
#######################################################
#                                                     #
#                        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        4.48     4.48
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31       7_B - 37_B        1.78     5.48
  LCS_AVERAGE:     74.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21       7_B - 27_B        0.98     5.90
  LCS_AVERAGE:     47.92

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      0    3   37      0    0    3    3    3    4    4    9   10   11   12   14   15   18   25   26   32   33   34   34 
LCS_GDT     E     3_C     E     3_B      3    3   37      0    3    3    3   12   15   15   17   18   20   24   26   31   34   35   35   36   36   36   36 
LCS_GDT     A     4_C     A     4_B      3    3   37      3    6    7   11   12   15   16   20   26   28   31   33   33   34   35   35   36   36   36   36 
LCS_GDT     E     5_C     E     5_B      3    3   37      3    3    3    5    9   13   16   20   24   27   29   32   32   34   35   35   36   36   36   36 
LCS_GDT     Q     6_C     Q     6_B      3   26   37      3    3    3    4    7   13   17   27   30   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     E     7_C     E     7_B     21   31   37      8   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     K     8_C     K     8_B     21   31   37      8   17   21   25   27   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     D     9_C     D     9_B     21   31   37     10   17   21   25   27   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     Q    10_C     Q    10_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    11_C     L    11_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     R    12_C     R    12_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     T    13_C     T    13_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     Q    14_C     Q    14_B     21   31   37      8   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     V    15_C     V    15_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     V    16_C     V    16_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     R    17_C     R    17_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    18_C     L    18_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     Q    19_C     Q    19_B     21   31   37     10   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     A    20_C     A    20_B     21   31   37      6   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     E    21_C     E    21_B     21   31   37      9   17   21   24   27   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     K    22_C     K    22_B     21   31   37      7   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     A    23_C     A    23_B     21   31   37      7   17   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     D    24_C     D    24_B     21   31   37      7   14   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    25_C     L    25_B     21   31   37      7   14   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    26_C     L    26_B     21   31   37      8   14   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     G    27_C     G    27_B     21   31   37      7   14   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     I    28_C     I    28_B     20   31   37      7   14   20   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     V    29_C     V    29_B     20   31   37      7   14   20   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     S    30_C     S    30_B     20   31   37      8   14   21   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     E    31_C     E    31_B     20   31   37      7   14   20   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    32_C     L    32_B     20   31   37      8   14   20   23   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     Q    33_C     Q    33_B     20   31   37      8   14   20   23   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    34_C     L    34_B     20   31   37      8   14   20   25   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     K    35_C     K    35_B     20   31   37      8   14   20   23   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     L    36_C     L    36_B     20   31   37      8   13   20   22   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     N    37_C     N    37_B     20   31   37      8   11   16   21   28   30   31   31   31   32   32   33   33   34   35   35   36   36   36   36 
LCS_GDT     S    38_C     S    38_B      3   26   37      3    3    3    3    4    4    6   10   15   22   25   29   32   32   33   34   36   36   36   36 
LCS_AVERAGE  LCS_A:  74.26  (  47.92   74.87  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     10     17     21     25     28     30     31     31     31     32     32     33     33     34     35     35     36     36     36     36 
GDT PERCENT_AT  27.03  45.95  56.76  67.57  75.68  81.08  83.78  83.78  83.78  86.49  86.49  89.19  89.19  91.89  94.59  94.59  97.30  97.30  97.30  97.30
GDT RMS_LOCAL   10.01   0.54   0.98   1.33   1.57   1.71   1.78   1.78   1.78   2.21   2.21   2.82   2.82   3.25   3.62   3.62   3.87   3.87   3.87   3.87
GDT RMS_ALL_AT   7.24   6.57   5.90   5.53   5.60   5.45   5.48   5.48   5.48   5.21   5.21   4.88   4.88   4.68   4.55   4.55   4.56   4.56   4.56   4.56

# Checking swapping
#   possible swapping detected:  E     3_C      E     3_B
#   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    19.678     0    0.488   0.504    21.591    0.000    0.000
LGA    E     3_C      E     3_B    13.987     0    0.594   1.342    15.903    0.000    0.000
LGA    A     4_C      A     4_B    11.771     0    0.589   0.563    12.760    0.000    0.000
LGA    E     5_C      E     5_B    12.469     0    0.586   1.142    15.678    0.000    0.000
LGA    Q     6_C      Q     6_B     8.230     0    0.612   1.254    13.189    8.929    4.339
LGA    E     7_C      E     7_B     1.786     0    0.598   0.812     6.830   61.905   46.402
LGA    K     8_C      K     8_B     3.048     0    0.091   1.217     7.078   57.262   43.439
LGA    D     9_C      D     9_B     2.487     0    0.026   1.083     6.823   66.905   48.214
LGA    Q    10_C      Q    10_B     0.941     0    0.036   0.623     3.244   88.214   76.667
LGA    L    11_C      L    11_B     1.129     0    0.060   0.252     2.086   83.690   77.262
LGA    R    12_C      R    12_B     2.043     0    0.043   1.978    10.379   70.833   39.481
LGA    T    13_C      T    13_B     1.800     0    0.027   1.296     4.254   77.143   64.830
LGA    Q    14_C      Q    14_B     0.664     0    0.032   1.128     4.243   88.214   68.677
LGA    V    15_C      V    15_B     0.417     0    0.041   0.124     1.613   97.619   92.041
LGA    V    16_C      V    16_B     1.112     0    0.052   0.100     2.397   81.548   75.510
LGA    R    17_C      R    17_B     2.421     0    0.031   1.639    12.984   64.881   31.429
LGA    L    18_C      L    18_B     2.412     0    0.072   0.832     5.849   64.762   50.774
LGA    Q    19_C      Q    19_B     1.189     0    0.034   1.121     5.596   81.429   70.529
LGA    A    20_C      A    20_B     2.028     0    0.034   0.047     2.606   66.786   64.857
LGA    E    21_C      E    21_B     3.119     0    0.043   1.027     4.132   55.357   48.783
LGA    K    22_C      K    22_B     2.338     0    0.058   0.094     3.112   66.905   63.228
LGA    A    23_C      A    23_B     1.226     0    0.027   0.036     1.559   79.286   79.714
LGA    D    24_C      D    24_B     1.820     0    0.027   0.481     3.762   75.000   66.250
LGA    L    25_C      L    25_B     1.867     0    0.037   1.050     4.920   77.143   67.917
LGA    L    26_C      L    26_B     0.953     0    0.048   1.418     4.500   90.595   72.917
LGA    G    27_C      G    27_B     0.538     0    0.044   0.044     0.545   90.476   90.476
LGA    I    28_C      I    28_B     0.544     0    0.045   0.624     1.487   92.857   90.595
LGA    V    29_C      V    29_B     0.202     0    0.035   0.105     0.399  100.000  100.000
LGA    S    30_C      S    30_B     0.334     0    0.038   0.062     0.875  100.000   96.825
LGA    E    31_C      E    31_B     1.090     0    0.035   0.647     1.358   83.690   86.455
LGA    L    32_C      L    32_B     1.588     0    0.031   0.223     3.088   75.000   70.060
LGA    Q    33_C      Q    33_B     1.352     0    0.043   1.146     5.552   79.286   60.899
LGA    L    34_C      L    34_B     0.561     0    0.084   0.102     1.041   90.476   89.345
LGA    K    35_C      K    35_B     2.041     0    0.056   1.818     7.497   66.786   49.365
LGA    L    36_C      L    36_B     3.001     0    0.170   0.959     3.792   53.810   57.500
LGA    N    37_C      N    37_B     2.515     0    0.186   0.318     4.774   50.595   49.821
LGA    S    38_C      S    38_B     8.202     0    0.096   0.615    11.914    7.619    5.079

# 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):     4.482          4.413                  5.099           64.730   56.748

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   38   37    4.0     31    1.78    72.973    76.293     1.652

LGA_LOCAL      RMSD:   1.776  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.476  Number of assigned atoms:   37 
Std_ASGN_ATOMS RMSD:   4.482  Standard rmsd on all 37 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.727357 * X  +   0.453555 * Y  +  -0.515015 * Z  +  21.411861
  Y_new =  -0.664614 * X  +   0.278557 * Y  +  -0.693321 * Z  +  29.958660
  Z_new =  -0.170999 * X  +   0.846578 * Y  +   0.504049 * Z  + -54.194538 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.740354  0.171843  1.033769   [DEG:  -42.4191    9.8459   59.2306 ]
ZXZ: -0.638892  1.042516 -0.199306   [DEG:  -36.6058   59.7318  -11.4194 ]
 
# END of job
