
#######################################################
#                                                     #
#                        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 T0298TS550_4_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected   17 , name T0298_D1.pdb
# PARAMETERS: T0298TS550_4_2-D1.T0298_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:    17       316 - 332         4.13     4.13
  LCS_AVERAGE:     11.49

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       319 - 332         1.59     5.52
  LCS_AVERAGE:      8.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       320 - 332         0.30     6.07
  LCS_AVERAGE:      7.19

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:  148
LCS_GDT     V     316     V     316      3    3   17     3    3    3    3    3    4    4    6    9   11   12   15   17   17   17   17   17   17   17   17 
LCS_GDT     R     317     R     317      3    5   17     3    3    3    4    5    5    5    6    9   11   12   15   17   17   17   17   17   17   17   17 
LCS_GDT     K     318     K     318      3    5   17     3    3    3    4    5    5    5    5    9    9   12   14   17   17   17   17   17   17   17   17 
LCS_GDT     G     319     G     319      3   14   17     3    3    4    7   11   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     A     320     A     320     13   14   17     3   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     A     321     A     321     13   14   17    12   13   13   13   13   13   13   14   14   14   14   14   17   17   17   17   17   17   17   17 
LCS_GDT     L     322     L     322     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     N     323     N     323     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     A     324     A     324     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     V     325     V     325     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     L     326     L     326     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     L     327     L     327     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     G     328     G     328     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     E     329     E     329     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     L     330     L     330     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     L     331     L     331     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_GDT     I     332     I     332     13   14   17    12   13   13   13   13   13   13   14   14   14   14   15   17   17   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   9.00  (   7.19    8.31   11.49 )

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     12     13     13     13     13     13     13     14     14     14     14     15     17     17     17     17     17     17     17     17 
GDT PERCENT_CA   8.11   8.78   8.78   8.78   8.78   8.78   8.78   9.46   9.46   9.46   9.46  10.14  11.49  11.49  11.49  11.49  11.49  11.49  11.49  11.49
GDT RMS_LOCAL    0.27   0.30   0.30   0.30   0.30   0.30   0.30   1.59   1.59   1.59   1.59   3.72   4.13   4.13   4.13   4.13   4.13   4.13   4.13   4.13
GDT RMS_ALL_CA   6.08   6.07   6.07   6.07   6.07   6.07   6.07   5.52   5.52   5.52   5.52   4.14   4.13   4.13   4.13   4.13   4.13   4.13   4.13   4.13

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316         11.535
LGA    R     317      R     317         11.070
LGA    K     318      K     318          9.309
LGA    G     319      G     319          2.714
LGA    A     320      A     320          3.700
LGA    A     321      A     321          2.370
LGA    L     322      L     322          2.299
LGA    N     323      N     323          2.459
LGA    A     324      A     324          1.914
LGA    V     325      V     325          0.668
LGA    L     326      L     326          1.394
LGA    L     327      L     327          1.479
LGA    G     328      G     328          0.999
LGA    E     329      E     329          1.085
LGA    L     330      L     330          0.526
LGA    L     331      L     331          1.278
LGA    I     332      I     332          2.244

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  148    4.0     14    1.59     9.628     9.168     0.826

LGA_LOCAL      RMSD =  1.594  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.836  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  4.128  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.169536 * X  +  -0.961476 * Y  +  -0.216383 * Z  + -50.305103
  Y_new =   0.384604 * X  +   0.137604 * Y  +  -0.912768 * Z  +  77.624084
  Z_new =   0.907380 * X  +  -0.237968 * Y  +   0.346458 * Z  +  13.021990 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.601853    2.539740  [ DEG:   -34.4836    145.5164 ]
  Theta =  -1.137007   -2.004586  [ DEG:   -65.1457   -114.8543 ]
  Phi   =   1.985978   -1.155614  [ DEG:   113.7882    -66.2118 ]
 
# 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: T0298TS550_4_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS550_4_2-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  148   4.0   14   1.59   9.168     4.13
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS550_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1u28_C
ATOM    661  N   VAL   316     -12.860  68.845  -9.378  1.00  0.00
ATOM    662  CA  VAL   316     -12.996  68.675  -7.920  1.00  0.00
ATOM    663  C   VAL   316     -13.889  69.765  -7.337  1.00  0.00
ATOM    664  O   VAL   316     -13.989  70.858  -7.897  1.00  0.00
ATOM    665  N   ARG   317     -14.544  69.432  -6.227  1.00  0.00
ATOM    666  CA  ARG   317     -15.307  70.406  -5.438  1.00  0.00
ATOM    667  C   ARG   317     -14.829  70.294  -3.990  1.00  0.00
ATOM    668  O   ARG   317     -15.220  69.363  -3.283  1.00  0.00
ATOM    669  N   LYS   318     -13.988  71.230  -3.568  1.00  0.00
ATOM    670  CA  LYS   318     -13.305  71.122  -2.271  1.00  0.00
ATOM    671  C   LYS   318     -14.049  71.769  -1.119  1.00  0.00
ATOM    672  O   LYS   318     -13.780  72.909  -0.748  1.00  0.00
ATOM    673  N   GLY   319     -14.237  70.950   0.241  1.00  0.00
ATOM    674  CA  GLY   319     -14.919  71.446   1.422  1.00  0.00
ATOM    675  C   GLY   319     -15.902  70.409   1.954  1.00  0.00
ATOM    676  O   GLY   319     -15.959  69.275   1.456  1.00  0.00
ATOM    677  N   ALA   320     -16.684  70.788   2.957  1.00  0.00
ATOM    678  CA  ALA   320     -17.655  69.885   3.540  1.00  0.00
ATOM    679  C   ALA   320     -18.690  69.445   2.508  1.00  0.00
ATOM    680  O   ALA   320     -19.310  70.273   1.851  1.00  0.00
ATOM    681  N   ALA   321     -19.144  67.935   2.541  1.00  0.00
ATOM    682  CA  ALA   321     -20.113  67.356   1.624  1.00  0.00
ATOM    683  C   ALA   321     -21.506  67.907   1.858  1.00  0.00
ATOM    684  O   ALA   321     -22.314  67.998   0.930  1.00  0.00
ATOM    685  N   LEU   322     -21.798  68.254   3.111  1.00  0.00
ATOM    686  CA  LEU   322     -23.075  68.841   3.483  1.00  0.00
ATOM    687  C   LEU   322     -23.113  70.303   3.011  1.00  0.00
ATOM    688  O   LEU   322     -24.093  70.725   2.384  1.00  0.00
ATOM    689  N   ASN   323     -22.054  71.055   3.286  1.00  0.00
ATOM    690  CA  ASN   323     -21.961  72.471   2.891  1.00  0.00
ATOM    691  C   ASN   323     -21.983  72.680   1.377  1.00  0.00
ATOM    692  O   ASN   323     -22.758  73.488   0.856  1.00  0.00
ATOM    693  N   ALA   324     -21.123  71.945   0.670  1.00  0.00
ATOM    694  CA  ALA   324     -21.035  72.007  -0.784  1.00  0.00
ATOM    695  C   ALA   324     -22.369  71.744  -1.473  1.00  0.00
ATOM    696  O   ALA   324     -22.721  72.444  -2.419  1.00  0.00
ATOM    697  N   VAL   325     -23.108  70.754  -0.993  1.00  0.00
ATOM    698  CA  VAL   325     -24.340  70.330  -1.639  1.00  0.00
ATOM    699  C   VAL   325     -25.475  71.320  -1.355  1.00  0.00
ATOM    700  O   VAL   325     -26.253  71.654  -2.260  1.00  0.00
ATOM    701  N   LEU   326     -25.562  71.784  -0.103  1.00  0.00
ATOM    702  CA  LEU   326     -26.470  72.868   0.282  1.00  0.00
ATOM    703  C   LEU   326     -26.280  74.078  -0.625  1.00  0.00
ATOM    704  O   LEU   326     -27.246  74.620  -1.157  1.00  0.00
ATOM    705  N   LEU   327     -25.016  74.495  -0.786  1.00  0.00
ATOM    706  CA  LEU   327     -24.670  75.628  -1.654  1.00  0.00
ATOM    707  C   LEU   327     -25.120  75.412  -3.112  1.00  0.00
ATOM    708  O   LEU   327     -25.619  76.339  -3.752  1.00  0.00
ATOM    709  N   GLY   328     -24.930  74.202  -3.611  1.00  0.00
ATOM    710  CA  GLY   328     -25.282  73.858  -4.996  1.00  0.00
ATOM    711  C   GLY   328     -26.795  73.947  -5.217  1.00  0.00
ATOM    712  O   GLY   328     -27.239  74.383  -6.279  1.00  0.00
ATOM    713  N   GLU   329     -27.579  73.536  -4.220  1.00  0.00
ATOM    714  CA  GLU   329     -29.046  73.640  -4.285  1.00  0.00
ATOM    715  C   GLU   329     -29.520  75.104  -4.420  1.00  0.00
ATOM    716  O   GLU   329     -30.489  75.379  -5.137  1.00  0.00
ATOM    717  N   LEU   330     -28.860  76.006  -3.710  1.00  0.00
ATOM    718  CA  LEU   330     -29.204  77.428  -3.727  1.00  0.00
ATOM    719  C   LEU   330     -28.871  78.033  -5.100  1.00  0.00
ATOM    720  O   LEU   330     -29.621  78.870  -5.617  1.00  0.00
ATOM    721  N   LEU   331     -27.767  77.589  -5.697  1.00  0.00
ATOM    722  CA  LEU   331     -27.399  77.962  -7.054  1.00  0.00
ATOM    723  C   LEU   331     -28.296  77.331  -8.122  1.00  0.00
ATOM    724  O   LEU   331     -28.272  77.752  -9.277  1.00  0.00
ATOM    725  N   ILE   332     -29.064  76.318  -7.748  1.00  0.00
ATOM    726  CA  ILE   332     -29.974  75.638  -8.666  1.00  0.00
ATOM    727  C   ILE   332     -31.305  76.408  -8.767  1.00  0.00
ATOM    728  O   ILE   332     -32.022  76.287  -9.765  1.00  0.00
TER
END
