
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0356AL243_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected   12 , name T0356_D2.pdb
# PARAMETERS: T0356AL243_4-D2.T0356_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:    12       132 - 147         4.07     4.07
  LCS_AVERAGE:      6.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       134 - 143         2.00     5.51
  LONGEST_CONTINUOUS_SEGMENT:     7       135 - 144         1.76     5.98
  LCS_AVERAGE:      3.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       140 - 144         0.30     8.97
  LCS_AVERAGE:      1.74

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:  192
LCS_GDT     Q     132     Q     132      3    4   12     3    3    3    4    6    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     K     133     K     133      3    4   12     3    3    3    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     I     134     I     134      3    7   12     3    4    4    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     V     135     V     135      3    7   12     3    4    4    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     S     136     S     136      3    7   12     3    3    3    4    7    7    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     V     140     V     140      5    7   12     5    5    5    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     D     141     D     141      5    7   12     5    5    5    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     L     142     L     142      5    7   12     5    5    5    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     N     143     N     143      5    7   12     5    5    5    6    7    8    9   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     R     144     R     144      5    7   12     5    5    5    5    7    7    8   10   10   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     P     146     P     146      0    6   12     0    0    3    5    5    6    8    8    9   11   11   11   11   11   12   12   12   12   12   12 
LCS_GDT     I     147     I     147      0    5   12     0    1    3    5    5    5    6    6    7    7    7   10   10   10   12   12   12   12   12   12 
LCS_AVERAGE  LCS_A:   3.75  (   1.74    3.26    6.25 )

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      5      5      5      6      7      8      9     10     10     11     11     11     11     11     12     12     12     12     12     12 
GDT PERCENT_CA   2.60   2.60   2.60   3.12   3.65   4.17   4.69   5.21   5.21   5.73   5.73   5.73   5.73   5.73   6.25   6.25   6.25   6.25   6.25   6.25
GDT RMS_LOCAL    0.30   0.30   0.30   1.39   1.72   2.07   2.32   2.68   2.68   3.23   3.23   3.23   3.23   3.23   4.07   4.07   4.07   4.07   4.07   4.07
GDT RMS_ALL_CA   8.97   8.97   8.97   6.74   6.27   5.66   5.65   5.22   5.22   4.34   4.34   4.34   4.34   4.34   4.07   4.07   4.07   4.07   4.07   4.07

#      Molecule1      Molecule2       DISTANCE
LGA    Q     132      Q     132          1.861
LGA    K     133      K     133          3.278
LGA    I     134      I     134          3.004
LGA    V     135      V     135          1.852
LGA    S     136      S     136          3.864
LGA    V     140      V     140          2.255
LGA    D     141      D     141          1.259
LGA    L     142      L     142          2.948
LGA    N     143      N     143          2.038
LGA    R     144      R     144          3.658
LGA    P     146      P     146          8.182
LGA    I     147      I     147         13.217

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  192    4.0     10    2.68     4.297     4.138     0.360

LGA_LOCAL      RMSD =  2.677  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.132  Number of atoms =   12 
Std_ALL_ATOMS  RMSD =  4.074  (standard rmsd on all 12 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.400516 * X  +  -0.806411 * Y  +  -0.435073 * Z  +  75.562561
  Y_new =  -0.911746 * X  +  -0.303515 * Y  +  -0.276762 * Z  +  77.194313
  Z_new =   0.091133 * X  +   0.507524 * Y  +  -0.856805 * Z  +  86.779999 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.606821   -0.534772  [ DEG:   149.3598    -30.6402 ]
  Theta =  -0.091260   -3.050333  [ DEG:    -5.2288   -174.7712 ]
  Phi   =  -1.156889    1.984704  [ DEG:   -66.2849    113.7151 ]
 
# 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: T0356AL243_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL243_4-D2.T0356_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  192   4.0   10   2.68   4.138     4.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL243_4-D2
REMARK Aligment from pdb entry: 1f1zA
ATOM    381  N   GLN   132      85.256  71.705  95.756  1.00  0.00              
ATOM    382  CA  GLN   132      86.006  72.125  94.580  1.00  0.00              
ATOM    383  C   GLN   132      86.301  70.987  93.623  1.00  0.00              
ATOM    384  O   GLN   132      86.836  71.214  92.541  1.00  0.00              
ATOM    385  N   LYS   133      85.998  69.759  94.038  1.00  0.00              
ATOM    386  CA  LYS   133      86.190  68.607  93.163  1.00  0.00              
ATOM    387  C   LYS   133      87.471  67.809  93.281  1.00  0.00              
ATOM    388  O   LYS   133      87.673  66.833  92.548  1.00  0.00              
ATOM    389  N   ILE   134      88.325  68.191  94.222  1.00  0.00              
ATOM    390  CA  ILE   134      89.587  67.493  94.425  1.00  0.00              
ATOM    391  C   ILE   134      89.341  66.173  95.163  1.00  0.00              
ATOM    392  O   ILE   134      90.119  65.217  95.038  1.00  0.00              
ATOM    393  N   VAL   135      88.219  66.125  95.879  1.00  0.00              
ATOM    394  CA  VAL   135      87.785  64.949  96.631  1.00  0.00              
ATOM    395  C   VAL   135      86.388  64.580  96.103  1.00  0.00              
ATOM    396  O   VAL   135      85.533  65.459  95.985  1.00  0.00              
ATOM    397  N   SER   136      86.174  63.312  95.752  1.00  0.00              
ATOM    398  CA  SER   136      84.875  62.823  95.261  1.00  0.00              
ATOM    399  C   SER   136      84.360  61.830  96.297  1.00  0.00              
ATOM    400  O   SER   136      85.143  61.078  96.874  1.00  0.00              
ATOM    401  N   VAL   140      83.053  61.805  96.525  1.00  0.00              
ATOM    402  CA  VAL   140      82.469  60.869  97.481  1.00  0.00              
ATOM    403  C   VAL   140      81.162  60.274  96.947  1.00  0.00              
ATOM    404  O   VAL   140      80.718  60.606  95.843  1.00  0.00              
ATOM    405  N   ASP   141      80.538  59.409  97.735  1.00  0.00              
ATOM    406  CA  ASP   141      79.287  58.800  97.327  1.00  0.00              
ATOM    407  C   ASP   141      78.170  59.815  97.559  1.00  0.00              
ATOM    408  O   ASP   141      77.599  59.883  98.642  1.00  0.00              
ATOM    409  N   LEU   142      77.888  60.618  96.539  1.00  0.00              
ATOM    410  CA  LEU   142      76.855  61.653  96.605  1.00  0.00              
ATOM    411  C   LEU   142      75.445  61.145  96.912  1.00  0.00              
ATOM    412  O   LEU   142      74.583  61.915  97.325  1.00  0.00              
ATOM    413  N   ASN   143      75.196  59.864  96.676  1.00  0.00              
ATOM    414  CA  ASN   143      73.880  59.293  96.939  1.00  0.00              
ATOM    415  C   ASN   143      73.705  58.887  98.401  1.00  0.00              
ATOM    416  O   ASN   143      72.672  58.337  98.792  1.00  0.00              
ATOM    417  N   ARG   144      74.718  59.177  99.205  1.00  0.00              
ATOM    418  CA  ARG   144      74.692  58.871 100.621  1.00  0.00              
ATOM    419  C   ARG   144      75.102  60.187 101.243  1.00  0.00              
ATOM    420  O   ARG   144      75.862  60.936 100.633  1.00  0.00              
ATOM    421  N   PRO   146      74.544  60.515 102.401  1.00  0.00              
ATOM    422  CA  PRO   146      74.914  61.755 103.061  1.00  0.00              
ATOM    423  C   PRO   146      76.411  61.709 103.272  1.00  0.00              
ATOM    424  O   PRO   146      76.979  60.642 103.539  1.00  0.00              
ATOM    425  N   ILE   147      77.043  62.868 103.180  1.00  0.00              
ATOM    426  CA  ILE   147      78.476  62.942 103.356  1.00  0.00              
ATOM    427  C   ILE   147      78.852  62.416 104.733  1.00  0.00              
ATOM    428  O   ILE   147      79.805  61.644 104.884  1.00  0.00              
END
