
#######################################################
#                                                     #
#                        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    6 (   40),  selected    6 , name T0301TS186_2-D2
# Molecule2: number of CA atoms  191 ( 1389),  selected    6 , name T0301_D2.pdb
# PARAMETERS: T0301TS186_2-D2.T0301_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:     6       187 - 192         2.47     2.47
  LCS_AVERAGE:      3.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       188 - 192         1.71     3.52
  LCS_AVERAGE:      2.53

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       187 - 189         0.26     7.27
  LONGEST_CONTINUOUS_SEGMENT:     3       188 - 190         0.22     3.93
  LONGEST_CONTINUOUS_SEGMENT:     3       189 - 191         0.61     4.69
  LONGEST_CONTINUOUS_SEGMENT:     3       190 - 192         0.26     6.64
  LCS_AVERAGE:      1.57

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:  191
LCS_GDT     D     187     D     187      3    4    6     3    3    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     188     G     188      3    5    6     3    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     G     189     G     189      3    5    6     3    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     190     A     190      3    5    6     3    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     191     I     191      3    5    6     3    3    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F     192     F     192      3    5    6     3    4    4    4    4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   2.41  (   1.57    2.53    3.14 )

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      4      4      4      4      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   1.57   2.09   2.09   2.09   2.09   2.62   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14
GDT RMS_LOCAL    0.22   0.59   0.59   0.59   0.59   1.71   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47
GDT RMS_ALL_CA   3.93   3.57   3.57   3.57   3.57   3.52   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47   2.47

#      Molecule1      Molecule2       DISTANCE
LGA    D     187      D     187          1.801
LGA    G     188      G     188          1.967
LGA    G     189      G     189          2.592
LGA    A     190      A     190          3.571
LGA    I     191      I     191          2.662
LGA    F     192      F     192          1.688

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  191    4.0      6    2.47     2.618     2.653     0.234

LGA_LOCAL      RMSD =  2.467  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.467  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.467  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.852672 * X  +  -0.027393 * Y  +  -0.521729 * Z  +   0.823015
  Y_new =   0.522287 * X  +   0.019951 * Y  +   0.852536 * Z  + -61.344151
  Z_new =  -0.012945 * X  +  -0.999426 * Y  +   0.031319 * Z  +  12.728105 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.539470    1.602123  [ DEG:   -88.2051     91.7949 ]
  Theta =   0.012945    3.128647  [ DEG:     0.7417    179.2583 ]
  Phi   =   0.549582   -2.592011  [ DEG:    31.4887   -148.5113 ]
 
# 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: T0301TS186_2-D2                               
REMARK     2: T0301_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS186_2-D2.T0301_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  191   4.0    6   2.47   2.653     2.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS186_2-D2
PFRMAT TS
TARGET T0301
MODEL  2
PARENT 1fcf_A
ATOM   1394  N   ASP   187      95.195  13.726  -3.312  1.00  0.00
ATOM   1395  CA  ASP   187      94.098  13.323  -2.454  1.00  0.00
ATOM   1396  C   ASP   187      93.674  11.848  -2.677  1.00  0.00
ATOM   1397  O   ASP   187      92.622  11.411  -2.250  1.00  0.00
ATOM   1398  CB  ASP   187      92.867  14.194  -2.714  1.00  0.00
ATOM   1399  CG  ASP   187      92.331  14.038  -4.124  1.00  0.00
ATOM   1400  OD1 ASP   187      92.929  13.269  -4.906  1.00  0.00
ATOM   1401  OD2 ASP   187      91.313  14.686  -4.447  1.00  0.00
ATOM   1402  N   GLY   188      94.483  11.046  -3.363  1.00  0.00
ATOM   1403  CA  GLY   188      94.127   9.662  -3.645  1.00  0.00
ATOM   1404  C   GLY   188      93.683   8.938  -2.414  1.00  0.00
ATOM   1405  O   GLY   188      94.195   9.229  -1.355  1.00  0.00
ATOM   1406  N   GLY   189      92.782   7.982  -2.557  1.00  0.00
ATOM   1407  CA  GLY   189      92.300   7.213  -1.428  1.00  0.00
ATOM   1408  C   GLY   189      93.276   6.183  -0.977  1.00  0.00
ATOM   1409  O   GLY   189      94.033   5.624  -1.760  1.00  0.00
ATOM   1410  N   ALA   190      93.235   6.005   0.317  1.00  0.00
ATOM   1411  CA  ALA   190      94.086   5.123   1.050  1.00  0.00
ATOM   1412  C   ALA   190      93.438   3.765   1.001  1.00  0.00
ATOM   1413  O   ALA   190      92.860   3.277   1.978  1.00  0.00
ATOM   1414  CB  ALA   190      94.226   5.596   2.488  1.00  0.00
ATOM   1415  N   ILE   191      93.563   3.205  -0.178  1.00  0.00
ATOM   1416  CA  ILE   191      92.989   1.924  -0.578  1.00  0.00
ATOM   1417  C   ILE   191      93.266   0.718   0.333  1.00  0.00
ATOM   1418  O   ILE   191      92.369  -0.100   0.609  1.00  0.00
ATOM   1419  CB  ILE   191      93.504   1.483  -1.961  1.00  0.00
ATOM   1420  CG1 ILE   191      93.035   2.459  -3.041  1.00  0.00
ATOM   1421  CG2 ILE   191      92.982   0.096  -2.305  1.00  0.00
ATOM   1422  CD1 ILE   191      91.533   2.504  -3.213  1.00  0.00
ATOM   1423  N   PHE   192      94.523   0.563   0.756  1.00  0.00
ATOM   1424  CA  PHE   192      95.037  -0.526   1.553  1.00  0.00
ATOM   1425  C   PHE   192      95.274  -0.220   3.032  1.00  0.00
ATOM   1426  O   PHE   192      94.386   0.270   3.745  1.00  0.00
ATOM   1427  CB  PHE   192      96.372  -0.896   0.955  1.00  0.00
ATOM   1428  CG  PHE   192      96.239  -1.385  -0.463  1.00  0.00
ATOM   1429  CD1 PHE   192      96.102  -0.499  -1.528  1.00  0.00
ATOM   1430  CD2 PHE   192      96.287  -2.746  -0.744  1.00  0.00
ATOM   1431  CE1 PHE   192      96.015  -0.995  -2.828  1.00  0.00
ATOM   1432  CE2 PHE   192      96.173  -3.254  -2.032  1.00  0.00
ATOM   1433  CZ  PHE   192      96.014  -2.367  -3.093  1.00  0.00
TER
END
