
#######################################################
#                                                     #
#                        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   17 (   68),  selected   17 , name T0316AL333_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   17 , name T0316_D3.pdb
# PARAMETERS: T0316AL333_2-D3.T0316_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       363 - 373         4.70     8.73
  LCS_AVERAGE:     11.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       365 - 369         1.93    10.57
  LCS_AVERAGE:      4.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       284 - 286         0.91    13.82
  LONGEST_CONTINUOUS_SEGMENT:     3       285 - 287         0.22    17.94
  LONGEST_CONTINUOUS_SEGMENT:     3       362 - 364         0.78    12.79
  LONGEST_CONTINUOUS_SEGMENT:     3       363 - 365         0.85     8.64
  LONGEST_CONTINUOUS_SEGMENT:     3       364 - 366         0.61    13.00
  LONGEST_CONTINUOUS_SEGMENT:     3       365 - 367         0.02    12.72
  LONGEST_CONTINUOUS_SEGMENT:     3       366 - 368         0.18    13.51
  LONGEST_CONTINUOUS_SEGMENT:     3       367 - 369         0.78     9.83
  LONGEST_CONTINUOUS_SEGMENT:     3       368 - 370         0.57    15.30
  LONGEST_CONTINUOUS_SEGMENT:     3       369 - 371         0.54    11.52
  LONGEST_CONTINUOUS_SEGMENT:     3       370 - 372         0.13    12.88
  LONGEST_CONTINUOUS_SEGMENT:     3       371 - 373         0.03     9.29
  LCS_AVERAGE:      3.33

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:   90
LCS_GDT     M     284     M     284      3    3    8     0    3    3    3    3    4    4    5    7   10   10   11   11   12   12   13   14   15   16   16 
LCS_GDT     S     285     S     285      3    3    8     3    3    3    3    3    4    4    5    7   10   10   11   12   13   14   14   14   15   16   16 
LCS_GDT     T     286     T     286      3    3   10     3    3    3    3    4    5    6    8    8   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     S     287     S     287      3    3   10     3    3    3    5    5    5    6    8    8   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     D     361     D     361      3    3   10     0    3    3    3    3    3    4    4    7    7    7    9   10   11   13   14   14   14   15   15 
LCS_GDT     N     362     N     362      3    3   10     0    3    3    3    3    3    5    5    7    8    9   11   11   13   14   14   14   15   16   16 
LCS_GDT     A     363     A     363      3    3   11     0    3    4    5    5    5    6    8    8   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     Y     364     Y     364      3    4   11     1    3    4    5    5    5    6    8    8   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     R     365     R     365      3    5   11     3    4    4    5    5    6    6    9    9   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     D     366     D     366      3    5   11     3    3    4    4    4    4    5    9    9    9    9   10   11   12   13   14   14   14   16   16 
LCS_GDT     G     367     G     367      3    5   11     3    4    4    4    4    4    5    9    9   10   10   11   12   13   14   14   14   15   16   16 
LCS_GDT     Q     368     Q     368      3    5   11     3    4    4    5    5    5    6    9    9   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     V     369     V     369      3    5   11     3    4    4    4    5    6    6    9    9   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     C     370     C     370      3    4   11     3    3    3    4    4    6    6    9    9   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     Q     371     Q     371      3    4   11     3    3    3    4    5    6    6    9    9   10   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     Y     372     Y     372      3    4   11     3    3    3    4    5    6    6    9    9    9   11   11   12   13   14   14   14   15   16   16 
LCS_GDT     I     373     I     373      3    4   11     3    3    3    4    5    6    6    9    9   10   11   11   12   13   14   14   14   15   16   16 
LCS_AVERAGE  LCS_A:   6.41  (   3.33    4.31   11.57 )

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      4      4      5      5      6      6      9      9     10     11     11     12     13     14     14     14     15     16     16 
GDT PERCENT_CA   3.33   4.44   4.44   5.56   5.56   6.67   6.67  10.00  10.00  11.11  12.22  12.22  13.33  14.44  15.56  15.56  15.56  16.67  17.78  17.78
GDT RMS_LOCAL    0.02   0.74   0.74   1.48   1.48   2.01   2.01   3.46   3.46   3.88   4.20   4.20   4.60   4.98   5.39   5.39   5.39   5.84   6.16   6.16
GDT RMS_ALL_CA  12.72   9.21   9.21   7.99   7.99   9.90   9.90  10.29  10.29   7.60   7.68   7.68   7.60   7.32   7.10   7.10   7.10   6.96   6.96   6.96

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         19.157
LGA    S     285      S     285         15.018
LGA    T     286      T     286         11.848
LGA    S     287      S     287         14.104
LGA    D     361      D     361         21.382
LGA    N     362      N     362         15.305
LGA    A     363      A     363         11.820
LGA    Y     364      Y     364          8.008
LGA    R     365      R     365          2.178
LGA    D     366      D     366          3.994
LGA    G     367      G     367          3.972
LGA    Q     368      Q     368          3.890
LGA    V     369      V     369          3.561
LGA    C     370      C     370          3.517
LGA    Q     371      Q     371          3.235
LGA    Y     372      Y     372          3.123
LGA    I     373      I     373          3.600

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17   90    4.0      9    3.46     8.889     7.545     0.253

LGA_LOCAL      RMSD =  3.463  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.674  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  6.833  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.103730 * X  +  -0.429806 * Y  +   0.896943 * Z  +  55.498589
  Y_new =  -0.591283 * X  +  -0.698498 * Y  +  -0.403094 * Z  +  54.298798
  Z_new =   0.799765 * X  +  -0.572160 * Y  +  -0.181682 * Z  +  -2.914802 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.878263    1.263330  [ DEG:  -107.6165     72.3835 ]
  Theta =  -0.926904   -2.214689  [ DEG:   -53.1077   -126.8923 ]
  Phi   =  -1.744461    1.397131  [ DEG:   -99.9503     80.0497 ]
 
# 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: T0316AL333_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_2-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17   90   4.0    9   3.46   7.545     6.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_2-D3
REMARK Aligment from pdb entry: 1ni5_A
ATOM    805  N   MET   284      19.482  -8.029 -16.717  1.00  0.00              
ATOM    806  CA  MET   284      19.982  -7.023 -17.653  1.00  0.00              
ATOM    807  C   MET   284      19.914  -5.694 -16.923  1.00  0.00              
ATOM    808  O   MET   284      20.761  -4.819 -17.104  1.00  0.00              
ATOM    809  N   SER   285      18.890  -5.562 -16.089  1.00  0.00              
ATOM    810  CA  SER   285      18.692  -4.361 -15.302  1.00  0.00              
ATOM    811  C   SER   285      19.896  -4.198 -14.385  1.00  0.00              
ATOM    812  O   SER   285      20.477  -3.115 -14.307  1.00  0.00              
ATOM    813  N   THR   286      20.279  -5.269 -13.694  1.00  0.00              
ATOM    814  CA  THR   286      21.437  -5.190 -12.814  1.00  0.00              
ATOM    815  C   THR   286      22.692  -4.898 -13.629  1.00  0.00              
ATOM    816  O   THR   286      23.500  -4.044 -13.259  1.00  0.00              
ATOM    817  N   SER   287      22.868  -5.608 -14.736  1.00  0.00              
ATOM    818  CA  SER   287      24.040  -5.378 -15.560  1.00  0.00              
ATOM    819  C   SER   287      24.100  -3.896 -15.878  1.00  0.00              
ATOM    820  O   SER   287      25.129  -3.250 -15.687  1.00  0.00              
ATOM    821  N   ASP   361      22.978  -3.354 -16.338  1.00  0.00              
ATOM    822  CA  ASP   361      22.911  -1.952 -16.711  1.00  0.00              
ATOM    823  C   ASP   361      23.290  -1.031 -15.577  1.00  0.00              
ATOM    824  O   ASP   361      23.962  -0.022 -15.791  1.00  0.00              
ATOM    825  N   ASN   362      22.858  -1.363 -14.367  1.00  0.00              
ATOM    826  CA  ASN   362      23.167  -0.520 -13.216  1.00  0.00              
ATOM    827  C   ASN   362      24.651  -0.569 -12.857  1.00  0.00              
ATOM    828  O   ASN   362      25.227   0.434 -12.432  1.00  0.00              
ATOM    829  N   ALA   363      25.269  -1.733 -13.029  1.00  0.00              
ATOM    830  CA  ALA   363      26.678  -1.863 -12.740  1.00  0.00              
ATOM    831  C   ALA   363      27.414  -0.975 -13.712  1.00  0.00              
ATOM    832  O   ALA   363      28.359  -0.276 -13.342  1.00  0.00              
ATOM    833  N   TYR   364      26.976  -1.002 -14.963  1.00  0.00              
ATOM    834  CA  TYR   364      27.594  -0.183 -15.990  1.00  0.00              
ATOM    835  C   TYR   364      27.451   1.301 -15.640  1.00  0.00              
ATOM    836  O   TYR   364      28.426   2.047 -15.696  1.00  0.00              
ATOM    837  N   ARG   365      26.253   1.734 -15.262  1.00  0.00              
ATOM    838  CA  ARG   365      26.066   3.132 -14.913  1.00  0.00              
ATOM    839  C   ARG   365      27.041   3.573 -13.837  1.00  0.00              
ATOM    840  O   ARG   365      27.567   4.681 -13.878  1.00  0.00              
ATOM    841  N   ASP   366      27.286   2.706 -12.868  1.00  0.00              
ATOM    842  CA  ASP   366      28.198   3.046 -11.785  1.00  0.00              
ATOM    843  C   ASP   366      29.643   3.131 -12.261  1.00  0.00              
ATOM    844  O   ASP   366      30.390   4.013 -11.840  1.00  0.00              
ATOM    845  N   GLY   367      30.048   2.212 -13.135  1.00  0.00              
ATOM    846  CA  GLY   367      31.421   2.234 -13.634  1.00  0.00              
ATOM    847  C   GLY   367      31.641   3.511 -14.428  1.00  0.00              
ATOM    848  O   GLY   367      32.730   4.074 -14.415  1.00  0.00              
ATOM    849  N   GLN   368      30.605   3.979 -15.109  1.00  0.00              
ATOM    850  CA  GLN   368      30.746   5.195 -15.884  1.00  0.00              
ATOM    851  C   GLN   368      30.745   6.371 -14.925  1.00  0.00              
ATOM    852  O   GLN   368      31.349   7.401 -15.209  1.00  0.00              
ATOM    853  N   VAL   369      30.067   6.217 -13.788  1.00  0.00              
ATOM    854  CA  VAL   369      30.037   7.284 -12.793  1.00  0.00              
ATOM    855  C   VAL   369      31.475   7.440 -12.319  1.00  0.00              
ATOM    856  O   VAL   369      31.986   8.556 -12.223  1.00  0.00              
ATOM    857  N   CYS   370      32.131   6.320 -12.036  1.00  0.00              
ATOM    858  CA  CYS   370      33.518   6.369 -11.608  1.00  0.00              
ATOM    859  C   CYS   370      34.366   6.952 -12.717  1.00  0.00              
ATOM    860  O   CYS   370      35.282   7.722 -12.448  1.00  0.00              
ATOM    861  N   GLN   371      34.070   6.585 -13.961  1.00  0.00              
ATOM    862  CA  GLN   371      34.826   7.117 -15.091  1.00  0.00              
ATOM    863  C   GLN   371      34.845   8.642 -14.988  1.00  0.00              
ATOM    864  O   GLN   371      35.891   9.294 -15.105  1.00  0.00              
ATOM    865  N   TYR   372      33.669   9.203 -14.758  1.00  0.00              
ATOM    866  CA  TYR   372      33.529  10.634 -14.626  1.00  0.00              
ATOM    867  C   TYR   372      34.366  11.067 -13.436  1.00  0.00              
ATOM    868  O   TYR   372      35.316  11.825 -13.571  1.00  0.00              
ATOM    869  N   ILE   373      34.028  10.538 -12.271  1.00  0.00              
ATOM    870  CA  ILE   373      34.711  10.876 -11.034  1.00  0.00              
ATOM    871  C   ILE   373      36.214  10.724 -11.000  1.00  0.00              
ATOM    872  O   ILE   373      36.881  11.421 -10.233  1.00  0.00              
END
