
#######################################################
#                                                     #
#                        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   21 (  162),  selected   21 , name T0311TS490_1_2-D1
# Molecule2: number of CA atoms   64 (  486),  selected   21 , name T0311_D1.pdb
# PARAMETERS: T0311TS490_1_2-D1.T0311_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:    21        51 - 71          2.51     2.51
  LCS_AVERAGE:     32.81

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        51 - 69          1.41     2.89
  LCS_AVERAGE:     27.60

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        54 - 68          0.98     3.41
  LCS_AVERAGE:     20.54

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:   64
LCS_GDT     E      51     E      51     13   19   21     9   10   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     M      52     M      52     13   19   21     9   10   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A      53     A      53     13   19   21     9   10   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     I      54     I      54     15   19   21     9   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     K      55     K      55     15   19   21     9   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L      56     L      56     15   19   21     9   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     S      57     S      57     15   19   21     9   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     V      58     V      58     15   19   21     9   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     V      59     V      59     15   19   21     9   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     I      60     I      60     15   19   21     3   10   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G      61     G      61     15   19   21     3    8   14   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     S      62     S      62     15   19   21     5   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     S      63     S      63     15   19   21     6   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     P      64     P      64     15   19   21     6   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     Q      65     Q      65     15   19   21     6   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     M      66     M      66     15   19   21     6   11   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     W      67     W      67     15   19   21     3    8   13   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L      68     L      68     15   19   21     6   10   15   18   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     N      69     N      69      4   19   21     4    5   12   15   18   19   19   19   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L      70     L      70      4    5   21     4    4    4    4    5    7    9   15   16   21   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     Q      71     Q      71      4    5   21     4    4    4    4    6    7   13   18   20   21   21   21   21   21   21   21   21   21   21   21 
LCS_AVERAGE  LCS_A:  26.98  (  20.54   27.60   32.81 )

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      9     11     15     18     18     19     19     19     20     21     21     21     21     21     21     21     21     21     21     21 
GDT PERCENT_CA  14.06  17.19  23.44  28.12  28.12  29.69  29.69  29.69  31.25  32.81  32.81  32.81  32.81  32.81  32.81  32.81  32.81  32.81  32.81  32.81
GDT RMS_LOCAL    0.20   0.80   1.03   1.21   1.21   1.41   1.41   1.41   2.12   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51
GDT RMS_ALL_CA   3.80   3.31   3.11   3.15   3.15   2.89   2.89   2.89   2.59   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51   2.51

#      Molecule1      Molecule2       DISTANCE
LGA    E      51      E      51          1.283
LGA    M      52      M      52          1.756
LGA    A      53      A      53          1.579
LGA    I      54      I      54          0.436
LGA    K      55      K      55          0.648
LGA    L      56      L      56          1.093
LGA    S      57      S      57          1.116
LGA    V      58      V      58          0.737
LGA    V      59      V      59          0.638
LGA    I      60      I      60          1.062
LGA    G      61      G      61          1.837
LGA    S      62      S      62          0.983
LGA    S      63      S      63          0.185
LGA    P      64      P      64          1.389
LGA    Q      65      Q      65          1.536
LGA    M      66      M      66          1.267
LGA    W      67      W      67          2.132
LGA    L      68      L      68          1.377
LGA    N      69      N      69          2.948
LGA    L      70      L      70          8.591
LGA    Q      71      Q      71          8.003

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   64    4.0     19    1.41    26.953    28.331     1.259

LGA_LOCAL      RMSD =  1.410  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.892  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  2.513  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.832572 * X  +  -0.164437 * Y  +   0.528947 * Z  +  27.428318
  Y_new =   0.366218 * X  +   0.879846 * Y  +  -0.302911 * Z  +   3.790026
  Z_new =  -0.415582 * X  +   0.445905 * Y  +   0.792755 * Z  +   5.490054 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.512370   -2.629222  [ DEG:    29.3566   -150.6434 ]
  Theta =   0.428583    2.713010  [ DEG:    24.5560    155.4440 ]
  Phi   =   0.414393   -2.727200  [ DEG:    23.7429   -156.2570 ]
 
# 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: T0311TS490_1_2-D1                             
REMARK     2: T0311_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0311TS490_1_2-D1.T0311_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   64   4.0   19   1.41  28.331     2.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0311TS490_1_2-D1
REMARK PARENT number 2
PFRMAT     TS
TARGET     T0311
PARENT     1lmb30           
ATOM    380  N   GLU    51      31.238  -3.655  -1.143  1.00  0.36
ATOM    381  CA  GLU    51      29.814  -3.562  -1.011  1.00  0.36
ATOM    382  C   GLU    51      29.433  -3.190   0.391  1.00  0.36
ATOM    383  O   GLU    51      28.606  -2.302   0.598  1.00  0.36
ATOM    384  CB  GLU    51      29.101  -4.867  -1.396  1.00  0.36
ATOM    385  CG  GLU    51      27.605  -4.685  -1.652  1.00  0.36
ATOM    386  CD  GLU    51      27.148  -5.881  -2.472  1.00  0.36
ATOM    387  OE1 GLU    51      27.829  -6.937  -2.404  1.00  0.36
ATOM    388  OE2 GLU    51      26.117  -5.751  -3.185  1.00  0.36
ATOM    389  N   MET    52      30.045  -3.845   1.398  1.00  0.19
ATOM    390  CA  MET    52      29.713  -3.588   2.774  1.00  0.19
ATOM    391  C   MET    52      30.088  -2.180   3.097  1.00  0.19
ATOM    392  O   MET    52      29.372  -1.492   3.822  1.00  0.19
ATOM    393  CB  MET    52      30.488  -4.467   3.776  1.00  0.19
ATOM    394  CG  MET    52      30.158  -5.963   3.736  1.00  0.19
ATOM    395  SD  MET    52      31.156  -6.957   4.892  1.00  0.19
ATOM    396  CE  MET    52      30.620  -8.585   4.288  1.00  0.19
ATOM    397  N   ALA    53      31.236  -1.715   2.572  1.00  0.21
ATOM    398  CA  ALA    53      31.692  -0.394   2.893  1.00  0.21
ATOM    399  C   ALA    53      30.684   0.602   2.408  1.00  0.21
ATOM    400  O   ALA    53      30.340   1.540   3.127  1.00  0.21
ATOM    401  CB  ALA    53      33.041  -0.047   2.239  1.00  0.21
ATOM    402  N   ILE    54      30.169   0.419   1.176  1.00  0.44
ATOM    403  CA  ILE    54      29.241   1.382   0.657  1.00  0.44
ATOM    404  C   ILE    54      27.961   1.348   1.444  1.00  0.44
ATOM    405  O   ILE    54      27.326   2.379   1.644  1.00  0.44
ATOM    406  CB  ILE    54      28.932   1.227  -0.804  1.00  0.44
ATOM    407  CG1 ILE    54      28.243   2.505  -1.322  1.00  0.44
ATOM    408  CG2 ILE    54      28.114  -0.058  -0.992  1.00  0.44
ATOM    409  CD1 ILE    54      28.234   2.636  -2.844  1.00  0.44
ATOM    410  N   LYS    55      27.523   0.162   1.901  1.00  0.58
ATOM    411  CA  LYS    55      26.302   0.096   2.656  1.00  0.58
ATOM    412  C   LYS    55      26.474   0.861   3.933  1.00  0.58
ATOM    413  O   LYS    55      25.599   1.625   4.337  1.00  0.58
ATOM    414  CB  LYS    55      25.925  -1.349   3.015  1.00  0.58
ATOM    415  CG  LYS    55      25.456  -2.155   1.803  1.00  0.58
ATOM    416  CD  LYS    55      24.118  -1.675   1.245  1.00  0.58
ATOM    417  CE  LYS    55      22.952  -2.588   1.626  1.00  0.58
ATOM    418  NZ  LYS    55      22.983  -2.874   3.079  1.00  0.58
ATOM    419  N   LEU    56      27.628   0.688   4.600  1.00  0.32
ATOM    420  CA  LEU    56      27.875   1.319   5.866  1.00  0.32
ATOM    421  C   LEU    56      27.920   2.807   5.668  1.00  0.32
ATOM    422  O   LEU    56      27.452   3.562   6.520  1.00  0.32
ATOM    423  CB  LEU    56      29.202   0.863   6.502  1.00  0.32
ATOM    424  CG  LEU    56      29.355  -0.675   6.574  1.00  0.32
ATOM    425  CD1 LEU    56      30.501  -1.090   7.513  1.00  0.32
ATOM    426  CD2 LEU    56      28.024  -1.380   6.873  1.00  0.32
ATOM    427  N   SER    57      28.478   3.271   4.531  1.00  0.23
ATOM    428  CA  SER    57      28.578   4.684   4.296  1.00  0.23
ATOM    429  C   SER    57      27.199   5.258   4.308  1.00  0.23
ATOM    430  O   SER    57      26.956   6.277   4.950  1.00  0.23
ATOM    431  CB  SER    57      29.174   5.055   2.920  1.00  0.23
ATOM    432  OG  SER    57      28.263   4.763   1.871  1.00  0.23
ATOM    433  N   VAL    58      26.250   4.607   3.604  1.00  0.46
ATOM    434  CA  VAL    58      24.936   5.168   3.506  1.00  0.46
ATOM    435  C   VAL    58      24.273   5.162   4.845  1.00  0.46
ATOM    436  O   VAL    58      23.595   6.123   5.204  1.00  0.46
ATOM    437  CB  VAL    58      24.022   4.468   2.535  1.00  0.46
ATOM    438  CG1 VAL    58      24.679   4.494   1.145  1.00  0.46
ATOM    439  CG2 VAL    58      23.661   3.072   3.059  1.00  0.46
ATOM    440  N   VAL    59      24.454   4.082   5.631  1.00  0.58
ATOM    441  CA  VAL    59      23.780   4.012   6.897  1.00  0.58
ATOM    442  C   VAL    59      24.290   5.102   7.788  1.00  0.58
ATOM    443  O   VAL    59      23.532   5.659   8.581  1.00  0.58
ATOM    444  CB  VAL    59      23.965   2.717   7.637  1.00  0.58
ATOM    445  CG1 VAL    59      23.458   1.571   6.746  1.00  0.58
ATOM    446  CG2 VAL    59      25.425   2.589   8.096  1.00  0.58
ATOM    447  N   ILE    60      25.587   5.454   7.673  1.00  0.47
ATOM    448  CA  ILE    60      26.150   6.414   8.584  1.00  0.47
ATOM    449  C   ILE    60      26.088   7.782   7.975  1.00  0.47
ATOM    450  O   ILE    60      26.430   8.764   8.634  1.00  0.47
ATOM    451  CB  ILE    60      27.608   6.185   8.822  1.00  0.47
ATOM    452  CG1 ILE    60      28.345   6.373   7.485  1.00  0.47
ATOM    453  CG2 ILE    60      27.799   4.802   9.469  1.00  0.47
ATOM    454  CD1 ILE    60      29.856   6.524   7.616  1.00  0.47
ATOM    455  N   GLY    61      25.631   7.894   6.714  1.00  0.32
ATOM    456  CA  GLY    61      25.486   9.188   6.108  1.00  0.32
ATOM    457  C   GLY    61      26.824   9.820   5.859  1.00  0.32
ATOM    458  O   GLY    61      26.975  11.028   6.028  1.00  0.32
ATOM    459  N   SER    62      27.838   9.026   5.458  1.00  0.37
ATOM    460  CA  SER    62      29.128   9.592   5.174  1.00  0.37
ATOM    461  C   SER    62      29.611   9.003   3.886  1.00  0.37
ATOM    462  O   SER    62      28.954   8.144   3.299  1.00  0.37
ATOM    463  CB  SER    62      30.182   9.298   6.256  1.00  0.37
ATOM    464  OG  SER    62      29.816   9.939   7.467  1.00  0.37
ATOM    465  N   SER    63      30.769   9.482   3.391  1.00  0.55
ATOM    466  CA  SER    63      31.303   8.945   2.172  1.00  0.55
ATOM    467  C   SER    63      32.272   7.875   2.558  1.00  0.55
ATOM    468  O   SER    63      32.823   7.871   3.658  1.00  0.55
ATOM    469  CB  SER    63      32.059   9.969   1.313  1.00  0.55
ATOM    470  OG  SER    63      33.237  10.380   1.988  1.00  0.55
ATOM    471  N   PRO    64      32.468   6.941   1.674  1.00  0.71
ATOM    472  CA  PRO    64      33.344   5.848   1.979  1.00  0.71
ATOM    473  C   PRO    64      34.763   6.252   2.197  1.00  0.71
ATOM    474  O   PRO    64      35.413   5.676   3.071  1.00  0.71
ATOM    475  CB  PRO    64      33.130   4.827   0.863  1.00  0.71
ATOM    476  CG  PRO    64      31.672   5.074   0.431  1.00  0.71
ATOM    477  CD  PRO    64      31.425   6.563   0.735  1.00  0.71
ATOM    478  N   GLN    65      35.272   7.236   1.435  1.00  0.64
ATOM    479  CA  GLN    65      36.649   7.590   1.617  1.00  0.64
ATOM    480  C   GLN    65      36.851   8.206   2.964  1.00  0.64
ATOM    481  O   GLN    65      37.977   8.521   3.342  1.00  0.64
ATOM    482  CB  GLN    65      37.174   8.565   0.550  1.00  0.64
ATOM    483  CG  GLN    65      36.445   9.910   0.514  1.00  0.64
ATOM    484  CD  GLN    65      35.240   9.759  -0.403  1.00  0.64
ATOM    485  OE1 GLN    65      34.927   8.662  -0.861  1.00  0.64
ATOM    486  NE2 GLN    65      34.554  10.897  -0.691  1.00  0.64
ATOM    487  N   MET    66      35.775   8.376   3.747  1.00  0.48
ATOM    488  CA  MET    66      35.936   8.962   5.038  1.00  0.48
ATOM    489  C   MET    66      36.640   7.983   5.924  1.00  0.48
ATOM    490  O   MET    66      37.414   8.365   6.800  1.00  0.48
ATOM    491  CB  MET    66      34.597   9.416   5.643  1.00  0.48
ATOM    492  CG  MET    66      34.003  10.567   4.820  1.00  0.48
ATOM    493  SD  MET    66      32.469  11.308   5.455  1.00  0.48
ATOM    494  CE  MET    66      32.380  12.584   4.164  1.00  0.48
ATOM    495  N   TRP    67      36.371   6.680   5.732  1.00  0.50
ATOM    496  CA  TRP    67      37.017   5.705   6.556  1.00  0.50
ATOM    497  C   TRP    67      38.023   4.943   5.755  1.00  0.50
ATOM    498  O   TRP    67      39.089   4.614   6.277  1.00  0.50
ATOM    499  CB  TRP    67      36.043   4.704   7.148  1.00  0.50
ATOM    500  CG  TRP    67      35.155   4.066   6.121  1.00  0.50
ATOM    501  CD1 TRP    67      35.293   2.933   5.381  1.00  0.50
ATOM    502  CD2 TRP    67      33.908   4.657   5.753  1.00  0.50
ATOM    503  NE1 TRP    67      34.194   2.778   4.566  1.00  0.50
ATOM    504  CE2 TRP    67      33.337   3.833   4.788  1.00  0.50
ATOM    505  CE3 TRP    67      33.297   5.793   6.192  1.00  0.50
ATOM    506  CZ2 TRP    67      32.124   4.139   4.240  1.00  0.50
ATOM    507  CZ3 TRP    67      32.079   6.100   5.636  1.00  0.50
ATOM    508  CH2 TRP    67      31.511   5.288   4.682  1.00  0.50
ATOM    509  N   LEU    68      37.713   4.592   4.486  1.00  0.43
ATOM    510  CA  LEU    68      38.749   3.903   3.772  1.00  0.43
ATOM    511  C   LEU    68      38.932   4.480   2.408  1.00  0.43
ATOM    512  O   LEU    68      38.074   4.340   1.536  1.00  0.43
ATOM    513  CB  LEU    68      38.540   2.407   3.535  1.00  0.43
ATOM    514  CG  LEU    68      39.845   1.749   3.038  1.00  0.43
ATOM    515  CD1 LEU    68      40.998   2.020   4.017  1.00  0.43
ATOM    516  CD2 LEU    68      39.677   0.244   2.795  1.00  0.43
ATOM    517  N   ASN    69      40.100   5.112   2.192  1.00  0.37
ATOM    518  CA  ASN    69      40.449   5.705   0.935  1.00  0.37
ATOM    519  C   ASN    69      40.628   4.620  -0.075  1.00  0.37
ATOM    520  O   ASN    69      40.250   4.763  -1.237  1.00  0.37
ATOM    521  CB  ASN    69      41.805   6.429   0.967  1.00  0.37
ATOM    522  CG  ASN    69      41.734   7.553   1.982  1.00  0.37
ATOM    523  OD1 ASN    69      40.648   8.008   2.336  1.00  0.37
ATOM    524  ND2 ASN    69      42.918   8.010   2.469  1.00  0.37
ATOM    525  N   LEU    70      41.232   3.495   0.349  1.00  0.46
ATOM    526  CA  LEU    70      41.541   2.420  -0.548  1.00  0.46
ATOM    527  C   LEU    70      40.287   1.881  -1.152  1.00  0.46
ATOM    528  O   LEU    70      40.224   1.678  -2.364  1.00  0.46
ATOM    529  CB  LEU    70      42.284   1.269   0.163  1.00  0.46
ATOM    530  CG  LEU    70      42.489  -0.021  -0.665  1.00  0.46
ATOM    531  CD1 LEU    70      41.211  -0.874  -0.738  1.00  0.46
ATOM    532  CD2 LEU    70      43.063   0.294  -2.056  1.00  0.46
ATOM    533  N   GLN    71      39.253   1.639  -0.327  1.00  0.42
ATOM    534  CA  GLN    71      38.043   1.050  -0.825  1.00  0.42
ATOM    535  C   GLN    71      37.389   1.960  -1.806  1.00  0.42
ATOM    536  O   GLN    71      36.947   1.514  -2.864  1.00  0.42
ATOM    537  CB  GLN    71      36.983   0.802   0.259  1.00  0.42
ATOM    538  CG  GLN    71      37.286  -0.358   1.200  1.00  0.42
ATOM    539  CD  GLN    71      36.199  -0.360   2.263  1.00  0.42
ATOM    540  OE1 GLN    71      35.835   0.687   2.796  1.00  0.42
ATOM    541  NE2 GLN    71      35.655  -1.567   2.568  1.00  0.42
TER
END
