
#######################################################
#                                                     #
#                        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   41 (  340),  selected   41 , name one
# Molecule2: number of CA atoms  141 ( 1112),  selected   41 , 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:    32      24_A - 55_A        4.81    13.07
  LCS_AVERAGE:     20.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      27_A - 46_A        1.73    15.49
  LCS_AVERAGE:     11.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      30_A - 45_A        0.98    16.05
  LONGEST_CONTINUOUS_SEGMENT:    16      31_A - 46_A        0.82    15.92
  LCS_AVERAGE:      7.91

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     D    15_A     D    15_A      3    4   17      0    3    3    3    4    4    5    9   11   12   14   15   16   17   17   17   17   17   18   18 
LCS_GDT     F    16_A     F    16_A      4   12   17      0    4    8   11   11   12   12   12   12   13   14   15   16   17   17   17   17   17   18   18 
LCS_GDT     L    17_A     L    17_A      4   12   17      3    3    4    4   11   12   12   12   12   13   14   15   16   17   17   17   17   17   18   18 
LCS_GDT     A    18_A     A    18_A      4   12   17      3    3    8   11   11   12   12   12   12   13   14   15   16   17   17   17   17   17   18   18 
LCS_GDT     E    19_A     E    19_A      4   12   17      3    4    5   11   11   12   12   12   12   13   14   15   16   17   17   17   17   17   18   18 
LCS_GDT     I    20_A     I    20_A      8   12   17      5    8    8   11   11   12   12   12   12   13   14   15   16   17   17   17   17   17   18   18 
LCS_GDT     F    21_A     F    21_A      8   12   17      5    8    8   11   11   12   12   12   12   13   14   15   16   17   17   17   17   17   18   19 
LCS_GDT     K    22_A     K    22_A      8   12   17      5    8    8   11   11   12   12   12   12   13   14   15   16   17   19   20   22   28   30   34 
LCS_GDT     K    23_A     K    23_A      8   12   28      5    8    8   11   11   12   12   12   12   13   14   15   16   17   17   21   29   31   32   34 
LCS_GDT     I    24_A     I    24_A      8   12   32      5    8    8   11   11   12   12   12   12   13   14   15   16   17   19   20   22   24   30   34 
LCS_GDT     G    25_A     G    25_A      8   12   32      4    8    8   11   11   12   12   12   12   13   18   24   28   29   31   31   31   31   32   34 
LCS_GDT     S    26_A     S    26_A      8   12   32      4    8    8   11   11   12   16   19   19   23   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     K    27_A     K    27_A      8   20   32      4    8    9   15   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     E    28_A     E    28_A      6   20   32      4   10   14   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     N    29_A     N    29_A      6   20   32      4    4    9   15   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     T    30_A     T    30_A     16   20   32      3    8    8   14   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     K    31_A     K    31_A     16   20   32      3    4   15   16   17   19   20   21   24   24   25   27   29   29   31   31   31   31   32   34 
LCS_GDT     E    32_A     E    32_A     16   20   32     11   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     G    33_A     G    33_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     L    34_A     L    34_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     A    35_A     A    35_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     E    36_A     E    36_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     L    37_A     L    37_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     Y    38_A     Y    38_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     E    39_A     E    39_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     Y    40_A     Y    40_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     K    41_A     K    41_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     K    42_A     K    42_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     K    43_A     K    43_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     Y    44_A     Y    44_A     16   20   32     12   13   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     S    45_A     S    45_A     16   20   32      4   11   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     D    46_A     D    46_A     16   20   32      4    9   15   16   17   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     A    47_A     A    47_A     10   18   32      5    8   10   11   16   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     D    48_A     D    48_A     10   11   32      4    8   10   10   11   16   19   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     I    49_A     I    49_A     10   11   32      5    8   10   12   16   19   20   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     E    50_A     E    50_A     10   11   32      4    8   10   10   11   11   13   16   22   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     P    51_A     P    51_A     10   11   32      4    8   10   10   11   11   13   16   21   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     F    52_A     F    52_A     10   11   32      4    8   10   10   11   16   19   22   24   25   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     L    53_A     L    53_A     10   11   32      4    8   10   10   11   11   12   15   19   23   27   28   29   29   31   31   31   31   32   34 
LCS_GDT     K    54_A     K    54_A     10   11   32      3    8   10   10   11   11   12   14   15   19   20   25   27   29   31   31   31   31   32   34 
LCS_GDT     N    55_A     N    55_A     10   11   32      3    6   10   10   11   11   13   16   19   23   26   28   29   29   31   31   31   31   32   34 
LCS_AVERAGE  LCS_A:  13.19  (   7.91   11.11   20.55 )

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     12     13     15     16     17     19     20     22     24     25     27     28     29     29     31     31     31     31     32     34 
GDT PERCENT_AT   8.51   9.22  10.64  11.35  12.06  13.48  14.18  15.60  17.02  17.73  19.15  19.86  20.57  20.57  21.99  21.99  21.99  21.99  22.70  24.11
GDT RMS_LOCAL    0.31   0.38   0.63   0.82   1.06   1.61   1.73   2.65   2.87   3.23   3.57   3.75   3.86   3.86   4.33   4.33   4.33   4.33   4.85   5.81
GDT RMS_ALL_AT  15.78  15.75  16.00  15.92  15.53  15.70  15.49  13.97  14.18  13.82  13.52  13.38  13.47  13.47  13.20  13.20  13.20  13.20  12.95  12.53

# Checking swapping
#   possible swapping detected:  F    21_A      F    21_A
#   possible swapping detected:  E    28_A      E    28_A
#   possible swapping detected:  Y    38_A      Y    38_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  Y    44_A      Y    44_A
#   possible swapping detected:  D    46_A      D    46_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    15_A      D    15_A    33.847     0    0.605   1.257    34.785    0.000    0.000
LGA    F    16_A      F    16_A    36.202     0    0.587   0.652    39.850    0.000    0.000
LGA    L    17_A      L    17_A    36.028     0    0.605   0.573    42.889    0.000    0.000
LGA    A    18_A      A    18_A    31.275     0    0.417   0.407    33.173    0.000    0.000
LGA    E    19_A      E    19_A    27.119     0    0.602   1.158    31.509    0.000    0.000
LGA    I    20_A      I    20_A    23.803     0    0.056   0.754    27.981    0.000    0.000
LGA    F    21_A      F    21_A    21.054     0    0.031   1.230    23.465    0.000    0.000
LGA    K    22_A      K    22_A    18.684     0    0.076   0.082    22.935    0.000    0.000
LGA    K    23_A      K    23_A    14.594     0    0.082   0.612    21.273    0.000    0.000
LGA    I    24_A      I    24_A    13.945     0    0.110   0.157    20.835    0.000    0.000
LGA    G    25_A      G    25_A    11.158     0    0.097   0.097    12.341    0.833    0.833
LGA    S    26_A      S    26_A     8.418     0    0.601   0.917     9.935    8.929    6.508
LGA    K    27_A      K    27_A     5.503     0    0.087   1.117    10.121   32.500   17.725
LGA    E    28_A      E    28_A     2.266     0    0.113   0.422     8.834   65.833   38.519
LGA    N    29_A      N    29_A     3.166     0    0.106   1.067     8.536   59.167   34.464
LGA    T    30_A      T    30_A     4.258     0    0.169   1.210     8.348   44.167   28.844
LGA    K    31_A      K    31_A     4.562     0    0.128   0.888    10.301   42.024   24.286
LGA    E    32_A      E    32_A     2.044     0    0.025   1.074     4.195   75.238   60.635
LGA    G    33_A      G    33_A     2.244     0    0.085   0.085     2.566   67.024   67.024
LGA    L    34_A      L    34_A     3.411     0    0.041   0.107     6.477   55.357   38.571
LGA    A    35_A      A    35_A     2.873     0    0.015   0.024     3.843   64.881   60.571
LGA    E    36_A      E    36_A     1.386     0    0.050   0.903     6.419   83.690   57.460
LGA    L    37_A      L    37_A     2.014     0    0.077   0.376     6.421   72.976   52.083
LGA    Y    38_A      Y    38_A     2.385     0    0.037   0.165     7.264   68.810   40.833
LGA    E    39_A      E    39_A     2.079     0    0.030   0.119     5.584   72.976   52.963
LGA    Y    40_A      Y    40_A     1.635     0    0.044   1.386    12.570   77.143   35.556
LGA    K    41_A      K    41_A     1.858     0    0.040   1.040    10.251   77.143   45.291
LGA    K    42_A      K    42_A     2.070     0    0.013   0.620     5.764   75.119   52.540
LGA    K    43_A      K    43_A     2.033     0    0.033   1.140     4.266   70.952   58.730
LGA    Y    44_A      Y    44_A     2.332     0    0.027   0.214     6.155   63.095   44.603
LGA    S    45_A      S    45_A     2.492     0    0.069   0.132     3.669   57.738   60.159
LGA    D    46_A      D    46_A     3.346     0    0.468   1.179     6.902   69.762   42.560
LGA    A    47_A      A    47_A     1.826     0    0.288   0.343     3.491   69.524   65.619
LGA    D    48_A      D    48_A     3.531     0    0.073   0.933     7.108   52.143   35.060
LGA    I    49_A      I    49_A     0.866     0    0.026   0.610     5.435   68.571   57.321
LGA    E    50_A      E    50_A     6.018     0    0.036   1.357    10.232   18.690    9.683
LGA    P    51_A      P    51_A     8.132     0    0.041   0.047     8.510    7.381    7.211
LGA    F    52_A      F    52_A     4.649     0    0.053   0.159     5.525   26.310   51.818
LGA    L    53_A      L    53_A     6.644     0    0.131   0.569     9.414    9.762   10.476
LGA    K    54_A      K    54_A    11.035     0    0.034   1.017    13.566    0.357    0.159
LGA    N    55_A      N    55_A    10.084     0    0.566   0.598    12.150    0.476    0.476

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     340    340  100.00               141
SUMMARY(RMSD_GDC):    11.152         10.839                 12.224           11.054    8.217

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   41  141    4.0     22    2.65    14.539    14.018     0.801

LGA_LOCAL      RMSD:   2.645  Number of atoms:   22  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.973  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:  11.152  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.010776 * X  +  -0.565424 * Y  +  -0.824730 * Z  +  40.035999
  Y_new =  -0.356474 * X  +   0.772760 * Y  +  -0.525136 * Z  +  -4.308654
  Z_new =   0.934243 * X  +   0.288336 * Y  +  -0.209886 * Z  +  -6.100408 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.601016 -1.206131  2.200016   [DEG:  -91.7315  -69.1062  126.0517 ]
ZXZ: -1.003801  1.782254  1.271441   [DEG:  -57.5136  102.1157   72.8482 ]
 
# END of job
