
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0386AL243_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   11 , name T0386_D2.pdb
# PARAMETERS: T0386AL243_1-D2.T0386_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:    11       219 - 229         3.56     3.56
  LCS_AVERAGE:     13.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       224 - 229         0.27     7.27
  LCS_AVERAGE:      6.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       224 - 229         0.27     7.27
  LCS_AVERAGE:      6.29

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:   81
LCS_GDT     N     219     N     219      4    4   11     3    4    4    4    4    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     P     220     P     220      4    4   11     3    4    4    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     221     E     221      4    5   11     4    4    5    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     K     222     K     222      4    5   11     4    4    5    5    5    5    7    7    7   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     I     223     I     223      4    5   11     4    4    5    5    5    5    7    7    7    8   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     R     224     R     224      6    6   11     6    6    6    6    6    6    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     225     L     225      6    6   11     6    6    6    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     L     226     L     226      6    6   11     6    6    6    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     K     227     K     227      6    6   11     6    6    6    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     228     E     228      6    6   11     6    6    6    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     F     229     F     229      6    6   11     6    6    6    6    6    7    8    9    9   10   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:   8.83  (   6.29    6.62   13.58 )

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      6      6      6      6      6      7      8      9      9     10     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA   7.41   7.41   7.41   7.41   7.41   8.64   9.88  11.11  11.11  12.35  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58  13.58
GDT RMS_LOCAL    0.27   0.27   0.27   0.27   0.27   2.04   2.52   2.73   2.73   3.17   3.56   3.56   3.56   3.56   3.56   3.56   3.56   3.56   3.56   3.56
GDT RMS_ALL_CA   7.27   7.27   7.27   7.27   7.27   4.00   3.77   3.75   3.75   3.63   3.56   3.56   3.56   3.56   3.56   3.56   3.56   3.56   3.56   3.56

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          3.092
LGA    P     220      P     220          2.252
LGA    E     221      E     221          2.138
LGA    K     222      K     222          5.124
LGA    I     223      I     223          5.863
LGA    R     224      R     224          3.837
LGA    L     225      L     225          2.581
LGA    L     226      L     226          2.539
LGA    K     227      K     227          3.667
LGA    E     228      E     228          3.201
LGA    F     229      F     229          2.840

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   81    4.0      9    2.73     9.877     9.236     0.318

LGA_LOCAL      RMSD =  2.726  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.560  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  3.560  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.508777 * X  +   0.381678 * Y  +  -0.771666 * Z  + -13.733232
  Y_new =  -0.218900 * X  +   0.924244 * Y  +   0.312820 * Z  +  11.244073
  Z_new =   0.832604 * X  +   0.009762 * Y  +   0.553783 * Z  +  81.997833 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.017627   -3.123966  [ DEG:     1.0099   -178.9901 ]
  Theta =  -0.983792   -2.157800  [ DEG:   -56.3671   -123.6329 ]
  Phi   =  -0.406308    2.735285  [ DEG:   -23.2797    156.7203 ]
 
# 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: T0386AL243_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL243_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   81   4.0    9   2.73   9.236     3.56
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL243_1-D2
REMARK Aligment from pdb entry: 2g03A
ATOM    657  N   ASN   219       2.927  58.392  70.941  1.00  0.00              
ATOM    658  CA  ASN   219       3.398  57.670  72.118  1.00  0.00              
ATOM    659  C   ASN   219       2.326  57.807  73.177  1.00  0.00              
ATOM    660  O   ASN   219       1.675  58.837  73.255  1.00  0.00              
ATOM    661  N   PRO   220       2.117  56.790  74.005  1.00  0.00              
ATOM    662  CA  PRO   220       1.208  57.001  75.121  1.00  0.00              
ATOM    663  C   PRO   220       1.916  57.384  76.408  1.00  0.00              
ATOM    664  O   PRO   220       1.290  57.471  77.455  1.00  0.00              
ATOM    665  N   GLU   221       3.208  57.663  76.310  1.00  0.00              
ATOM    666  CA  GLU   221       3.980  58.101  77.470  1.00  0.00              
ATOM    667  C   GLU   221       3.875  59.638  77.542  1.00  0.00              
ATOM    668  O   GLU   221       4.856  60.341  77.324  1.00  0.00              
ATOM    669  N   LYS   222       2.680  60.139  77.855  1.00  0.00              
ATOM    670  CA  LYS   222       2.291  61.519  77.536  1.00  0.00              
ATOM    671  C   LYS   222       2.938  62.564  78.458  1.00  0.00              
ATOM    672  O   LYS   222       2.917  63.770  78.143  1.00  0.00              
ATOM    673  N   ILE   223       3.504  62.105  79.573  1.00  0.00              
ATOM    674  CA  ILE   223       4.052  62.994  80.592  1.00  0.00              
ATOM    675  C   ILE   223       5.543  62.776  80.810  1.00  0.00              
ATOM    676  O   ILE   223       6.111  63.263  81.775  1.00  0.00              
ATOM    677  N   ARG   224       6.164  62.041  79.908  1.00  0.00              
ATOM    678  CA  ARG   224       7.580  61.760  79.995  1.00  0.00              
ATOM    679  C   ARG   224       8.417  63.025  79.731  1.00  0.00              
ATOM    680  O   ARG   224       8.232  63.705  78.722  1.00  0.00              
ATOM    681  N   LEU   225       9.309  63.358  80.661  1.00  0.00              
ATOM    682  CA  LEU   225      10.129  64.565  80.544  1.00  0.00              
ATOM    683  C   LEU   225      10.926  64.642  79.224  1.00  0.00              
ATOM    684  O   LEU   225      11.004  65.704  78.614  1.00  0.00              
ATOM    685  N   LEU   226      11.487  63.525  78.775  1.00  0.00              
ATOM    686  CA  LEU   226      12.303  63.520  77.572  1.00  0.00              
ATOM    687  C   LEU   226      11.469  63.760  76.305  1.00  0.00              
ATOM    688  O   LEU   226      11.866  64.532  75.415  1.00  0.00              
ATOM    689  N   LYS   227      10.307  63.111  76.227  1.00  0.00              
ATOM    690  CA  LYS   227       9.375  63.315  75.126  1.00  0.00              
ATOM    691  C   LYS   227       8.877  64.753  75.120  1.00  0.00              
ATOM    692  O   LYS   227       8.837  65.386  74.063  1.00  0.00              
ATOM    693  N   GLU   228       8.502  65.282  76.283  1.00  0.00              
ATOM    694  CA  GLU   228       8.039  66.671  76.345  1.00  0.00              
ATOM    695  C   GLU   228       9.163  67.647  75.898  1.00  0.00              
ATOM    696  O   GLU   228       9.001  68.404  74.946  1.00  0.00              
ATOM    697  N   PHE   229      10.313  67.593  76.544  1.00  0.00              
ATOM    698  CA  PHE   229      11.350  68.583  76.282  1.00  0.00              
ATOM    699  C   PHE   229      12.101  68.460  74.943  1.00  0.00              
ATOM    700  O   PHE   229      12.368  69.477  74.321  1.00  0.00              
END
