
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   38 (  302),  selected   37 , name one
# Molecule2: number of CA atoms   37 (  291),  selected   37 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       2_B - 38_B        3.82     3.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33       6_B - 38_B        1.89     4.58
  LCS_AVERAGE:     80.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        0.47     4.81
  LCS_AVERAGE:     71.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   37
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     A     2_C     A     2_B      3    3   37      0    3    3    3    3    4    4    8    9    9   11   13   14   16   21   22   24   27   31   32 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3    3    4    5   16   19   24   28   31   35   35   35   35   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    3    3    3    6    6    8   20   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    4    6    8   12   20   27   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   33   37      3    3    3    4    8   16   23   29   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     31   33   37     10   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     31   33   37     21   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     31   33   37     22   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     31   33   37     23   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     31   33   37     24   31   31   31   31   31   31   31   33   34   34   34   35   35   35   35   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   33   37      3    3    3    3    4    4    6    7    9   19   25   32   32   32   34   35   36   36   36   36 
LCS_AVERAGE  LCS_A:  83.98  (  71.51   80.42  100.00 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     24     31     31     31     31     31     31     31     33     34     34     34     35     35     35     35     36     36     36     36 
GDT PERCENT_AT  64.86  83.78  83.78  83.78  83.78  83.78  83.78  83.78  89.19  91.89  91.89  91.89  94.59  94.59  94.59  94.59  97.30  97.30  97.30  97.30
GDT RMS_LOCAL    0.36   0.47   0.47   0.47   0.47   0.47   0.47   0.47   1.99   2.40   2.40   2.40   2.86   2.86   2.86   2.70   3.12   3.12   3.12   3.12
GDT RMS_ALL_AT   4.94   4.81   4.81   4.81   4.81   4.81   4.81   4.81   4.21   4.02   4.02   4.02   3.89   3.89   3.89   4.05   3.90   3.90   3.90   3.90

# Checking swapping
#   possible swapping detected:  E     5_C      E     5_B
#   possible swapping detected:  D     9_C      D     9_B
#   possible swapping detected:  E    21_C      E    21_B
#   possible swapping detected:  E    31_C      E    31_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_C      A     2_B    18.598     0    0.446   0.438    20.161    0.000    0.000
LGA    E     3_C      E     3_B    12.975     0    0.600   1.017    14.829    0.000    0.000
LGA    A     4_C      A     4_B     9.984     0    0.630   0.585    11.206    0.119    0.095
LGA    E     5_C      E     5_B    10.739     0    0.603   0.755    13.927    0.714    0.317
LGA    Q     6_C      Q     6_B     7.721     0    0.600   1.270    15.435   14.048    6.561
LGA    E     7_C      E     7_B     0.489     0    0.584   0.960     8.237   82.738   51.217
LGA    K     8_C      K     8_B     0.655     0    0.060   1.369     7.366   92.857   67.460
LGA    D     9_C      D     9_B     0.828     0    0.053   0.178     2.461   90.476   81.726
LGA    Q    10_C      Q    10_B     0.700     0    0.062   0.419     2.222   90.476   84.603
LGA    L    11_C      L    11_B     0.326     0    0.010   0.056     0.752  100.000   96.429
LGA    R    12_C      R    12_B     0.464     0    0.015   0.381     1.848  100.000   88.268
LGA    T    13_C      T    13_B     0.319     0    0.019   0.935     2.629  100.000   88.639
LGA    Q    14_C      Q    14_B     0.453     0    0.014   0.755     3.921  100.000   81.905
LGA    V    15_C      V    15_B     0.455     0    0.021   0.057     0.736  100.000   95.918
LGA    V    16_C      V    16_B     0.366     0    0.018   0.111     0.685  100.000   98.639
LGA    R    17_C      R    17_B     0.148     0    0.051   1.530     8.209  100.000   66.710
LGA    L    18_C      L    18_B     0.318     0    0.013   0.082     0.672  100.000   97.619
LGA    Q    19_C      Q    19_B     0.410     0    0.019   0.178     0.868  100.000   95.767
LGA    A    20_C      A    20_B     0.374     0    0.074   0.084     0.587   97.619   98.095
LGA    E    21_C      E    21_B     0.339     0    0.015   0.114     1.028   95.238   93.704
LGA    K    22_C      K    22_B     0.617     0    0.024   0.122     1.018   90.476   89.471
LGA    A    23_C      A    23_B     0.621     0    0.025   0.033     0.673   90.476   90.476
LGA    D    24_C      D    24_B     0.432     0    0.028   0.270     1.534  100.000   95.417
LGA    L    25_C      L    25_B     0.447     0    0.010   0.053     0.622  100.000   96.429
LGA    L    26_C      L    26_B     0.354     0    0.040   0.088     0.811  100.000   96.429
LGA    G    27_C      G    27_B     0.441     0    0.089   0.089     0.444  100.000  100.000
LGA    I    28_C      I    28_B     0.394     0    0.025   0.086     0.566  100.000   97.619
LGA    V    29_C      V    29_B     0.277     0    0.035   0.054     0.517  100.000   98.639
LGA    S    30_C      S    30_B     0.260     0    0.028   0.125     0.743  100.000   98.413
LGA    E    31_C      E    31_B     0.335     0    0.015   0.897     4.739  100.000   76.349
LGA    L    32_C      L    32_B     0.190     0    0.007   0.043     0.568  100.000   98.810
LGA    Q    33_C      Q    33_B     0.535     0    0.037   1.047     3.027   92.857   85.079
LGA    L    34_C      L    34_B     0.669     0    0.056   0.203     1.128   90.476   89.345
LGA    K    35_C      K    35_B     0.517     0    0.026   0.500     2.435   92.857   89.788
LGA    L    36_C      L    36_B     0.541     0    0.052   0.081     0.559   90.476   92.857
LGA    N    37_C      N    37_B     0.518     0    0.322   0.833     6.614   68.571   51.488
LGA    S    38_C      S    38_B     7.719     0    0.609   0.790     9.694   10.714    7.460

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       37     148    148  100.00     291    291  100.00                37
SUMMARY(RMSD_GDC):     3.816          3.727                  4.250           80.843   74.263

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    0.47    86.486    85.563     5.441

LGA_LOCAL      RMSD:   0.470  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.808  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   3.816  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.832161 * X  +  -0.497930 * Y  +   0.244079 * Z  + -12.519794
  Y_new =  -0.102534 * X  +  -0.294400 * Y  +  -0.950166 * Z  +  33.422302
  Z_new =   0.544973 * X  +  -0.815717 * Y  +   0.193933 * Z  + -38.020775 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.018996 -0.576357 -1.337384   [DEG: -172.9757  -33.0228  -76.6265 ]
ZXZ:  0.251444  1.375627  2.552605   [DEG:   14.4067   78.8176  146.2535 ]
 
# END of job
