
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS249_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    9 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_1_2-D1.T0372_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:     9       290 - 298         2.05     2.05
  LCS_AVERAGE:      7.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       290 - 297         1.55     2.24
  LCS_AVERAGE:      5.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       291 - 295         0.97     2.76
  LONGEST_CONTINUOUS_SEGMENT:     5       293 - 297         0.96     3.69
  LCS_AVERAGE:      3.70

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:  126
LCS_GDT     K     290     K     290      4    8    9     0    3    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     Y     291     Y     291      5    8    9     3    4    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     M     292     M     292      5    8    9     3    4    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     A     293     A     293      5    8    9     3    4    6    6    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     C     294     C     294      5    8    9     3    4    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     L     295     L     295      5    8    9     3    4    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     K     296     K     296      5    8    9     0    4    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     D     297     D     297      5    8    9     0    4    7    7    8    8    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_GDT     H     298     H     298      3    3    9     0    3    3    3    3    4    8    9    9    9    9    9    9    9    9    9    9    9    9    9 
LCS_AVERAGE  LCS_A:   5.58  (   3.70    5.91    7.14 )

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      3      4      7      7      8      8      8      9      9      9      9      9      9      9      9      9      9      9      9      9 
GDT PERCENT_CA   2.38   3.17   5.56   5.56   6.35   6.35   6.35   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14   7.14
GDT RMS_LOCAL    0.23   0.46   1.19   1.19   1.55   1.55   1.55   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05
GDT RMS_ALL_CA   2.57   2.46   2.36   2.36   2.24   2.24   2.24   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05   2.05

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290          1.479
LGA    Y     291      Y     291          1.170
LGA    M     292      M     292          0.975
LGA    A     293      A     293          2.471
LGA    C     294      C     294          1.613
LGA    L     295      L     295          1.673
LGA    K     296      K     296          2.247
LGA    D     297      D     297          1.674
LGA    H     298      H     298          3.712

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    9  126    4.0      9    2.05     5.754     6.145     0.420

LGA_LOCAL      RMSD =  2.045  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.045  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  2.045  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.039802 * X  +   0.679050 * Y  +   0.733013 * Z  +  33.217159
  Y_new =   0.412614 * X  +  -0.656957 * Y  +   0.630997 * Z  +  59.040344
  Z_new =   0.910036 * X  +   0.327566 * Y  +  -0.254038 * Z  +   0.786306 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.230438   -0.911155  [ DEG:   127.7947    -52.2053 ]
  Theta =  -1.143371   -1.998222  [ DEG:   -65.5103   -114.4897 ]
  Phi   =   1.666961   -1.474632  [ DEG:    95.5098    -84.4902 ]
 
# 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: T0372TS249_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_1_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    9  126   4.0    9   2.05   6.145     2.05
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      26.885  46.331   7.777  1.00  0.00
ATOM   1036  CA  LYS   290      27.448  46.073   6.505  1.00  0.00
ATOM   1037  C   LYS   290      26.326  46.260   5.569  1.00  0.00
ATOM   1038  O   LYS   290      25.605  45.321   5.234  1.00  0.00
ATOM   1039  CB  LYS   290      27.983  44.643   6.317  1.00  0.00
ATOM   1040  CG  LYS   290      29.420  44.444   6.804  1.00  0.00
ATOM   1041  CD  LYS   290      29.626  44.607   8.307  1.00  0.00
ATOM   1042  CE  LYS   290      31.072  44.358   8.736  1.00  0.00
ATOM   1043  NZ  LYS   290      31.465  42.975   8.384  1.00  0.00
ATOM   1044  N   TYR   291      26.143  47.512   5.131  1.00  0.00
ATOM   1045  CA  TYR   291      25.117  47.705   4.175  1.00  0.00
ATOM   1046  C   TYR   291      25.889  47.605   2.919  1.00  0.00
ATOM   1047  O   TYR   291      26.399  48.596   2.400  1.00  0.00
ATOM   1048  CB  TYR   291      24.463  49.098   4.240  1.00  0.00
ATOM   1049  CG  TYR   291      23.329  49.107   3.274  1.00  0.00
ATOM   1050  CD1 TYR   291      22.147  48.482   3.597  1.00  0.00
ATOM   1051  CD2 TYR   291      23.433  49.744   2.059  1.00  0.00
ATOM   1052  CE1 TYR   291      21.088  48.480   2.722  1.00  0.00
ATOM   1053  CE2 TYR   291      22.376  49.747   1.178  1.00  0.00
ATOM   1054  CZ  TYR   291      21.203  49.111   1.508  1.00  0.00
ATOM   1055  OH  TYR   291      20.118  49.111   0.606  1.00  0.00
ATOM   1056  N   MET   292      26.031  46.362   2.430  1.00  0.00
ATOM   1057  CA  MET   292      26.819  46.185   1.260  1.00  0.00
ATOM   1058  C   MET   292      25.885  46.161   0.103  1.00  0.00
ATOM   1059  O   MET   292      25.692  45.125  -0.532  1.00  0.00
ATOM   1060  CB  MET   292      27.622  44.869   1.256  1.00  0.00
ATOM   1061  CG  MET   292      28.595  44.731   0.080  1.00  0.00
ATOM   1062  SD  MET   292      29.727  43.308   0.190  1.00  0.00
ATOM   1063  CE  MET   292      28.458  42.045  -0.107  1.00  0.00
ATOM   1064  N   ALA   293      25.258  47.319  -0.180  1.00  0.00
ATOM   1065  CA  ALA   293      24.477  47.429  -1.372  1.00  0.00
ATOM   1066  C   ALA   293      25.535  47.587  -2.411  1.00  0.00
ATOM   1067  O   ALA   293      26.553  48.225  -2.144  1.00  0.00
ATOM   1068  CB  ALA   293      23.575  48.675  -1.420  1.00  0.00
ATOM   1069  N   CYS   294      25.319  47.061  -3.632  1.00  0.00
ATOM   1070  CA  CYS   294      26.444  46.990  -4.520  1.00  0.00
ATOM   1071  C   CYS   294      26.383  47.923  -5.704  1.00  0.00
ATOM   1072  O   CYS   294      25.665  48.921  -5.722  1.00  0.00
ATOM   1073  CB  CYS   294      26.669  45.573  -5.070  1.00  0.00
ATOM   1074  SG  CYS   294      27.056  44.378  -3.753  1.00  0.00
ATOM   1075  N   LEU   295      27.196  47.550  -6.725  1.00  0.00
ATOM   1076  CA  LEU   295      27.629  48.268  -7.904  1.00  0.00
ATOM   1077  C   LEU   295      26.673  48.306  -9.080  1.00  0.00
ATOM   1078  O   LEU   295      25.606  47.699  -9.069  1.00  0.00
ATOM   1079  CB  LEU   295      29.000  47.733  -8.384  1.00  0.00
ATOM   1080  CG  LEU   295      29.720  48.539  -9.483  1.00  0.00
ATOM   1081  CD1 LEU   295      30.085  49.949  -8.995  1.00  0.00
ATOM   1082  CD2 LEU   295      30.938  47.775 -10.022  1.00  0.00
ATOM   1083  N   LYS   296      27.045  49.117 -10.114  1.00  0.00
ATOM   1084  CA  LYS   296      26.326  49.319 -11.354  1.00  0.00
ATOM   1085  C   LYS   296      27.270  49.246 -12.540  1.00  0.00
ATOM   1086  O   LYS   296      28.465  49.520 -12.432  1.00  0.00
ATOM   1087  CB  LYS   296      25.610  50.680 -11.433  1.00  0.00
ATOM   1088  CG  LYS   296      24.991  50.939 -12.806  1.00  0.00
ATOM   1089  CD  LYS   296      23.908  49.926 -13.179  1.00  0.00
ATOM   1090  CE  LYS   296      23.627  49.863 -14.682  1.00  0.00
ATOM   1091  NZ  LYS   296      23.215  51.191 -15.178  1.00  0.00
ATOM   1092  N   ASP   297      26.705  48.896 -13.725  1.00  0.00
ATOM   1093  CA  ASP   297      27.365  48.638 -14.988  1.00  0.00
ATOM   1094  C   ASP   297      27.452  49.857 -15.854  1.00  0.00
ATOM   1095  O   ASP   297      28.135  50.837 -15.562  1.00  0.00
ATOM   1096  CB  ASP   297      26.613  47.631 -15.875  1.00  0.00
ATOM   1097  CG  ASP   297      26.714  46.249 -15.272  1.00  0.00
ATOM   1098  OD1 ASP   297      27.482  46.087 -14.289  1.00  0.00
ATOM   1099  OD2 ASP   297      26.029  45.331 -15.796  1.00  0.00
ATOM   1100  N   HIS   298      26.793  49.737 -17.026  1.00  0.00
ATOM   1101  CA  HIS   298      26.725  50.716 -18.074  1.00  0.00
ATOM   1102  C   HIS   298      26.045  51.934 -17.526  1.00  0.00
ATOM   1103  O   HIS   298      25.604  51.952 -16.381  1.00  0.00
ATOM   1104  CB  HIS   298      25.945  50.214 -19.301  1.00  0.00
ATOM   1105  CG  HIS   298      26.628  49.048 -19.948  1.00  0.00
ATOM   1106  ND1 HIS   298      26.514  47.747 -19.511  1.00  0.00
ATOM   1107  CD2 HIS   298      27.471  49.009 -21.015  1.00  0.00
ATOM   1108  CE1 HIS   298      27.293  46.992 -20.325  1.00  0.00
ATOM   1109  NE2 HIS   298      27.894  47.714 -21.254  1.00  0.00
TER
END
