
#######################################################
#                                                     #
#                        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   14 (  112),  selected   14 , name T0318TS193_5_2-D1
# Molecule2: number of CA atoms  154 ( 1200),  selected   14 , name T0318_D1.pdb
# PARAMETERS: T0318TS193_5_2-D1.T0318_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:    14       142 - 155         4.89     4.89
  LCS_AVERAGE:      9.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       146 - 154         1.82     6.32
  LCS_AVERAGE:      5.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       144 - 147         0.10    13.53
  LONGEST_CONTINUOUS_SEGMENT:     4       150 - 153         0.91    11.38
  LONGEST_CONTINUOUS_SEGMENT:     4       151 - 154         0.92    15.16
  LCS_AVERAGE:      2.23

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:  154
LCS_GDT     R     142     R     142      3    4   14     3    3    3    3    4    4    5    6    6    6    7    7   10   10   10   11   11   12   12   12 
LCS_GDT     E     143     E     143      3    4   14     3    3    3    3    4    4    5    6    9   10   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     144     L     144      4    8   14     4    4    5    7    8    8    8    9   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     N     145     N     145      4    8   14     4    4    5    7    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     146     V     146      4    9   14     4    5    6    7    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     N     147     N     147      4    9   14     4    4    5    6    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     I     148     I     148      3    9   14     3    5    6    7    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     149     D     149      3    9   14     3    5    6    7    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     150     V     150      4    9   14     3    4    5    7    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     V     151     V     151      4    9   14     3    5    6    7    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     C     152     C     152      4    9   14     3    5    6    6    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     D     153     D     153      4    9   14     3    4    6    6    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     K     154     K     154      4    9   14     3    3    6    6    8    8   10   10   11   11   11   13   13   13   13   13   13   13   13   13 
LCS_GDT     L     155     L     155      0    4   14     0    0    3    3    4    4    5    5    5    5    6   13   13   13   13   13   13   13   13   13 
LCS_AVERAGE  LCS_A:   5.46  (   2.23    5.06    9.09 )

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      6      7      8      8     10     10     11     11     11     13     13     13     13     13     13     13     13     13 
GDT PERCENT_CA   2.60   3.25   3.90   4.55   5.19   5.19   6.49   6.49   7.14   7.14   7.14   8.44   8.44   8.44   8.44   8.44   8.44   8.44   8.44   8.44
GDT RMS_LOCAL    0.10   0.65   0.87   1.21   1.47   1.47   2.14   2.14   2.68   2.68   2.68   3.85   3.85   3.85   3.85   3.85   3.85   3.85   3.85   3.85
GDT RMS_ALL_CA  13.53   5.96   6.27   7.94   8.18   8.18   6.19   6.19   5.61   5.61   5.61   5.08   5.08   5.08   5.08   5.08   5.08   5.08   5.08   5.08

#      Molecule1      Molecule2       DISTANCE
LGA    R     142      R     142         16.511
LGA    E     143      E     143          9.772
LGA    L     144      L     144          6.969
LGA    N     145      N     145          3.075
LGA    V     146      V     146          1.999
LGA    N     147      N     147          2.750
LGA    I     148      I     148          1.403
LGA    D     149      D     149          0.708
LGA    V     150      V     150          3.147
LGA    V     151      V     151          1.709
LGA    C     152      C     152          1.431
LGA    D     153      D     153          2.047
LGA    K     154      K     154          1.785
LGA    L     155      L     155          8.641

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  154    4.0     10    2.14     5.682     5.775     0.447

LGA_LOCAL      RMSD =  2.138  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.194  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  4.894  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.177864 * X  +   0.036144 * Y  +  -0.983391 * Z  +  29.624611
  Y_new =  -0.145853 * X  +  -0.989256 * Y  +  -0.009980 * Z  +  42.158318
  Z_new =  -0.973186 * X  +   0.141656 * Y  +   0.181225 * Z  +  11.315760 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.663456   -2.478137  [ DEG:    38.0132   -141.9868 ]
  Theta =   1.338699    1.802894  [ DEG:    76.7018    103.2982 ]
  Phi   =  -2.454759    0.686834  [ DEG:  -140.6473     39.3527 ]
 
# 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: T0318TS193_5_2-D1                             
REMARK     2: T0318_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS193_5_2-D1.T0318_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  154   4.0   10   2.14   5.775     4.89
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS193_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1097  N   ARG   142      38.306  41.934   6.799  1.00  0.00
ATOM   1098  CA  ARG   142      37.500  41.506   7.937  1.00  0.00
ATOM   1099  C   ARG   142      36.918  42.701   8.681  1.00  0.00
ATOM   1100  O   ARG   142      35.757  42.686   9.088  1.00  0.00
ATOM   1101  CB  ARG   142      38.348  40.701   8.923  1.00  0.00
ATOM   1102  CG  ARG   142      38.745  39.323   8.419  1.00  0.00
ATOM   1103  CD  ARG   142      39.646  38.610   9.415  1.00  0.00
ATOM   1104  NE  ARG   142      40.060  37.294   8.933  1.00  0.00
ATOM   1105  CZ  ARG   142      40.904  36.495   9.576  1.00  0.00
ATOM   1106  NH1 ARG   142      41.223  35.315   9.062  1.00  0.00
ATOM   1107  NH2 ARG   142      41.430  36.878  10.733  1.00  0.00
ATOM   1108  N   GLU   143      37.733  43.737   8.855  1.00  0.00
ATOM   1109  CA  GLU   143      37.307  44.933   9.572  1.00  0.00
ATOM   1110  C   GLU   143      36.001  45.479   9.008  1.00  0.00
ATOM   1111  O   GLU   143      35.036  45.687   9.743  1.00  0.00
ATOM   1112  CB  GLU   143      38.368  46.030   9.459  1.00  0.00
ATOM   1113  CG  GLU   143      38.018  47.310  10.202  1.00  0.00
ATOM   1114  CD  GLU   143      39.108  48.358  10.101  1.00  0.00
ATOM   1115  OE1 GLU   143      40.153  48.071   9.480  1.00  0.00
ATOM   1116  OE2 GLU   143      38.918  49.467  10.645  1.00  0.00
ATOM   1117  N   LEU   144      35.977  45.707   7.699  1.00  0.00
ATOM   1118  CA  LEU   144      34.780  46.203   7.031  1.00  0.00
ATOM   1119  C   LEU   144      33.607  45.252   7.223  1.00  0.00
ATOM   1120  O   LEU   144      32.479  45.683   7.465  1.00  0.00
ATOM   1121  CB  LEU   144      35.029  46.352   5.529  1.00  0.00
ATOM   1122  CG  LEU   144      36.167  47.288   5.119  1.00  0.00
ATOM   1123  CD1 LEU   144      36.381  47.247   3.614  1.00  0.00
ATOM   1124  CD2 LEU   144      35.852  48.722   5.515  1.00  0.00
ATOM   1125  N   ASN   145      33.900  45.834   9.203  1.00  0.00
ATOM   1126  CA  ASN   145      32.893  46.338  10.128  1.00  0.00
ATOM   1127  C   ASN   145      33.353  47.628  10.794  1.00  0.00
ATOM   1128  O   ASN   145      34.348  47.643  11.519  1.00  0.00
ATOM   1129  CB  ASN   145      32.613  45.311  11.227  1.00  0.00
ATOM   1130  CG  ASN   145      31.404  45.672  12.068  1.00  0.00
ATOM   1131  OD1 ASN   145      30.519  46.400  11.619  1.00  0.00
ATOM   1132  ND2 ASN   145      31.365  45.164  13.294  1.00  0.00
ATOM   1133  N   VAL   146      35.990  46.716  12.747  1.00  0.00
ATOM   1134  CA  VAL   146      35.299  45.445  12.917  1.00  0.00
ATOM   1135  C   VAL   146      35.462  44.913  14.335  1.00  0.00
ATOM   1136  O   VAL   146      36.581  44.731  14.815  1.00  0.00
ATOM   1137  CB  VAL   146      35.845  44.372  11.955  1.00  0.00
ATOM   1138  CG1 VAL   146      35.178  43.031  12.218  1.00  0.00
ATOM   1139  CG2 VAL   146      35.577  44.767  10.511  1.00  0.00
ATOM   1140  N   ASN   147      34.339  44.666  15.001  1.00  0.00
ATOM   1141  CA  ASN   147      34.356  44.154  16.367  1.00  0.00
ATOM   1142  C   ASN   147      33.381  42.995  16.532  1.00  0.00
ATOM   1143  O   ASN   147      32.176  43.153  16.338  1.00  0.00
ATOM   1144  CB  ASN   147      33.959  45.253  17.355  1.00  0.00
ATOM   1145  CG  ASN   147      34.019  44.788  18.797  1.00  0.00
ATOM   1146  OD1 ASN   147      33.263  43.908  19.208  1.00  0.00
ATOM   1147  ND2 ASN   147      34.922  45.380  19.571  1.00  0.00
ATOM   1148  N   ILE   148      33.909  41.831  16.895  1.00  0.00
ATOM   1149  CA  ILE   148      33.085  40.646  17.099  1.00  0.00
ATOM   1150  C   ILE   148      32.911  40.344  18.582  1.00  0.00
ATOM   1151  O   ILE   148      33.830  39.853  19.236  1.00  0.00
ATOM   1152  CB  ILE   148      33.713  39.403  16.443  1.00  0.00
ATOM   1153  CG1 ILE   148      35.085  39.112  17.055  1.00  0.00
ATOM   1154  CG2 ILE   148      33.889  39.621  14.948  1.00  0.00
ATOM   1155  CD1 ILE   148      35.675  37.786  16.628  1.00  0.00
ATOM   1156  N   ASP   149      33.914  38.017  17.938  1.00  0.00
ATOM   1157  CA  ASP   149      32.888  37.301  18.687  1.00  0.00
ATOM   1158  C   ASP   149      33.459  36.056  19.351  1.00  0.00
ATOM   1159  O   ASP   149      33.973  35.162  18.678  1.00  0.00
ATOM   1160  CB  ASP   149      31.752  36.866  17.759  1.00  0.00
ATOM   1161  CG  ASP   149      30.592  36.243  18.509  1.00  0.00
ATOM   1162  OD1 ASP   149      30.715  36.050  19.738  1.00  0.00
ATOM   1163  OD2 ASP   149      29.561  35.947  17.871  1.00  0.00
ATOM   1164  N   VAL   150      33.366  36.001  20.675  1.00  0.00
ATOM   1165  CA  VAL   150      33.776  34.819  21.424  1.00  0.00
ATOM   1166  C   VAL   150      32.642  34.304  22.303  1.00  0.00
ATOM   1167  O   VAL   150      32.087  35.045  23.115  1.00  0.00
ATOM   1168  CB  VAL   150      34.975  35.120  22.341  1.00  0.00
ATOM   1169  CG1 VAL   150      36.225  35.380  21.516  1.00  0.00
ATOM   1170  CG2 VAL   150      34.698  36.348  23.195  1.00  0.00
ATOM   1171  N   VAL   151      31.022  33.329  24.105  1.00  0.00
ATOM   1172  CA  VAL   151      30.774  32.616  22.856  1.00  0.00
ATOM   1173  C   VAL   151      29.824  31.445  23.070  1.00  0.00
ATOM   1174  O   VAL   151      29.722  30.909  24.173  1.00  0.00
ATOM   1175  CB  VAL   151      32.078  32.053  22.261  1.00  0.00
ATOM   1176  CG1 VAL   151      31.771  31.078  21.134  1.00  0.00
ATOM   1177  CG2 VAL   151      32.938  33.177  21.702  1.00  0.00
ATOM   1178  N   CYS   152      29.131  31.052  22.007  1.00  0.00
ATOM   1179  CA  CYS   152      28.244  29.894  22.056  1.00  0.00
ATOM   1180  C   CYS   152      28.547  28.921  20.924  1.00  0.00
ATOM   1181  O   CYS   152      28.603  29.309  19.757  1.00  0.00
ATOM   1182  CB  CYS   152      26.784  30.332  21.929  1.00  0.00
ATOM   1183  SG  CYS   152      26.203  31.397  23.268  1.00  0.00
ATOM   1184  N   ASP   153      28.741  27.654  21.274  1.00  0.00
ATOM   1185  CA  ASP   153      29.061  26.626  20.291  1.00  0.00
ATOM   1186  C   ASP   153      27.871  26.348  19.381  1.00  0.00
ATOM   1187  O   ASP   153      26.724  26.340  19.827  1.00  0.00
ATOM   1188  CB  ASP   153      29.442  25.319  20.988  1.00  0.00
ATOM   1189  CG  ASP   153      30.057  24.311  20.037  1.00  0.00
ATOM   1190  OD1 ASP   153      30.373  24.691  18.890  1.00  0.00
ATOM   1191  OD2 ASP   153      30.223  23.139  20.439  1.00  0.00
ATOM   1192  N   LYS   154      27.929  24.884  21.049  1.00  0.00
ATOM   1193  CA  LYS   154      26.851  23.908  21.159  1.00  0.00
ATOM   1194  C   LYS   154      25.728  24.424  22.050  1.00  0.00
ATOM   1195  O   LYS   154      24.557  24.114  21.832  1.00  0.00
ATOM   1196  CB  LYS   154      27.372  22.601  21.760  1.00  0.00
ATOM   1197  CG  LYS   154      27.748  22.700  23.230  1.00  0.00
ATOM   1198  CD  LYS   154      28.365  21.404  23.731  1.00  0.00
ATOM   1199  CE  LYS   154      28.819  21.532  25.175  1.00  0.00
ATOM   1200  NZ  LYS   154      29.401  20.261  25.689  1.00  0.00
ATOM   1201  N   LEU   155      25.592  22.298  22.664  1.00  0.00
ATOM   1202  CA  LEU   155      24.369  21.514  22.778  1.00  0.00
ATOM   1203  C   LEU   155      23.388  22.160  23.748  1.00  0.00
ATOM   1204  O   LEU   155      22.174  22.004  23.616  1.00  0.00
ATOM   1205  CB  LEU   155      24.680  20.105  23.287  1.00  0.00
ATOM   1206  CG  LEU   155      25.452  19.194  22.331  1.00  0.00
ATOM   1207  CD1 LEU   155      25.837  17.894  23.020  1.00  0.00
ATOM   1208  CD2 LEU   155      24.607  18.854  21.112  1.00  0.00
TER
END
