T0372TS464_4_2-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   29 , name T0372_D2.pdb
# PARAMETERS: T0372TS464_4_2-D2.T0372_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:    13       219 - 231         4.88    16.09
  LONGEST_CONTINUOUS_SEGMENT:    13       220 - 232         4.59    15.76
  LONGEST_CONTINUOUS_SEGMENT:    13       225 - 237         4.66    16.20
  LONGEST_CONTINUOUS_SEGMENT:    13       226 - 238         4.94    16.55
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       221 - 227         1.94    18.06
  LONGEST_CONTINUOUS_SEGMENT:     7       222 - 228         1.96    18.95
  LCS_AVERAGE:      3.01

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       226 - 230         0.53    16.32
  LCS_AVERAGE:      2.06

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:  172
LCS_GDT     V     213     V     213      3    4   11     3    3    3    5    6    6    6    7    8    9    9   10   11   11   12   14   14   15   18   22 
LCS_GDT     N     214     N     214      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   11   11   11   14   14   15   16   17 
LCS_GDT     G     215     G     215      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   10   11   11   12   13   14   15   16 
LCS_GDT     K     216     K     216      3    4   11     3    3    3    4    4    5    6    7    8    9    9   10   11   11   11   14   14   15   16   17 
LCS_GDT     I     217     I     217      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   11   11   12   14   15   18   19   22 
LCS_GDT     V     218     V     218      3    4   11     3    3    3    4    4    5    6    6    7    9    9   10   10   11   11   14   14   18   18   22 
LCS_GDT     A     219     A     219      3    4   13     3    3    3    4    4    4    6    6    7    9    9   10   10   11   12   13   14   18   18   22 
LCS_GDT     F     220     F     220      3    4   13     0    3    3    4    4    4    6    6    7    9    9   12   12   12   13   14   15   18   19   22 
LCS_GDT     T     221     T     221      3    7   13     1    3    3    4    6    7   10   10   11   11   11   12   12   12   13   14   15   18   18   22 
LCS_GDT     F     222     F     222      3    7   13     2    3    4    5    7    8   10   10   11   11   11   12   12   12   13   14   15   18   19   22 
LCS_GDT     G     223     G     223      3    7   13     3    3    5    5    7    8   10   10   11   11   11   12   12   12   13   14   15   18   18   20 
LCS_GDT     M     224     M     224      4    7   13     3    3    5    5    7    8   10   10   11   11   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     P     225     P     225      4    7   13     3    3    5    5    7    8   10   10   11   11   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     I     226     I     226      5    7   13     3    5    5    6    7    8   10   10   11   11   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     N     227     N     227      5    7   13     3    5    5    6    7    8   10   10   11   11   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     H     228     H     228      5    7   13     3    5    5    6    7    8   10   10   11   11   11   12   12   13   14   16   16   18   18   19 
LCS_GDT     E     229     E     229      5    6   13     3    5    5    6    6    8   10   10   11   11   11   12   12   13   14   16   16   18   18   22 
LCS_GDT     T     230     T     230      5    6   13     3    5    5    6    6    8   10   10   11   11   11   12   12   14   14   16   16   18   19   22 
LCS_GDT     F     231     F     231      3    6   13     1    4    5    6    6    6    6   10   11   11   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     G     232     G     232      3    3   13     3    3    3    3    3    4    6    9    9    9   11   11   13   14   15   16   16   18   19   22 
LCS_GDT     V     233     V     233      3    4   13     3    3    3    4    4    5    6    9    9    9   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     H     234     H     234      3    4   13     3    3    3    4    4    5    6    9    9    9   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     V     235     V     235      3    4   13     3    3    3    4    4    4    5    8    9    9   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     E     236     E     236      3    4   13     3    3    3    4    4    5    6    8    9    9   11   12   13   14   15   16   16   18   19   22 
LCS_GDT     K     237     K     237      3    5   13     3    3    4    5    6    6    6    7    8    9   10   12   13   14   15   16   16   18   19   22 
LCS_GDT     A     238     A     238      4    5   13     3    4    4    4    6    6    6    7    8    9   10   12   13   14   15   16   16   18   19   22 
LCS_GDT     D     239     D     239      4    5   10     3    4    4    5    6    6    6    7    8    8   10   11   12   13   15   16   16   18   19   21 
LCS_GDT     T     240     T     240      4    5   10     3    4    4    5    6    6    6    7    8    9   10   12   13   14   15   16   16   18   19   22 
LCS_GDT     S     241     S     241      4    5   10     3    4    4    5    6    6    6    7    8    8   10   11   12   13   15   16   16   18   19   21 
LCS_AVERAGE  LCS_A:   4.07  (   2.06    3.01    7.14 )

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      5      5      6      7      8     10     10     11     11     11     12     13     14     15     16     16     18     19     22 
GDT PERCENT_CA   1.74   2.91   2.91   3.49   4.07   4.65   5.81   5.81   6.40   6.40   6.40   6.98   7.56   8.14   8.72   9.30   9.30  10.47  11.05  12.79
GDT RMS_LOCAL    0.05   0.53   0.53   1.16   1.96   2.12   2.54   2.54   2.91   2.91   2.91   3.67   4.84   5.18   5.38   5.66   5.66   6.26   7.37   8.49
GDT RMS_ALL_CA  22.57  16.32  16.32  15.15  18.95  19.03  17.73  17.73  17.16  17.16  17.16  16.62  12.35  12.29  11.51  11.49  11.49  11.79  10.10   9.70

#      Molecule1      Molecule2       DISTANCE
LGA    V     213      V     213         22.944
LGA    N     214      N     214         24.362
LGA    G     215      G     215         26.257
LGA    K     216      K     216         23.587
LGA    I     217      I     217         16.785
LGA    V     218      V     218         15.319
LGA    A     219      A     219         13.764
LGA    F     220      F     220          9.562
LGA    T     221      T     221          3.117
LGA    F     222      F     222          1.997
LGA    G     223      G     223          2.743
LGA    M     224      M     224          3.180
LGA    P     225      P     225          2.457
LGA    I     226      I     226          3.058
LGA    N     227      N     227          1.623
LGA    H     228      H     228          1.325
LGA    E     229      E     229          2.901
LGA    T     230      T     230          2.194
LGA    F     231      F     231          5.691
LGA    G     232      G     232         12.713
LGA    V     233      V     233         15.077
LGA    H     234      H     234         15.872
LGA    V     235      V     235         20.694
LGA    E     236      E     236         23.688
LGA    K     237      K     237         25.662
LGA    A     238      A     238         24.410
LGA    D     239      D     239         29.225
LGA    T     240      T     240         30.937
LGA    S     241      S     241         34.094

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29  172    4.0     10    2.54     5.378     4.783     0.379

LGA_LOCAL      RMSD =  2.537  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.732  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  9.512  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.224491 * X  +   0.585688 * Y  +   0.778828 * Z  + -65.599785
  Y_new =  -0.533745 * X  +   0.742582 * Y  +  -0.404583 * Z  +  69.090683
  Z_new =  -0.815303 * X  +  -0.324870 * Y  +   0.479312 * Z  + 102.214592 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.595661    2.545932  [ DEG:   -34.1288    145.8712 ]
  Theta =   0.953253    2.188340  [ DEG:    54.6174    125.3826 ]
  Phi   =  -1.172661    1.968931  [ DEG:   -67.1885    112.8115 ]
 
# 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: T0372TS464_4_2-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_2-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29  172   4.0   10   2.54   4.783     9.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM     19  CA  VAL   213      36.057  53.557  32.695  1.00  0.00
ATOM     20  CA  ASN   214      34.400  50.295  31.877  1.00  0.00
ATOM     21  CA  GLY   215      34.503  51.040  28.185  1.00  0.00
ATOM     22  CA  LYS   216      38.262  51.737  28.602  1.00  0.00
ATOM     23  CA  ILE   217      38.875  48.213  29.930  1.00  0.00
ATOM     24  CA  VAL   218      37.109  45.804  27.531  1.00  0.00
ATOM     25  CA  ALA   219      38.714  47.352  24.433  1.00  0.00
ATOM     26  CA  PHE   220      42.129  47.501  26.406  1.00  0.00
ATOM     27  CA  THR   221      41.182  43.824  26.587  1.00  0.00
ATOM     28  CA  PHE   222      39.903  43.598  23.086  1.00  0.00
ATOM     29  CA  GLY   223      42.754  45.723  21.681  1.00  0.00
ATOM     30  CA  MET   224      40.226  47.672  19.622  1.00  0.00
ATOM     31  CA  PRO   225      39.761  51.345  20.329  1.00  0.00
ATOM     32  CA  ILE   226      36.708  53.539  19.917  1.00  0.00
ATOM     33  CA  ASN   227      35.729  56.962  18.619  1.00  0.00
ATOM     34  CA  HIS   228      34.319  59.673  20.748  1.00  0.00
ATOM     35  CA  GLU   229      31.081  59.154  19.023  1.00  0.00
ATOM     36  CA  THR   230      30.936  55.482  19.746  1.00  0.00
ATOM     37  CA  PHE   231      31.807  56.187  23.321  1.00  0.00
ATOM     38  CA  GLY   232      29.008  58.721  23.701  1.00  0.00
ATOM     39  CA  VAL   233      26.445  56.620  21.996  1.00  0.00
ATOM     40  CA  HIS   234      27.185  53.580  24.112  1.00  0.00
ATOM     41  CA  VAL   235      27.182  55.737  27.219  1.00  0.00
ATOM     42  CA  GLU   236      23.854  57.056  26.261  1.00  0.00
ATOM     43  CA  LYS   237      22.140  53.687  26.040  1.00  0.00
ATOM     44  CA  ALA   238      23.598  51.498  28.741  1.00  0.00
ATOM     45  CA  ASP   239      24.633  53.850  31.505  1.00  0.00
ATOM     46  CA  THR   240      21.418  53.711  33.489  1.00  0.00
ATOM     47  CA  SER   241      22.634  55.589  36.634  1.00  0.00
TER
END
