
#######################################################
#                                                     #
#                        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   47 (  365),  selected   47 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   47 , 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:    29      25_A - 53_A        4.99    11.90
  LONGEST_CONTINUOUS_SEGMENT:    29      26_A - 54_A        4.91    12.78
  LONGEST_CONTINUOUS_SEGMENT:    29      29_A - 57_A        4.95    14.30
  LONGEST_CONTINUOUS_SEGMENT:    29      30_A - 58_A        4.93    15.16
  LCS_AVERAGE:     45.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      27_A - 46_A        1.98    13.30
  LCS_AVERAGE:     27.77

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      30_A - 43_A        0.82    13.52
  LONGEST_CONTINUOUS_SEGMENT:    14      45_A - 58_A        0.78    20.20
  LCS_AVERAGE:     19.33

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   47
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    12_A     A    12_A     10   14   22      7   10   10   10   14   14   14   14   16   18   20   21   23   25   27   31   31   34   35   35 
LCS_GDT     V    13_A     V    13_A     10   14   22      7   10   10   10   14   14   14   14   16   17   17   18   20   21   27   31   31   34   35   35 
LCS_GDT     K    14_A     K    14_A     10   14   22      7   10   10   10   14   14   14   14   16   17   17   22   23   26   27   30   31   34   35   35 
LCS_GDT     A    15_A     A    15_A     10   14   22      7   10   10   10   14   14   14   14   16   18   20   22   23   26   27   31   31   34   35   35 
LCS_GDT     R    16_A     R    16_A     10   14   22      7   10   10   10   14   14   14   14   16   18   20   22   23   26   27   31   31   34   35   35 
LCS_GDT     V    17_A     V    17_A     10   14   22      7   10   10   10   14   14   14   14   16   18   20   22   23   26   27   31   31   34   35   35 
LCS_GDT     E    18_A     E    18_A     10   14   22      7   10   10   10   14   14   14   14   16   17   18   22   23   26   27   30   31   34   35   35 
LCS_GDT     K    19_A     K    19_A     10   14   22      6   10   10   10   14   14   14   14   16   17   18   21   23   25   27   30   31   34   35   35 
LCS_GDT     L    20_A     L    20_A     10   14   24      5   10   10   10   14   14   14   14   16   18   21   22   23   26   27   31   31   34   35   35 
LCS_GDT     A    21_A     A    21_A     10   14   24      5   10   10   10   14   14   14   14   16   18   21   22   23   26   27   31   31   34   35   35 
LCS_GDT     P    22_A     P    22_A      5   14   24      4    5    5    9   14   14   14   14   16   17   21   22   23   25   27   30   31   34   35   35 
LCS_GDT     E    23_A     E    23_A      5   14   24      4    5    5    9   14   14   14   14   16   18   20   22   23   26   27   31   31   34   35   35 
LCS_GDT     A    24_A     A    24_A      5   14   27      4    5    5    9   14   14   14   14   16   18   21   22   23   26   27   31   31   34   35   35 
LCS_GDT     V    25_A     V    25_A      5   14   29      3    4    5    9   14   14   14   14   16   18   21   22   23   26   27   31   31   34   35   35 
LCS_GDT     P    26_A     P    26_A      5    7   29      3    4    5    8   10   12   15   17   20   22   22   23   25   26   27   31   31   34   35   35 
LCS_GDT     Q    27_A     Q    27_A      5   20   29      3    4    5    5    9   15   17   19   21   22   22   23   26   27   27   28   28   30   32   34 
LCS_GDT     K    28_A     K    28_A      5   20   29      3    5   15   16   17   18   19   20   21   22   22   23   26   27   27   28   28   30   32   32 
LCS_GDT     L    29_A     L    29_A      5   20   29      3    4    5   11   16   16   18   20   21   22   22   23   25   27   27   28   28   30   32   34 
LCS_GDT     K    30_A     K    30_A     14   20   29      4   12   15   16   17   18   19   20   21   22   22   24   26   27   27   31   31   33   35   35 
LCS_GDT     R    31_A     R    31_A     14   20   29      4    6   15   16   17   18   19   20   21   22   22   24   26   27   27   31   31   34   35   35 
LCS_GDT     A    32_A     A    32_A     14   20   29      4   12   15   16   17   18   19   20   21   22   22   24   26   27   27   31   31   34   35   35 
LCS_GDT     L    33_A     L    33_A     14   20   29      4   10   15   16   17   18   19   20   21   22   22   24   26   27   27   31   31   34   35   35 
LCS_GDT     K    34_A     K    34_A     14   20   29     10   12   15   16   17   18   19   20   21   22   22   24   26   27   27   31   31   34   35   35 
LCS_GDT     I    35_A     I    35_A     14   20   29     10   12   15   16   17   18   19   20   21   22   22   24   26   27   27   31   31   34   35   35 
LCS_GDT     A    36_A     A    36_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     E    37_A     E    37_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     R    38_A     R    38_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     E    39_A     E    39_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     Q    40_A     Q    40_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     G    41_A     G    41_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     E    42_A     E    42_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     G    43_A     G    43_A     14   20   29     10   12   15   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     E    44_A     E    44_A     13   20   29      4    5   11   14   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     F    45_A     F    45_A     14   20   29      4    9   14   16   17   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     D    46_A     D    46_A     14   20   29      7   11   14   14   16   17   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     E    47_A     E    47_A     14   15   29      9   12   14   14   14   15   15   16   19   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     C    48_A     C    48_A     14   15   29      9   12   14   14   14   15   15   15   19   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     L    49_A     L    49_A     14   15   29      9   12   14   14   16   18   19   20   21   22   23   24   26   27   27   31   31   34   35   35 
LCS_GDT     E    50_A     E    50_A     14   15   29      7   12   14   14   14   15   15   16   19   22   23   24   26   27   27   28   30   32   33   34 
LCS_GDT     A    51_A     A    51_A     14   15   29      8   12   14   14   14   15   15   15   19   22   23   23   24   25   27   27   28   29   30   34 
LCS_GDT     L    52_A     L    52_A     14   15   29      9   12   14   14   14   15   15   15   19   22   23   24   26   27   27   28   30   32   33   34 
LCS_GDT     D    53_A     D    53_A     14   15   29      9   12   14   14   14   15   15   16   19   22   23   24   26   27   27   28   29   30   32   34 
LCS_GDT     D    54_A     D    54_A     14   15   29      9   12   14   14   14   15   15   15   19   22   23   23   24   25   27   27   28   29   30   31 
LCS_GDT     A    55_A     A    55_A     14   15   29      9   12   14   14   14   15   15   15   19   22   23   23   24   25   25   26   28   29   30   31 
LCS_GDT     K    56_A     K    56_A     14   15   29      9   12   14   14   14   15   15   16   19   22   23   24   26   27   27   28   28   29   30   31 
LCS_GDT     R    57_A     R    57_A     14   15   29      9   12   14   14   14   15   15   16   19   22   23   24   25   25   27   28   28   29   30   31 
LCS_GDT     A    58_A     A    58_A     14   15   29      8   12   14   14   14   15   15   15   19   22   23   23   24   25   25   26   28   29   29   30 
LCS_AVERAGE  LCS_A:  30.89  (  19.33   27.77   45.57 )

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     10     12     15     16     17     18     19     20     21     22     23     24     26     27     27     31     31     34     35     35 
GDT PERCENT_AT  16.67  20.00  25.00  26.67  28.33  30.00  31.67  33.33  35.00  36.67  38.33  40.00  43.33  45.00  45.00  51.67  51.67  56.67  58.33  58.33
GDT RMS_LOCAL    0.29   0.42   0.92   1.09   1.22   1.43   1.69   1.88   2.07   2.55   3.78   3.62   3.84   3.97   3.97   5.75   5.52   6.04   6.16   6.16
GDT RMS_ALL_AT  13.21  20.91  13.55  13.54  13.47  13.47  13.43  13.46  13.26  12.74  16.32  13.61  13.30  13.26  13.26  10.86  11.21  11.18  11.26  11.26

# Checking swapping
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  D    46_A      D    46_A
#   possible swapping detected:  D    53_A      D    53_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    12_A      A    12_A    17.635     0    0.064   0.067    18.448    0.000    0.000
LGA    V    13_A      V    13_A    17.890     0    0.017   0.027    19.449    0.000    0.000
LGA    K    14_A      K    14_A    22.209     0    0.018   0.222    28.692    0.000    0.000
LGA    A    15_A      A    15_A    22.392     0    0.026   0.030    23.098    0.000    0.000
LGA    R    16_A      R    16_A    19.853     0    0.014   1.470    22.318    0.000    0.000
LGA    V    17_A      V    17_A    21.595     0    0.032   0.083    23.929    0.000    0.000
LGA    E    18_A      E    18_A    26.278     0    0.129   1.049    30.706    0.000    0.000
LGA    K    19_A      K    19_A    25.761     0    0.036   1.040    26.597    0.000    0.000
LGA    L    20_A      L    20_A    23.282     0    0.033   1.369    25.795    0.000    0.000
LGA    A    21_A      A    21_A    25.956     0    0.132   0.185    26.740    0.000    0.000
LGA    P    22_A      P    22_A    24.758     0    0.044   0.088    28.720    0.000    0.000
LGA    E    23_A      E    23_A    21.571     0    0.057   0.797    28.097    0.000    0.000
LGA    A    24_A      A    24_A    19.181     0    0.592   0.551    20.886    0.000    0.000
LGA    V    25_A      V    25_A    14.814     0    0.125   0.172    18.071    0.000    0.000
LGA    P    26_A      P    26_A     8.427     0    0.150   0.165    13.071    5.714    3.469
LGA    Q    27_A      Q    27_A     4.628     0    0.621   1.633     9.806   34.286   25.026
LGA    K    28_A      K    28_A     2.173     0    0.194   1.140     4.016   59.167   58.624
LGA    L    29_A      L    29_A     3.865     0    0.049   0.918     7.693   46.667   31.071
LGA    K    30_A      K    30_A     1.315     0    0.197   0.206     2.296   79.286   79.683
LGA    R    31_A      R    31_A     1.567     0    0.073   1.218     3.608   77.143   72.511
LGA    A    32_A      A    32_A     1.051     0    0.124   0.131     1.212   81.429   83.238
LGA    L    33_A      L    33_A     1.589     0    0.498   1.362     4.760   67.619   62.083
LGA    K    34_A      K    34_A     0.498     0    0.006   0.261     2.627   97.619   86.085
LGA    I    35_A      I    35_A     0.189     0    0.019   0.071     0.384  100.000  100.000
LGA    A    36_A      A    36_A     0.462     0    0.038   0.044     0.717  100.000   98.095
LGA    E    37_A      E    37_A     0.437     0    0.018   0.143     0.801   95.238   96.825
LGA    R    38_A      R    38_A     0.732     0    0.018   1.305     5.696   90.476   73.290
LGA    E    39_A      E    39_A     0.719     0    0.018   0.148     1.348   90.476   87.460
LGA    Q    40_A      Q    40_A     0.819     0    0.031   0.648     3.964   90.476   73.333
LGA    G    41_A      G    41_A     0.835     0    0.066   0.066     1.040   88.214   88.214
LGA    E    42_A      E    42_A     0.312     0    0.025   0.179     0.495  100.000  100.000
LGA    G    43_A      G    43_A     0.295     0    0.044   0.044     1.457   90.714   90.714
LGA    E    44_A      E    44_A     2.418     0    0.461   0.410     4.776   56.548   51.534
LGA    F    45_A      F    45_A     2.947     0    0.190   1.178    11.076   66.905   29.697
LGA    D    46_A      D    46_A     3.876     0    0.079   0.988     8.184   38.929   24.345
LGA    E    47_A      E    47_A     8.060     0    0.096   1.152    12.566    8.095    3.757
LGA    C    48_A      C    48_A     7.769     0    0.020   0.832    11.055   11.190    8.254
LGA    L    49_A      L    49_A     3.187     0    0.007   0.105     5.156   34.881   39.524
LGA    E    50_A      E    50_A     9.157     0    0.018   1.366    14.222    3.690    1.640
LGA    A    51_A      A    51_A    12.633     0    0.028   0.030    13.720    0.000    0.000
LGA    L    52_A      L    52_A     8.942     0    0.052   0.089    11.456    2.738    3.393
LGA    D    53_A      D    53_A     7.869     0    0.022   1.324    10.711    3.571    3.750
LGA    D    54_A      D    54_A    14.959     0    0.025   0.098    18.157    0.000    0.000
LGA    A    55_A      A    55_A    15.514     0    0.058   0.067    15.607    0.000    0.000
LGA    K    56_A      K    56_A    10.143     0    0.036   0.898    11.595    0.000   24.656
LGA    R    57_A      R    57_A    13.481     0    0.069   1.286    17.634    0.000    0.000
LGA    A    58_A      A    58_A    19.242     0    0.102   0.108    20.840    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       47     188    188  100.00     365    365  100.00                60
SUMMARY(RMSD_GDC):     9.257          9.223                 10.084           27.018   25.005

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   47   60    4.0     20    1.88    32.917    31.576     1.012

LGA_LOCAL      RMSD:   1.877  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.460  Number of assigned atoms:   47 
Std_ASGN_ATOMS RMSD:   9.257  Standard rmsd on all 47 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.968133 * X  +  -0.214066 * Y  +   0.129978 * Z  +  16.683813
  Y_new =  -0.229520 * X  +  -0.550771 * Y  +   0.802478 * Z  +   7.443104
  Z_new =  -0.100195 * X  +  -0.806738 * Y  +  -0.582352 * Z  + -12.830624 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.232777  0.100364 -2.196044   [DEG:  -13.3372    5.7504 -125.8240 ]
ZXZ:  2.981017  2.192416 -3.018027   [DEG:  170.7997  125.6162 -172.9202 ]
 
# END of job
