
#######################################################
#                                                     #
#                        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   31 (   31),  selected   31 , name T0314TS464_1_2-D1
# Molecule2: number of CA atoms  103 ( 1643),  selected   31 , name T0314_D1.pdb
# PARAMETERS: T0314TS464_1_2-D1.T0314_D1.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:    21        14 - 78          4.74     8.11
  LONGEST_CONTINUOUS_SEGMENT:    21        59 - 79          4.26    10.39
  LCS_AVERAGE:     17.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        64 - 78          1.71     9.76
  LCS_AVERAGE:      9.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        66 - 75          0.98    10.00
  LCS_AVERAGE:      5.98

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:  103
LCS_GDT     Q      10     Q      10      5    5   13     3    4    5    5    6    8    9   10   11   13   14   19   22   24   26   26   27   29   29   29 
LCS_GDT     A      11     A      11      5    5   13     4    4    5    5    6    8    9   10   13   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     A      12     A      12      5    5   13     4    4    5    5    6    8    9   10   11   13   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     D      13     D      13      5    5   13     4    4    5    5    6    8    9   10   11   15   18   19   20   22   26   26   27   29   29   29 
LCS_GDT     A      14     A      14      5    5   21     4    4    5    5    6    8   10   11   14   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     D      59     D      59      3    4   21     3    3    3    5    6    6    7    8   11   11   14   20   22   24   26   26   27   29   29   29 
LCS_GDT     D      60     D      60      3    4   21     3    3    4    5    6    6    7    8   11   13   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     V      61     V      61      3    4   21     3    3    4    5    6    6    7    8   12   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     M      62     M      62      3    4   21     2    3    4    5    6    6    7   13   15   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     R      63     R      63      3    3   21     3    3    4    4    8   11   14   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     L      64     L      64      3   15   21     3    3    4    4    8   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     G      65     G      65      5   15   21     3    4   10   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     R      66     R      66     10   15   21     4    7   11   12   14   14   15   15   16   17   18   20   21   24   26   26   27   29   29   29 
LCS_GDT     E      67     E      67     10   15   21     4    7   11   12   14   14   15   15   16   17   18   19   20   21   26   26   27   29   29   29 
LCS_GDT     Q      68     Q      68     10   15   21     4    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     L      69     L      69     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     Q      70     Q      70     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     I      71     I      71     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     L      72     L      72     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     L      73     L      73     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     E      74     E      74     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     Q      75     Q      75     10   15   21     5    8   11   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     N      76     N      76      9   15   21     4    7   10   12   14   14   15   15   16   17   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     I      77     I      77      9   15   21     4    4    8   12   14   14   15   15   16   17   18   19   20   21   23   25   26   29   29   29 
LCS_GDT     N      78     N      78      5   15   21     4    8   11   12   14   14   15   15   16   17   18   19   20   21   23   23   26   29   29   29 
LCS_GDT     E      79     E      79      5    6   21     3    3    5    5    5    6    7    8   11   16   16   17   17   20   20   20   21   21   22   22 
LCS_GDT     P      97     P      97      3    3   18     0    3    4    5    6    6    6    7   11   11   13   15   21   24   26   26   27   29   29   29 
LCS_GDT     E      98     E      98      3    3    5     3    3    3    4    6    6    7    8   11   11   13   14   22   24   26   26   27   29   29   29 
LCS_GDT     I      99     I      99      3    3    5     3    3    4    4    6    6    7    8   11   15   18   20   22   24   26   26   27   29   29   29 
LCS_GDT     T     100     T     100      3    3    5     3    3    4    4    4    4    6    7   11   11   12   14   18   20   23   26   27   29   29   29 
LCS_GDT     A     101     A     101      3    3    5     0    3    4    4    4    4    4    5    5    6    7    7   12   14   15   17   23   23   26   27 
LCS_AVERAGE  LCS_A:  10.78  (   5.98    9.08   17.29 )

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      5      8     11     12     14     14     15     15     16     17     18     20     22     24     26     26     27     29     29     29 
GDT PERCENT_CA   4.85   7.77  10.68  11.65  13.59  13.59  14.56  14.56  15.53  16.50  17.48  19.42  21.36  23.30  25.24  25.24  26.21  28.16  28.16  28.16
GDT RMS_LOCAL    0.25   0.57   0.96   1.11   1.39   1.39   1.71   1.71   2.18   2.76   3.08   4.67   5.11   5.32   5.57   5.57   5.74   6.17   6.17   6.17
GDT RMS_ALL_CA   9.31   9.54  10.00   9.87   9.82   9.82   9.76   9.76   9.76  10.00   9.96   7.17   7.19   7.19   7.16   7.16   7.14   6.97   6.97   6.97

#      Molecule1      Molecule2       DISTANCE
LGA    Q      10      Q      10         18.800
LGA    A      11      A      11         14.247
LGA    A      12      A      12         13.246
LGA    D      13      D      13         15.740
LGA    A      14      A      14         12.841
LGA    D      59      D      59         15.823
LGA    D      60      D      60         12.123
LGA    V      61      V      61          8.663
LGA    M      62      M      62          9.485
LGA    R      63      R      63          6.404
LGA    L      64      L      64          3.600
LGA    G      65      G      65          3.210
LGA    R      66      R      66          1.018
LGA    E      67      E      67          1.572
LGA    Q      68      Q      68          1.486
LGA    L      69      L      69          0.831
LGA    Q      70      Q      70          0.781
LGA    I      71      I      71          0.873
LGA    L      72      L      72          0.361
LGA    L      73      L      73          0.849
LGA    E      74      E      74          1.186
LGA    Q      75      Q      75          1.146
LGA    N      76      N      76          1.730
LGA    I      77      I      77          2.202
LGA    N      78      N      78          1.287
LGA    E      79      E      79          7.128
LGA    P      97      P      97         18.299
LGA    E      98      E      98         16.003
LGA    I      99      I      99         10.474
LGA    T     100      T     100         13.958
LGA    A     101      A     101         14.694

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31  103    4.0     15    1.71    14.806    13.649     0.827

LGA_LOCAL      RMSD =  1.715  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.762  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  6.911  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.498207 * X  +  -0.524211 * Y  +   0.690646 * Z  +   6.671106
  Y_new =   0.814911 * X  +  -0.011023 * Y  +   0.579481 * Z  +  11.314628
  Z_new =  -0.296157 * X  +   0.851517 * Y  +   0.432677 * Z  + -15.561964 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.100670   -2.040923  [ DEG:    63.0637   -116.9363 ]
  Theta =   0.300667    2.840926  [ DEG:    17.2269    162.7731 ]
  Phi   =   2.119529   -1.022063  [ DEG:   121.4401    -58.5599 ]
 
# 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: T0314TS464_1_2-D1                             
REMARK     2: T0314_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0314TS464_1_2-D1.T0314_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31  103   4.0   15   1.71  13.649     6.91
REMARK  ---------------------------------------------------------- 
MOLECULE T0314TS464_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0314
PARENT N/A
ATOM      1  CA  GLN    10      22.647   6.263 -18.916  1.00  0.00
ATOM      2  CA  ALA    11      20.052   5.624 -16.195  1.00  0.00
ATOM      3  CA  ALA    12      19.471   1.932 -16.972  1.00  0.00
ATOM      4  CA  ASP    13      23.144   1.382 -17.862  1.00  0.00
ATOM      5  CA  ALA    14      24.370   3.212 -14.805  1.00  0.00
ATOM      6  CA  ASP    59       1.181  14.161 -18.037  1.00  0.00
ATOM      7  CA  ASP    60       4.406  14.132 -20.090  1.00  0.00
ATOM      8  CA  VAL    61       6.462  13.554 -16.958  1.00  0.00
ATOM      9  CA  MET    62       4.338  10.502 -16.034  1.00  0.00
ATOM     10  CA  ARG    63       4.468   9.019 -19.520  1.00  0.00
ATOM     11  CA  LEU    64       8.264   9.378 -19.477  1.00  0.00
ATOM     12  CA  GLY    65       8.500   8.047 -15.884  1.00  0.00
ATOM     13  CA  ARG    66       6.513   4.998 -16.946  1.00  0.00
ATOM     14  CA  GLU    67       8.643   3.802 -19.850  1.00  0.00
ATOM     15  CA  GLN    68      11.746   4.289 -17.626  1.00  0.00
ATOM     16  CA  LEU    69      10.345   2.071 -14.861  1.00  0.00
ATOM     17  CA  GLN    70       9.414  -0.632 -17.327  1.00  0.00
ATOM     18  CA  ILE    71      13.014  -0.298 -18.521  1.00  0.00
ATOM     19  CA  LEU    72      14.734  -0.557 -15.228  1.00  0.00
ATOM     20  CA  LEU    73      12.489  -3.443 -14.082  1.00  0.00
ATOM     21  CA  GLU    74      13.336  -5.350 -17.247  1.00  0.00
ATOM     22  CA  GLN    75      16.941  -5.113 -16.127  1.00  0.00
ATOM     23  CA  ASN    76      16.930  -6.384 -12.564  1.00  0.00
ATOM     24  CA  ILE    77      16.858  -2.920 -11.007  1.00  0.00
ATOM     25  CA  ASN    78      14.309  -2.487  -8.213  1.00  0.00
ATOM     26  CA  GLU    79      12.552   0.779  -8.988  1.00  0.00
ATOM     27  CA  PRO    97      13.308   3.495  -6.180  1.00  0.00
ATOM     28  CA  GLU    98      14.421   7.036  -6.890  1.00  0.00
ATOM     29  CA  ILE    99      12.215   7.461  -9.921  1.00  0.00
ATOM     30  CA  THR   100       9.269   5.903  -8.094  1.00  0.00
ATOM     31  CA  ALA   101       9.837   8.314  -5.135  1.00  0.00
TER
END
