
#######################################################
#                                                     #
#                        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   32 (   32),  selected   32 , name T0301TS464_5_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   32 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_5_2-D1.T0301_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:    16        24 - 76          4.91    16.75
  LONGEST_CONTINUOUS_SEGMENT:    16        25 - 77          4.21    17.50
  LCS_AVERAGE:      6.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        25 - 31          1.87    16.71
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.32    17.83
  LCS_AVERAGE:      2.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        71 - 76          0.41    18.40
  LCS_AVERAGE:      2.22

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:  200
LCS_GDT     K      20     K      20      3    3   14     0    3    3    3    3    4    5    7    7   10   10   12   13   16   16   17   18   18   20   21 
LCS_GDT     G      21     G      21      3    3   14     3    3    3    3    3    4    5    7    7    9   10   12   13   16   16   17   18   18   20   21 
LCS_GDT     V      22     V      22      3    3   14     3    4    4    4    5    5    6    8    9   11   12   12   13   16   16   17   18   18   20   21 
LCS_GDT     F      23     F      23      3    3   15     3    4    4    4    6    7    7    8    9   11   12   12   13   16   16   17   18   18   20   21 
LCS_GDT     F      24     F      24      3    3   16     3    4    4    4    6    7    7    8    9   11   12   12   13   16   16   17   18   18   20   21 
LCS_GDT     R      25     R      25      5    7   16     5    5    5    6    7    7    7   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     L      26     L      26      5    7   16     5    5    5    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     E      27     E      27      5    7   16     5    5    5    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     D      28     D      28      5    7   16     5    5    5    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     L      29     L      29      5    7   16     5    5    5    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     P      30     P      30      5    7   16     4    4    5    6    7    8    9   10   11   12   13   15   15   16   16   16   17   17   18   19 
LCS_GDT     E      31     E      31      5    7   16     4    4    5    6    7    8    9   10   11   12   13   15   15   16   16   17   17   17   19   21 
LCS_GDT     S      32     S      32      5    6   16     4    4    5    6    6    8    8   10   11   12   13   14   15   16   16   17   18   18   19   21 
LCS_GDT     C      33     C      33      5    6   16     4    4    5    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   19   21 
LCS_GDT     C      71     C      71      6    7   16     4    6    6    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   19   21 
LCS_GDT     V      72     V      72      6    7   16     5    6    6    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     I      73     I      73      6    7   16     5    6    6    6    7    8    9   10   11   12   13   15   15   16   16   17   18   18   20   21 
LCS_GDT     L      74     L      74      6    7   16     5    6    6    6    7    8    9   10   11   12   13   15   15   16   16   16   17   17   17   19 
LCS_GDT     S      75     S      75      6    7   16     5    6    6    6    7    8    9    9   10   12   13   15   15   16   16   16   17   17   17   19 
LCS_GDT     K      76     K      76      6    7   16     5    6    6    6    7    8    9    9   10   12   13   15   15   16   16   16   16   17   17   18 
LCS_GDT     S      77     S      77      3    7   16     0    3    3    5    7    8    9    9   10   12   13   15   15   16   16   16   16   17   17   18 
LCS_GDT     G     110     G     110      3    4   11     3    3    3    4    6    7    7    8    8   10   10   12   13   16   16   17   18   18   20   21 
LCS_GDT     A     111     A     111      3    4   11     3    3    3    4    6    7    7    8    8   10   10   12   13   16   16   17   18   18   20   21 
LCS_GDT     G     112     G     112      3    4   11     3    3    3    3    4    7    7    7    8   10   10   12   13   16   16   17   18   18   20   21 
LCS_GDT     A     113     A     113      3    4   11     3    3    3    3    4    4    5    7    8    9    9   12   13   16   16   17   18   18   20   21 
LCS_GDT     F     114     F     114      3    3    8     3    3    3    3    3    4    5    5    6    6    6   10   11   13   16   17   18   18   20   20 
LCS_GDT     A     115     A     115      3    3    8     3    3    3    3    3    4    5    7    7    9    9   10   12   13   16   17   18   18   20   21 
LCS_GDT     I     141     I     141      5    5    8     5    5    5    5    5    5    5    6    7    7    9    9   11   12   13   13   15   16   18   18 
LCS_GDT     G     142     G     142      5    5    8     5    5    5    5    5    5    5    6    7    9   10   11   13   14   15   16   18   18   19   21 
LCS_GDT     K     143     K     143      5    5    6     5    5    5    5    5    5    6    8    8    9   10   11   13   15   15   16   18   18   19   21 
LCS_GDT     T     144     T     144      5    5    6     5    5    5    5    6    7    7    8    8   10   10   12   13   16   16   17   18   18   20   21 
LCS_GDT     I     145     I     145      5    5    6     5    5    5    5    5    5    7    7    7   10   10   12   13   16   16   17   18   18   20   21 
LCS_AVERAGE  LCS_A:   3.84  (   2.22    2.69    6.61 )

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      6      6      6      7      8      9     10     11     12     13     15     15     16     16     17     18     18     20     21 
GDT PERCENT_CA   2.50   3.00   3.00   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.50   7.50   8.00   8.00   8.50   9.00   9.00  10.00  10.50
GDT RMS_LOCAL    0.20   0.41   0.41   0.41   1.32   1.74   1.98   2.42   2.68   3.00   3.28   3.89   3.89   4.21   4.21   5.52   5.76   5.76   6.40   6.99
GDT RMS_ALL_CA  17.43  18.40  18.40  18.40  17.83  19.07  18.86  14.54  14.54  14.89  15.54  17.76  17.76  17.50  17.50  12.12  12.16  12.16  12.12  11.68

#      Molecule1      Molecule2       DISTANCE
LGA    K      20      K      20         24.638
LGA    G      21      G      21         20.077
LGA    V      22      V      22         14.133
LGA    F      23      F      23         12.785
LGA    F      24      F      24         10.615
LGA    R      25      R      25          5.248
LGA    L      26      L      26          2.632
LGA    E      27      E      27          1.783
LGA    D      28      D      28          3.329
LGA    L      29      L      29          0.316
LGA    P      30      P      30          5.082
LGA    E      31      E      31          1.027
LGA    S      32      S      32          3.904
LGA    C      33      C      33          1.377
LGA    C      71      C      71          1.986
LGA    V      72      V      72          1.963
LGA    I      73      I      73          3.977
LGA    L      74      L      74          6.996
LGA    S      75      S      75         10.232
LGA    K      76      K      76         13.319
LGA    S      77      S      77         15.113
LGA    G     110      G     110         24.973
LGA    A     111      A     111         18.420
LGA    G     112      G     112         21.141
LGA    A     113      A     113         20.723
LGA    F     114      F     114         20.536
LGA    A     115      A     115         18.017
LGA    I     141      I     141         21.413
LGA    G     142      G     142         19.355
LGA    K     143      K     143         19.372
LGA    T     144      T     144         18.784
LGA    I     145      I     145         18.472

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32  200    4.0     10    2.42     4.875     4.393     0.397

LGA_LOCAL      RMSD =  2.420  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.416  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 11.458  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.831208 * X  +   0.076158 * Y  +   0.550721 * Z  +  64.413475
  Y_new =   0.414940 * X  +   0.574304 * Y  +  -0.705691 * Z  +  20.896545
  Z_new =  -0.370025 * X  +   0.815092 * Y  +   0.445765 * Z  + -30.815626 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.070344   -2.071248  [ DEG:    61.3262   -118.6738 ]
  Theta =   0.379036    2.762557  [ DEG:    21.7171    158.2829 ]
  Phi   =   0.463008   -2.678585  [ DEG:    26.5284   -153.4716 ]
 
# 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: T0301TS464_5_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_5_2-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32  200   4.0   10   2.42   4.393    11.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  LYS    20      56.207  24.760   7.847  1.00  0.00
ATOM      2  CA  GLY    21      57.292  27.912   9.617  1.00  0.00
ATOM      3  CA  VAL    22      60.928  27.585   8.618  1.00  0.00
ATOM      4  CA  PHE    23      59.892  26.950   5.031  1.00  0.00
ATOM      5  CA  PHE    24      58.254  30.392   4.858  1.00  0.00
ATOM      6  CA  ARG    25      61.352  31.841   6.472  1.00  0.00
ATOM      7  CA  LEU    26      63.643  30.243   3.871  1.00  0.00
ATOM      8  CA  GLU    27      61.441  31.438   1.033  1.00  0.00
ATOM      9  CA  ASP    28      61.845  34.976   2.374  1.00  0.00
ATOM     10  CA  LEU    29      65.608  34.672   2.391  1.00  0.00
ATOM     11  CA  PRO    30      65.812  33.000  -1.028  1.00  0.00
ATOM     12  CA  GLU    31      63.560  35.650  -2.603  1.00  0.00
ATOM     13  CA  SER    32      65.484  38.523  -1.042  1.00  0.00
ATOM     14  CA  CYS    33      68.741  36.691  -1.767  1.00  0.00
ATOM     15  CA  CYS    71      77.654  30.827   5.640  1.00  0.00
ATOM     16  CA  VAL    72      75.513  28.398   7.637  1.00  0.00
ATOM     17  CA  ILE    73      71.971  27.097   8.068  1.00  0.00
ATOM     18  CA  LEU    74      71.599  25.174  11.301  1.00  0.00
ATOM     19  CA  SER    75      68.597  23.309  12.663  1.00  0.00
ATOM     20  CA  LYS    76      67.310  20.801  15.209  1.00  0.00
ATOM     21  CA  SER    77      64.224  18.573  15.475  1.00  0.00
ATOM     22  CA  GLY   110      57.919  27.685  -4.821  1.00  0.00
ATOM     23  CA  ALA   111      60.180  28.349  -1.832  1.00  0.00
ATOM     24  CA  GLY   112      62.861  30.070  -3.908  1.00  0.00
ATOM     25  CA  ALA   113      65.352  27.225  -4.168  1.00  0.00
ATOM     26  CA  PHE   114      67.678  27.982  -7.087  1.00  0.00
ATOM     27  CA  ALA   115      70.248  25.278  -6.494  1.00  0.00
ATOM     28  CA  ILE   141      63.765  24.671 -14.999  1.00  0.00
ATOM     29  CA  GLY   142      66.811  26.912 -15.338  1.00  0.00
ATOM     30  CA  LYS   143      68.202  25.894 -11.941  1.00  0.00
ATOM     31  CA  THR   144      71.594  24.636 -10.798  1.00  0.00
ATOM     32  CA  ILE   145      72.445  21.093  -9.779  1.00  0.00
TER
END
