
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30       6_A - 35_A        4.96     7.81
  LCS_AVERAGE:     82.86

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       3_A - 16_A        1.39    11.76
  LCS_AVERAGE:     28.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       4_A - 13_A        0.96    10.93
  LONGEST_CONTINUOUS_SEGMENT:    10       6_A - 15_A        0.83    12.06
  LCS_AVERAGE:     18.04

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     S     1_A     S     1_A      3    4   23      3    3    4    4    5    6    8   11   14   18   20   22   22   23   24   24   25   26   29   29 
LCS_GDT     D     2_A     D     2_A      3    4   23      3    3    4    4    4    5   10   11   14   18   20   22   22   23   24   24   26   29   30   32 
LCS_GDT     E     3_A     E     3_A      8   14   23      4    5    8   11   15   15   16   18   21   22   23   23   24   25   26   28   29   30   31   32 
LCS_GDT     M     4_A     M     4_A     10   14   23      4    8   11   13   15   17   18   19   21   22   23   24   25   27   28   29   29   30   31   32 
LCS_GDT     W     5_A     W     5_A     10   14   23      4    5    9   13   15   15   16   19   21   22   23   24   25   27   28   29   29   30   31   32 
LCS_GDT     F     6_A     F     6_A     10   14   30      6    8   11   13   15   17   18   19   21   22   23   24   25   27   28   29   29   30   31   32 
LCS_GDT     C     7_A     C     7_A     10   14   30      3    8   11   13   15   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     E     8_A     E     8_A     10   14   30      6    8   11   13   15   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     T     9_A     T     9_A     10   14   30      6    8   11   13   15   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     L    10_A     L    10_A     10   14   30      6    8   11   13   15   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     R    11_A     R    11_A     10   14   30      6    8   11   13   15   16   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     R    12_A     R    12_A     10   14   30      6    8   11   13   15   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     L    13_A     L    13_A     10   14   30      4    8   11   13   15   15   16   17   20   22   25   25   25   26   28   29   29   30   31   32 
LCS_GDT     L    14_A     L    14_A     10   14   30      4    8   11   13   15   15   16   16   18   19   21   24   25   26   26   29   29   30   31   32 
LCS_GDT     C    15_A     C    15_A     10   14   30      3    7   11   13   15   15   16   16   18   19   20   24   25   26   26   29   29   30   31   32 
LCS_GDT     P    16_A     P    16_A      6   14   30      3    5   10   11   15   15   16   16   20   21   23   24   25   26   27   29   29   30   31   32 
LCS_GDT     K    17_A     K    17_A      3    7   30      3    4    4   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     S    18_A     S    18_A      4    7   30      3    4    7   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     C    19_A     C    19_A      4    7   30      3    4    5    9   12   16   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     S    20_A     S    20_A      4    7   30      3    4    4    6   10   13   15   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     I    21_A     I    21_A      4    7   30      3    4    4    7    9   12   15   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     E    22_A     E    22_A      3    6   30      3    3    4    7    9   12   15   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     G    23_A     G    23_A      4    6   30      3    4    5    5    6   10   12   17   21   21   22   24   25   26   27   29   29   30   31   32 
LCS_GDT     G    24_A     G    24_A      4    6   30      3    4    4    7    9   13   15   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     C    25_A     C    25_A      4    9   30      3    4    4    7   11   14   17   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     P    26_A     P    26_A      5    9   30      3    4    6    9   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     E    27_A     E    27_A      5    9   30      3    4    7   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     V    28_A     V    28_A      5    9   30      4    4    7   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     C    29_A     C    29_A      5    9   30      4    4    7   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     S    30_A     S    30_A      5    9   30      3    4    7   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     H    31_A     H    31_A      5    9   30      3    4    6   11   13   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     M    32_A     M    32_A      5    9   30      3    4    6    8   10   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     C    33_A     C    33_A      5    9   30      3    4    9   11   14   17   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     P    34_A     P    34_A      4    9   30      0    3    5   13   15   15   18   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_GDT     L    35_A     L    35_A      3    6   30      0    5    5    6    9   11   15   19   21   22   25   25   25   27   28   29   29   30   31   32 
LCS_AVERAGE  LCS_A:  43.24  (  18.04   28.82   82.86 )

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      6      8     11     13     15     17     18     19     21     22     25     25     25     27     28     29     29     30     31     32 
GDT PERCENT_AT  17.14  22.86  31.43  37.14  42.86  48.57  51.43  54.29  60.00  62.86  71.43  71.43  71.43  77.14  80.00  82.86  82.86  85.71  88.57  91.43
GDT RMS_LOCAL    0.22   0.49   1.02   1.20   1.47   2.27   2.35   2.44   3.11   3.22   3.64   3.64   3.64   4.19   4.36   4.54   4.54   4.81   5.11   5.41
GDT RMS_ALL_AT  10.83  11.11  11.84  11.87  11.66   7.07   6.97   7.01   8.08   7.89   7.81   7.81   7.81   7.08   7.07   7.17   7.17   6.99   6.91   7.14

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E    27_A      E    27_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A    17.249     0    0.226   0.689    19.121    0.000    0.000
LGA    D     2_A      D     2_A    12.832     0    0.668   1.189    16.263    0.714    0.357
LGA    E     3_A      E     3_A     7.193     0    0.558   1.284    10.931   18.690    8.889
LGA    M     4_A      M     4_A     3.537     0    0.045   0.944     7.504   43.810   31.786
LGA    W     5_A      W     5_A     5.049     0    0.068   1.422    13.714   39.524   12.755
LGA    F     6_A      F     6_A     3.092     0    0.079   1.001     6.230   57.738   40.996
LGA    C     7_A      C     7_A     1.704     0    0.078   0.670     2.130   75.238   75.873
LGA    E     8_A      E     8_A     1.421     0    0.084   1.057     6.278   85.952   56.561
LGA    T     9_A      T     9_A     0.607     0    0.022   0.260     2.611   84.048   75.850
LGA    L    10_A      L    10_A     3.095     0    0.028   0.059     4.765   50.476   44.643
LGA    R    11_A      R    11_A     3.632     0    0.077   1.248     9.137   43.810   29.957
LGA    R    12_A      R    12_A     2.838     0    0.088   1.366     4.166   48.690   58.615
LGA    L    13_A      L    13_A     5.148     0    0.107   0.907     7.759   22.500   21.012
LGA    L    14_A      L    14_A     8.866     0    0.162   0.925    12.631    3.571    1.905
LGA    C    15_A      C    15_A     8.969     0    0.541   0.926     9.396    4.881    3.968
LGA    P    16_A      P    16_A     6.651     0    0.602   0.801    10.268   20.952   12.721
LGA    K    17_A      K    17_A     2.340     0    0.108   0.769    11.546   57.857   34.286
LGA    S    18_A      S    18_A     1.814     0    0.661   0.798     4.712   62.976   61.746
LGA    C    19_A      C    19_A     3.312     0    0.074   0.777     7.211   36.548   46.032
LGA    S    20_A      S    20_A     8.802     0    0.031   0.653    12.325    5.000    3.413
LGA    I    21_A      I    21_A    11.128     0    0.560   0.726    13.239    0.357    0.417
LGA    E    22_A      E    22_A    13.020     0    0.636   0.962    13.780    0.000    0.000
LGA    G    23_A      G    23_A    13.741     0    0.572   0.572    13.741    0.000    0.000
LGA    G    24_A      G    24_A    10.188     0    0.150   0.150    10.921    1.071    1.071
LGA    C    25_A      C    25_A     6.589     0    0.614   0.884     8.077   15.000   13.016
LGA    P    26_A      P    26_A     2.652     0    0.649   0.676     2.949   65.000   68.639
LGA    E    27_A      E    27_A     2.152     0    0.145   1.042     8.487   68.810   42.169
LGA    V    28_A      V    28_A     2.191     0    0.030   1.119     5.145   68.810   60.476
LGA    C    29_A      C    29_A     1.366     0    0.360   0.960     1.755   77.143   78.571
LGA    S    30_A      S    30_A     1.941     0    0.075   0.127     3.011   79.405   70.794
LGA    H    31_A      H    31_A     1.904     0    0.378   1.303     5.056   65.595   56.571
LGA    M    32_A      M    32_A     2.891     0    0.151   1.054     4.782   56.071   48.393
LGA    C    33_A      C    33_A     1.117     0    0.337   0.405     2.932   69.286   70.794
LGA    P    34_A      P    34_A     5.989     0    0.609   0.636     8.712   17.857   17.619
LGA    L    35_A      L    35_A     9.624     0    0.379   1.458    14.387    3.333    1.667

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     6.628          6.516                  7.042           38.592   32.902

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     19    2.44    49.286    46.189     0.748

LGA_LOCAL      RMSD:   2.441  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   7.006  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   6.628  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.243192 * X  +  -0.918185 * Y  +   0.312720 * Z  +   4.444936
  Y_new =   0.702308 * X  +  -0.389055 * Y  +  -0.596153 * Z  +   4.448896
  Z_new =   0.669044 * X  +   0.074646 * Y  +   0.739464 * Z  +  -9.835661 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.904149 -0.732922  0.100605   [DEG:  109.0997  -41.9933    5.7642 ]
ZXZ:  0.483104  0.738522  1.459685   [DEG:   27.6798   42.3142   83.6338 ]
 
# END of job
