
#######################################################
#                                                     #
#                        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   27 (   27),  selected   27 , name T0318TS464_5_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   27 , name T0318_D1.pdb
# PARAMETERS: T0318TS464_5_2-D1.T0318_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:    24        77 - 100         4.50    11.85
  LCS_AVERAGE:     14.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        87 - 100         1.86    13.44
  LCS_AVERAGE:      6.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        89 - 100         0.88    13.06
  LCS_AVERAGE:      4.91

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:  154
LCS_GDT     V      77     V      77      3    3   24     0    3    3    3    3    3    5    6   11   14   18   21   23   23   24   24   24   24   24   24 
LCS_GDT     P      78     P      78      3    4   24     3    3    4    7    7    9   11   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     D      79     D      79      3    4   24     3    4    4    4    5    5    8   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     A      80     A      80      3    4   24     3    4    4    4    5    6   11   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     S      81     S      81      3    4   24     0    3    4    7    7    9   11   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     S      82     S      82      3    4   24     3    3    3    3    5    9   10   13   15   18   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     R      83     R      83      3    7   24     3    3    5    6    6    7    7   10   13   16   20   22   22   23   24   24   24   24   24   24 
LCS_GDT     G      84     G      84      6    7   24     4    6    6    6    7    9   10   13   15   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     N      85     N      85      6    7   24     4    6    6    7    7    9   11   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     T      86     T      86      6    7   24     4    6    6   10   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     P      87     P      87      6   14   24     4    6    6    6    7   11   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     T      88     T      88      6   14   24     4    6    6    6    7    9   11   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     N      89     N      89     12   14   24     4    7   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     A      90     A      90     12   14   24     8   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     H      91     H      91     12   14   24     8   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     S      92     S      92     12   14   24     8   10   11   12   13   13   13   14   16   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     I      93     I      93     12   14   24     8   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     Y      94     Y      94     12   14   24     8   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     K      95     K      95     12   14   24     8   10   11   12   13   13   13   14   16   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     E      96     E      96     12   14   24     8   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     L      97     L      97     12   14   24     5   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     K      98     K      98     12   14   24     4   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     P      99     P      99     12   14   24     4    6   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     I     100     I     100     12   14   24     8   10   11   12   13   13   13   14   17   19   21   22   23   23   24   24   24   24   24   24 
LCS_GDT     D     153     D     153      3    3    3     3    3    3    3    4    5    5    6    7    8   10   10   11   12   12   13   15   17   20   20 
LCS_GDT     K     154     K     154      3    3    3     3    3    3    3    4    5    5    6    8    8   10   10   11   12   12   13   15   17   20   20 
LCS_GDT     L     155     L     155      3    3    3     3    3    3    3    4    5    7    7    8    8   10   10   11   12   13   15   15   19   20   21 
LCS_AVERAGE  LCS_A:   8.38  (   4.91    6.16   14.07 )

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      8     10     11     12     13     13     13     14     17     19     21     22     23     23     24     24     24     24     24     24 
GDT PERCENT_CA   5.19   6.49   7.14   7.79   8.44   8.44   8.44   9.09  11.04  12.34  13.64  14.29  14.94  14.94  15.58  15.58  15.58  15.58  15.58  15.58
GDT RMS_LOCAL    0.35   0.64   0.76   0.88   1.25   1.25   1.25   1.86   3.58   3.75   4.04   4.18   4.32   4.32   4.50   4.50   4.50   4.50   4.50   4.50
GDT RMS_ALL_CA  13.67  13.24  13.12  13.06  12.83  12.83  12.83  13.44  11.19  11.35  11.56  11.66  11.77  11.77  11.85  11.85  11.85  11.85  11.85  11.85

#      Molecule1      Molecule2       DISTANCE
LGA    V      77      V      77         15.801
LGA    P      78      P      78         18.044
LGA    D      79      D      79         15.266
LGA    A      80      A      80         15.091
LGA    S      81      S      81         17.557
LGA    S      82      S      82         21.922
LGA    R      83      R      83         20.498
LGA    G      84      G      84         18.731
LGA    N      85      N      85         12.643
LGA    T      86      T      86          6.128
LGA    P      87      P      87          3.483
LGA    T      88      T      88          3.961
LGA    N      89      N      89          2.713
LGA    A      90      A      90          0.755
LGA    H      91      H      91          1.411
LGA    S      92      S      92          0.605
LGA    I      93      I      93          0.444
LGA    Y      94      Y      94          1.080
LGA    K      95      K      95          0.708
LGA    E      96      E      96          0.606
LGA    L      97      L      97          1.898
LGA    K      98      K      98          2.569
LGA    P      99      P      99          2.168
LGA    I     100      I     100          1.732
LGA    D     153      D     153         30.738
LGA    K     154      K     154         28.633
LGA    L     155      L     155         25.701

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  154    4.0     14    1.86     9.740     9.155     0.715

LGA_LOCAL      RMSD =  1.859  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.980  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  8.691  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.704789 * X  +  -0.527143 * Y  +   0.474755 * Z  +  -9.223283
  Y_new =   0.707624 * X  +   0.474829 * Y  +  -0.523265 * Z  +  58.101238
  Z_new =   0.050408 * X  +   0.704740 * Y  +   0.707673 * Z  + -11.180686 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.783321   -2.358271  [ DEG:    44.8810   -135.1190 ]
  Theta =  -0.050429   -3.091163  [ DEG:    -2.8894   -177.1106 ]
  Phi   =   0.787405   -2.354187  [ DEG:    45.1150   -134.8850 ]
 
# 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: T0318TS464_5_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS464_5_2-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  154   4.0   14   1.86   9.155     8.69
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS464_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM      1  CA  VAL    77      15.572  39.986  21.918  1.00  0.00
ATOM      2  CA  PRO    78      18.240  40.090  19.237  1.00  0.00
ATOM      3  CA  ASP    79      21.048  40.306  21.829  1.00  0.00
ATOM      4  CA  ALA    80      19.916  37.049  23.520  1.00  0.00
ATOM      5  CA  SER    81      19.761  35.412  20.090  1.00  0.00
ATOM      6  CA  SER    82      23.145  36.359  18.645  1.00  0.00
ATOM      7  CA  ARG    83      24.989  35.847  21.972  1.00  0.00
ATOM      8  CA  GLY    84      22.811  33.362  23.836  1.00  0.00
ATOM      9  CA  ASN    85      22.390  35.633  26.863  1.00  0.00
ATOM     10  CA  THR    86      19.868  35.926  29.690  1.00  0.00
ATOM     11  CA  PRO    87      17.424  38.820  29.272  1.00  0.00
ATOM     12  CA  THR    88      19.214  40.703  32.109  1.00  0.00
ATOM     13  CA  ASN    89      22.747  40.440  30.568  1.00  0.00
ATOM     14  CA  ALA    90      21.237  41.853  27.344  1.00  0.00
ATOM     15  CA  HIS    91      19.925  44.938  29.226  1.00  0.00
ATOM     16  CA  SER    92      23.057  45.650  31.250  1.00  0.00
ATOM     17  CA  ILE    93      25.235  45.355  28.113  1.00  0.00
ATOM     18  CA  TYR    94      23.062  48.014  26.455  1.00  0.00
ATOM     19  CA  LYS    95      23.499  50.345  29.422  1.00  0.00
ATOM     20  CA  GLU    96      27.317  50.105  29.396  1.00  0.00
ATOM     21  CA  LEU    97      27.146  51.038  25.708  1.00  0.00
ATOM     22  CA  LYS    98      25.345  54.302  26.417  1.00  0.00
ATOM     23  CA  PRO    99      28.368  55.223  28.493  1.00  0.00
ATOM     24  CA  ILE   100      30.569  54.824  25.417  1.00  0.00
ATOM     25  CA  ASP   153      31.627  56.694  22.252  1.00  0.00
ATOM     26  CA  LYS   154      31.533  53.692  19.879  1.00  0.00
ATOM     27  CA  LEU   155      28.007  54.108  18.563  1.00  0.00
TER
END
