
#######################################################
#                                                     #
#                        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   50 (  424),  selected   45 , name one
# Molecule2: number of CA atoms   76 (  680),  selected   45 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32      27_B - 58_B        4.98    12.45
  LCS_AVERAGE:     39.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      37_B - 58_B        1.79    14.96
  LCS_AVERAGE:     22.54

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      41_B - 58_B        0.83    14.96
  LCS_AVERAGE:     17.98

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   45
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     E    21_B     E    21_B     15   15   19      8   13   14   15   15   15   15   15   15   16   16   17   18   19   20   21   22   22   23   24 
LCS_GDT     E    22_B     E    22_B     15   15   19      8   13   14   15   15   15   15   15   15   16   16   17   18   19   20   21   22   24   25   26 
LCS_GDT     L    23_B     L    23_B     15   15   19      8   13   14   15   15   15   15   15   15   16   16   17   18   19   20   21   22   22   23   24 
LCS_GDT     K    24_B     K    24_B     15   15   19      8   13   14   15   15   15   15   15   15   16   16   17   18   19   20   21   22   22   23   26 
LCS_GDT     K    25_B     K    25_B     15   15   19      8   13   14   15   15   15   15   15   15   16   16   17   18   19   20   22   25   25   29   31 
LCS_GDT     I    26_B     I    26_B     15   15   19      8   13   14   15   15   15   15   15   15   16   16   17   18   19   22   23   29   31   33   33 
LCS_GDT     R    27_B     R    27_B     15   15   32      8   13   14   15   15   15   15   15   15   16   16   17   18   19   20   23   29   31   33   33 
LCS_GDT     E    28_B     E    28_B     15   15   32      8   13   14   15   15   15   15   15   15   16   16   17   19   24   27   28   31   31   33   33 
LCS_GDT     R    29_B     R    29_B     15   15   32      8   13   14   15   15   15   15   15   15   16   22   24   26   29   30   30   31   31   33   33 
LCS_GDT     L    30_B     L    30_B     15   15   32      6   13   14   15   15   15   15   15   23   26   27   29   29   29   30   30   31   31   33   33 
LCS_GDT     L    31_B     L    31_B     15   15   32      4   13   14   15   15   15   15   23   25   26   28   29   29   29   30   30   31   31   33   34 
LCS_GDT     M    32_B     M    32_B     15   15   32      3    5   14   15   15   15   16   23   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     V    33_B     V    33_B     15   15   32      6   13   14   15   15   15   21   24   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     F    34_B     F    34_B     15   15   32      5   13   14   15   18   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     D    35_B     D    35_B     15   17   32      5    6   13   15   15   20   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    36_B     E    36_B      7   17   32      5    6   10   10   14   19   22   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    37_B     E    37_B      7   22   32      5    6   10   10   14   18   22   25   25   26   28   29   29   29   30   30   31   31   33   34 
LCS_GDT     R    38_B     R    38_B      7   22   32      5    6   12   19   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     V    39_B     V    39_B      7   22   32      5    9   15   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    40_B     E    40_B      7   22   32      5    9   16   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    41_B     E    41_B     18   22   32      5    6   10   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     Y    42_B     Y    42_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     M    43_B     M    43_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     K    44_B     K    44_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     I    45_B     I    45_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     M    46_B     M    46_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     K    47_B     K    47_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    48_B     E    48_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     V    49_B     V    49_B     18   22   32     13   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     I    50_B     I    50_B     18   22   32     13   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    51_B     E    51_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     K    52_B     K    52_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     I    53_B     I    53_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     L    54_B     L    54_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     E    55_B     E    55_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     N    56_B     N    56_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     R    57_B     R    57_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     K    58_B     K    58_B     18   22   32     15   17   17   20   21   22   23   25   25   26   28   29   29   29   30   30   31   32   33   34 
LCS_GDT     K    64_B     K    64_B      5    7   31      4    5    5    6    7    9   12   13   15   19   23   24   26   28   28   29   30   32   33   34 
LCS_GDT     V    65_B     V    65_B      5    7   31      4    5    5    6    7    9   12   13   15   19   23   24   26   28   28   29   30   32   33   34 
LCS_GDT     E    66_B     E    66_B      5    7   31      4    5    5    6    7    9   12   13   14   17   20   22   23   26   27   29   30   32   33   34 
LCS_GDT     I    67_B     I    67_B      5    7   31      4    5    5    6    7    9   12   13   15   17   20   22   25   28   28   29   30   32   33   34 
LCS_GDT     P    68_B     P    68_B      5    7   31      4    5    5    6    7    9   12   13   15   17   20   22   22   25   27   29   30   32   33   34 
LCS_GDT     P    69_B     P    69_B      3    4   31      3    3    3    4    4    5    6    6   10   12   16   19   21   25   27   29   30   32   33   34 
LCS_GDT     G    70_B     G    70_B      3    4   21      3    3    3    4    4    4    4    5    6    7    7    7    7    7    7   14   22   30   30   33 
LCS_AVERAGE  LCS_A:  26.62  (  17.98   22.54   39.33 )

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     15     17     17     20     21     22     23     25     25     26     28     29     29     29     30     30     31     32     33     34 
GDT PERCENT_AT  19.74  22.37  22.37  26.32  27.63  28.95  30.26  32.89  32.89  34.21  36.84  38.16  38.16  38.16  39.47  39.47  40.79  42.11  43.42  44.74
GDT RMS_LOCAL    0.29   0.37   0.37   1.11   1.27   1.57   1.84   2.23   2.23   2.60   3.16   3.41   3.41   3.41   3.97   3.97   4.53   5.37   5.53   5.78
GDT RMS_ALL_AT  15.02  14.89  14.89  14.78  15.01  14.49  14.47  14.42  14.42  13.92  13.25  13.04  13.04  13.04  12.77  12.77  12.56  14.54  14.72  14.33

# Checking swapping
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    37_B      E    37_B
#   possible swapping detected:  E    40_B      E    40_B
#   possible swapping detected:  E    41_B      E    41_B
#   possible swapping detected:  E    66_B      E    66_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E    21_B      E    21_B    38.326     0    0.046   1.044    46.722    0.000    0.000
LGA    E    22_B      E    22_B    32.763     0    0.031   1.263    35.200    0.000    0.000
LGA    L    23_B      L    23_B    28.535     0    0.066   1.411    30.505    0.000    0.000
LGA    K    24_B      K    24_B    29.752     0    0.078   0.162    35.353    0.000    0.000
LGA    K    25_B      K    25_B    28.434     0    0.018   0.881    38.119    0.000    0.000
LGA    I    26_B      I    26_B    22.325     0    0.026   0.045    24.930    0.000    0.000
LGA    R    27_B      R    27_B    19.700     0    0.015   1.036    24.714    0.000    0.000
LGA    E    28_B      E    28_B    20.686     0    0.024   0.978    29.435    0.000    0.000
LGA    R    29_B      R    29_B    19.008     0    0.030   1.307    23.319    0.000    0.000
LGA    L    30_B      L    30_B    12.504     0    0.100   0.132    15.084    0.714    0.357
LGA    L    31_B      L    31_B    10.345     0    0.251   1.397    13.038    2.500    1.250
LGA    M    32_B      M    32_B     9.971     0    0.177   0.262    14.389    0.833    0.417
LGA    V    33_B      V    33_B     8.211     0    0.024   0.281    11.978   10.595    6.667
LGA    F    34_B      F    34_B     2.871     0    0.689   1.274     4.188   48.690   52.771
LGA    D    35_B      D    35_B     3.210     0    0.021   0.766     6.568   57.381   43.631
LGA    E    36_B      E    36_B     4.085     0    0.032   0.729     5.575   45.357   35.344
LGA    E    37_B      E    37_B     4.159     0    0.020   0.889     9.596   43.452   23.122
LGA    R    38_B      R    38_B     2.122     0    0.171   0.778     6.470   66.905   48.571
LGA    V    39_B      V    39_B     1.240     0    0.015   0.047     2.324   79.286   74.218
LGA    E    40_B      E    40_B     1.454     0    0.025   0.967     6.130   75.119   57.937
LGA    E    41_B      E    41_B     2.168     0    0.044   0.633     5.234   63.095   48.624
LGA    Y    42_B      Y    42_B     2.357     0    0.206   1.360     9.480   64.881   40.397
LGA    M    43_B      M    43_B     3.333     0    0.027   0.761     7.553   51.786   36.250
LGA    K    44_B      K    44_B     3.018     0    0.026   0.589     4.712   57.381   47.619
LGA    I    45_B      I    45_B     1.521     0    0.016   0.068     2.060   77.381   78.393
LGA    M    46_B      M    46_B     1.430     0    0.018   0.652     4.086   81.429   65.357
LGA    K    47_B      K    47_B     2.151     0    0.066   0.067     5.041   72.976   56.190
LGA    E    48_B      E    48_B     1.673     0    0.024   0.443     3.280   77.143   67.831
LGA    V    49_B      V    49_B     0.544     0    0.027   0.076     1.008   90.595   93.265
LGA    I    50_B      I    50_B     0.782     0    0.018   0.050     1.788   90.476   84.881
LGA    E    51_B      E    51_B     0.682     0    0.046   0.098     1.408   90.476   86.455
LGA    K    52_B      K    52_B     1.302     0    0.030   1.100     9.965   81.548   51.429
LGA    I    53_B      I    53_B     1.477     0    0.023   0.074     2.397   79.286   73.036
LGA    L    54_B      L    54_B     0.792     0    0.018   1.416     5.131   92.857   73.274
LGA    E    55_B      E    55_B     1.146     0    0.026   0.847     6.516   79.405   56.032
LGA    N    56_B      N    56_B     2.622     0    0.026   0.909     3.262   61.071   58.214
LGA    R    57_B      R    57_B     2.501     0    0.024   0.995     7.089   60.952   46.667
LGA    K    58_B      K    58_B     0.829     0    0.081   0.237     2.656   83.690   80.952
LGA    K    64_B      K    64_B    17.544     0    0.055   0.199    23.715    0.000    0.000
LGA    V    65_B      V    65_B    15.409     0    0.063   0.075    17.675    0.000    0.000
LGA    E    66_B      E    66_B    18.698     0    0.082   0.816    25.823    0.000    0.000
LGA    I    67_B      I    67_B    17.292     0    0.619   0.658    18.335    0.000    0.000
LGA    P    68_B      P    68_B    18.671     0    0.680   0.753    20.219    0.000    0.000
LGA    P    69_B      P    69_B    17.197     0    0.654   0.804    21.675    0.000    0.000
LGA    G    70_B      G    70_B    15.279     0    0.685   0.685    15.981    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       45     180    180  100.00     387    387  100.00                76
SUMMARY(RMSD_GDC):    10.700         10.478                 11.515           23.517   19.594

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   50   76    4.0     25    2.23    30.263    28.680     1.074

LGA_LOCAL      RMSD:   2.227  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.416  Number of assigned atoms:   45 
Std_ASGN_ATOMS RMSD:  10.700  Standard rmsd on all 45 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.541126 * X  +  -0.042942 * Y  +   0.839844 * Z  + -61.187496
  Y_new =  -0.812427 * X  +  -0.231165 * Y  +  -0.535280 * Z  + -67.663826
  Z_new =   0.217128 * X  +  -0.971967 * Y  +   0.090202 * Z  +  55.974926 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.158380 -0.218872 -1.478257   [DEG: -123.6660  -12.5404  -84.6979 ]
ZXZ:  1.003361  1.480471  2.921810   [DEG:   57.4883   84.8248  167.4074 ]
 
# END of job
