
#######################################################
#                                                     #
#                        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   16 (   78),  selected   16 , name T0301TS239_2_1-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   16 , name T0301_D1.pdb
# PARAMETERS: T0301TS239_2_1-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       378 - 395         2.94     2.94
  LCS_AVERAGE:      8.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       383 - 391         1.84     5.22
  LONGEST_CONTINUOUS_SEGMENT:     9       384 - 392         1.94     5.97
  LCS_AVERAGE:      4.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       387 - 392         0.86     6.38
  LCS_AVERAGE:      2.28

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     R     378     R     378      4    7   16     4    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     S     379     S     379      4    7   16     4    4    5    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     A     380     A     380      4    7   16     4    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     R     381     R     381      4    7   16     4    4    5    8   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     I     382     I     382      4    7   16     3    3    7    9   11   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     L     383     L     383      4    9   16     3    3    5    8   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     M     384     M     384      3    9   16     3    4    6    8    8   10   13   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     385     E     385      5    9   16     3    5    6    8   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     G     386     G     386      5    9   16     3    4    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     W     387     W     387      6    9   16     4    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     V     388     V     388      6    9   16     4    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     R     389     R     389      6    9   16     4    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     V     390     V     390      6    9   16     3    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     P     391     P     391      6    9   16     3    5    8    9   12   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     G     392     G     392      6    9   16     0    5    6    7    8   13   14   15   15   15   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     F     395     F     395      0    3   16     0    0    0    3    3    5    9   10   13   14   15   16   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   4.76  (   2.28    4.00    8.00 )

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      4      5      8      9     12     13     14     15     15     15     15     16     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   2.00   2.50   4.00   4.50   6.00   6.50   7.00   7.50   7.50   7.50   7.50   8.00   8.00   8.00   8.00   8.00   8.00   8.00   8.00   8.00
GDT RMS_LOCAL    0.22   0.53   1.11   1.27   1.92   2.02   2.14   2.35   2.35   2.35   2.35   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94
GDT RMS_ALL_CA   3.22   3.88   3.29   3.33   3.03   3.02   3.08   3.11   3.11   3.11   3.11   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94   2.94

#      Molecule1      Molecule2       DISTANCE
LGA    R     378      R     378          1.689
LGA    S     379      S     379          2.317
LGA    A     380      A     380          0.748
LGA    R     381      R     381          2.275
LGA    I     382      I     382          3.263
LGA    L     383      L     383          2.382
LGA    M     384      M     384          3.969
LGA    E     385      E     385          2.154
LGA    G     386      G     386          2.607
LGA    W     387      W     387          2.774
LGA    V     388      V     388          1.269
LGA    R     389      R     389          1.271
LGA    V     390      V     390          1.643
LGA    P     391      P     391          1.534
LGA    G     392      G     392          3.032
LGA    F     395      F     395          8.482

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  200    4.0     15    2.35     5.625     5.649     0.613

LGA_LOCAL      RMSD =  2.347  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.108  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  2.935  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.510677 * X  +   0.736918 * Y  +  -0.442900 * Z  + 106.855270
  Y_new =   0.702551 * X  +   0.654613 * Y  +   0.279114 * Z  + -60.998463
  Z_new =   0.495612 * X  +  -0.168622 * Y  +  -0.852018 * Z  +  40.452396 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.946208    0.195385  [ DEG:  -168.8053     11.1947 ]
  Theta =  -0.518540   -2.623053  [ DEG:   -29.7101   -150.2899 ]
  Phi   =   2.199342   -0.942251  [ DEG:   126.0130    -53.9870 ]
 
# 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: T0301TS239_2_1-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS239_2_1-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  200   4.0   15   2.35   5.649     2.94
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS239_2_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0301
PARENT 1tm0_A
ATOM    669  N   ARG   378      80.294  16.830  19.327  1.00  9.99
ATOM    670  CA  ARG   378      79.065  17.369  19.911  1.00  9.99
ATOM    671  C   ARG   378      78.616  18.653  19.201  1.00  9.99
ATOM    672  O   ARG   378      79.374  19.622  19.142  1.00  9.99
ATOM    673  CB  ARG   378      79.447  17.581  21.382  1.00  9.99
ATOM    674  N   SER   379      77.398  18.633  18.644  1.00  9.99
ATOM    675  CA  SER   379      76.812  19.774  17.922  1.00  9.99
ATOM    676  C   SER   379      75.859  20.542  18.823  1.00  9.99
ATOM    677  O   SER   379      75.348  19.988  19.788  1.00  9.99
ATOM    678  CB  SER   379      76.040  19.306  16.684  1.00  9.99
ATOM    679  N   ALA   380      75.606  21.807  18.504  1.00  9.99
ATOM    680  CA  ALA   380      74.725  22.615  19.336  1.00  9.99
ATOM    681  C   ALA   380      74.255  23.867  18.617  1.00  9.99
ATOM    682  O   ALA   380      74.782  24.218  17.572  1.00  9.99
ATOM    683  CB  ALA   380      75.459  23.003  20.614  1.00  9.99
ATOM    684  N   ARG   381      73.257  24.532  19.189  1.00  9.99
ATOM    685  CA  ARG   381      72.709  25.739  18.600  1.00  9.99
ATOM    686  C   ARG   381      72.984  26.895  19.531  1.00  9.99
ATOM    687  O   ARG   381      72.603  26.855  20.696  1.00  9.99
ATOM    688  CB  ARG   381      71.220  25.588  18.378  1.00  9.99
ATOM    689  N   ILE   382      73.655  27.920  19.017  1.00  9.99
ATOM    690  CA  ILE   382      73.995  29.085  19.818  1.00  9.99
ATOM    691  C   ILE   382      72.763  29.946  20.043  1.00  9.99
ATOM    692  O   ILE   382      72.111  29.843  21.081  1.00  9.99
ATOM    693  CB  ILE   382      75.103  29.884  19.126  1.00  9.99
ATOM    694  N   LEU   383      72.434  30.789  19.072  1.00  9.99
ATOM    695  CA  LEU   383      71.268  31.651  19.195  1.00  9.99
ATOM    696  C   LEU   383      70.069  31.033  18.483  1.00  9.99
ATOM    697  O   LEU   383      70.229  30.258  17.545  1.00  9.99
ATOM    698  CB  LEU   383      71.573  33.024  18.599  1.00  9.99
ATOM    699  N   MET   384      68.869  31.375  18.938  1.00  9.99
ATOM    700  CA  MET   384      67.635  30.868  18.343  1.00  9.99
ATOM    701  C   MET   384      66.634  32.008  18.201  1.00  9.99
ATOM    702  O   MET   384      66.407  32.754  19.149  1.00  9.99
ATOM    703  CB  MET   384      67.030  29.770  19.223  1.00  9.99
ATOM    704  N   GLU   385      66.030  32.141  17.024  1.00  9.99
ATOM    705  CA  GLU   385      65.055  33.204  16.792  1.00  9.99
ATOM    706  C   GLU   385      65.560  34.518  17.373  1.00  9.99
ATOM    707  O   GLU   385      65.042  35.000  18.379  1.00  9.99
ATOM    708  CB  GLU   385      63.709  32.852  17.439  1.00  9.99
ATOM    709  N   GLY   386      66.584  35.088  16.752  1.00  9.99
ATOM    710  CA  GLY   386      67.125  36.351  17.217  1.00  9.99
ATOM    711  C   GLY   386      67.037  37.352  16.079  1.00  9.99
ATOM    712  O   GLY   386      67.264  37.009  14.922  1.00  9.99
ATOM    713  N   TRP   387      66.688  38.607  16.391  1.00  9.99
ATOM    714  CA  TRP   387      66.581  39.628  15.348  1.00  9.99
ATOM    715  C   TRP   387      67.912  39.771  14.624  1.00  9.99
ATOM    716  O   TRP   387      68.956  39.416  15.167  1.00  9.99
ATOM    717  CB  TRP   387      66.203  40.881  16.131  1.00  9.99
ATOM    718  N   VAL   388      67.869  40.289  13.401  1.00  9.99
ATOM    719  CA  VAL   388      69.078  40.469  12.603  1.00  9.99
ATOM    720  C   VAL   388      68.945  41.657  11.648  1.00  9.99
ATOM    721  O   VAL   388      68.248  41.581  10.637  1.00  9.99
ATOM    722  CB  VAL   388      69.369  39.190  11.817  1.00  9.99
ATOM    723  N   ARG   389      69.622  42.754  11.978  1.00  9.99
ATOM    724  CA  ARG   389      69.589  43.968  11.164  1.00  9.99
ATOM    725  C   ARG   389      70.342  43.792   9.843  1.00  9.99
ATOM    726  O   ARG   389      71.542  44.052   9.755  1.00  9.99
ATOM    727  CB  ARG   389      70.186  45.141  11.955  1.00  9.99
ATOM    728  N   VAL   390      69.623  43.353   8.816  1.00  9.99
ATOM    729  CA  VAL   390      70.218  43.145   7.504  1.00  9.99
ATOM    730  C   VAL   390      70.026  44.368   6.611  1.00  9.99
ATOM    731  O   VAL   390      68.898  44.762   6.313  1.00  9.99
ATOM    732  CB  VAL   390      69.605  41.909   6.811  1.00  9.99
ATOM    733  N   PRO   391      71.133  44.967   6.186  1.00  9.99
ATOM    734  CA  PRO   391      71.068  46.142   5.329  1.00  9.99
ATOM    735  C   PRO   391      70.371  45.809   4.010  1.00  9.99
ATOM    736  O   PRO   391      70.056  46.702   3.225  1.00  9.99
ATOM    737  CB  PRO   391      72.477  46.703   5.017  1.00  9.99
ATOM    738  N   GLY   392      70.128  44.521   3.771  1.00  9.99
ATOM    739  CA  GLY   392      69.469  44.107   2.543  1.00  9.99
ATOM    740  C   GLY   392      68.056  44.651   2.423  1.00  9.99
ATOM    741  O   GLY   392      67.783  45.508   1.584  1.00  9.99
ATOM    742  N   PHE   395      67.154  44.139   3.256  1.00  9.99
ATOM    743  CA  PHE   395      65.767  44.586   3.259  1.00  9.99
ATOM    744  C   PHE   395      65.044  44.041   4.482  1.00  9.99
ATOM    745  O   PHE   395      65.092  42.845   4.763  1.00  9.99
ATOM    746  CB  PHE   395      65.040  44.133   1.987  1.00  9.99
TER
END
