
#######################################################
#                                                     #
#                        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   65 (  516),  selected   51 , name one
# Molecule2: number of CA atoms   51 (  404),  selected   51 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:C  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        1.56     1.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    51       6_C - 56_C        1.56     1.56
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       7_C - 52_C        0.96     1.69
  LONGEST_CONTINUOUS_SEGMENT:    46       8_C - 53_C        0.78     1.63
  LONGEST_CONTINUOUS_SEGMENT:    46       9_C - 54_C        0.96     1.61
  LCS_AVERAGE:     85.93

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   51
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     P     6_C     P     6_C      7   51   51      3    5   12   26   43   46   47   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T     7_C     T     7_C     46   51   51      3    5    7   17   42   46   47   48   49   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K     8_C     K     8_C     46   51   51      3   22   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     I     9_C     I     9_C     46   51   51     24   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     L    10_C     L    10_C     46   51   51     24   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    11_C     P    11_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    12_C     C    12_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    13_C     P    13_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    14_C     R    14_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    15_C     C    15_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    16_C     N    16_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    17_C     S    17_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     M    18_C     M    18_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     E    19_C     E    19_C     46   51   51     23   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    20_C     T    20_C     46   51   51      9   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K    21_C     K    21_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     F    22_C     F    22_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    23_C     C    23_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    24_C     Y    24_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    25_C     Y    25_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    26_C     N    26_C     46   51   51     15   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    27_C     N    27_C     46   51   51     15   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    28_C     Y    28_C     46   51   51     24   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    29_C     N    29_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     V    30_C     V    30_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     N    31_C     N    31_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Q    32_C     Q    32_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    33_C     P    33_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    34_C     R    34_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     H    35_C     H    35_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     F    36_C     F    36_C     46   51   51     31   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    37_C     C    37_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     K    38_C     K    38_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     A    39_C     A    39_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     C    40_C     C    40_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Q    41_C     Q    41_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    42_C     R    42_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     Y    43_C     Y    43_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     W    44_C     W    44_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    45_C     T    45_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    46_C     S    46_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    47_C     G    47_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    48_C     G    48_C     46   51   51     29   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     T    49_C     T    49_C     46   51   51     16   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     M    50_C     M    50_C     46   51   51      5   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     R    51_C     R    51_C     46   51   51     32   42   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     S    52_C     S    52_C     46   51   51      3   16   44   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     V    53_C     V    53_C     46   51   51      3   16   41   46   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     P    54_C     P    54_C     46   51   51      3    5   13   31   44   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     I    55_C     I    55_C     11   51   51      3    7   21   41   46   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_GDT     G    56_C     G    56_C      9   51   51      3    3    9   18   32   47   48   49   50   51   51   51   51   51   51   51   51   51   51   51 
LCS_AVERAGE  LCS_A:  95.31  (  85.93  100.00  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     32     42     44     46     46     47     48     49     50     51     51     51     51     51     51     51     51     51     51     51 
GDT PERCENT_AT  62.75  82.35  86.27  90.20  90.20  92.16  94.12  96.08  98.04 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.48   0.59   0.78   0.78   0.94   1.12   1.24   1.40   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56
GDT RMS_ALL_AT   1.69   1.70   1.70   1.63   1.63   1.60   1.59   1.57   1.57   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56

# Checking swapping
#   possible swapping detected:  F    22_C      F    22_C
#   possible swapping detected:  F    36_C      F    36_C

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     6_C      P     6_C     3.786     2    0.140   0.140     4.980   35.833   27.619
LGA    T     7_C      T     7_C     5.159     0    0.173   0.302     7.008   29.048   24.218
LGA    K     8_C      K     8_C     2.401     4    0.208   0.209     2.872   66.905   36.931
LGA    I     9_C      I     9_C     1.024     0    0.065   0.720     3.464   83.690   79.762
LGA    L    10_C      L    10_C     0.754     0    0.051   0.230     1.908   90.476   87.143
LGA    P    11_C      P    11_C     0.275     0    0.016   0.062     0.593  100.000   97.279
LGA    C    12_C      C    12_C     0.447     0    0.041   0.113     0.899   95.238   95.238
LGA    P    13_C      P    13_C     0.645     0    0.056   0.278     1.464   90.476   89.184
LGA    R    14_C      R    14_C     0.794     0    0.141   0.566     3.533   88.214   75.411
LGA    C    15_C      C    15_C     0.582     0    0.057   0.164     0.855   92.857   92.063
LGA    N    16_C      N    16_C     0.330     0    0.045   0.256     0.882  100.000   96.429
LGA    S    17_C      S    17_C     0.394     0    0.096   0.142     0.596   97.619   98.413
LGA    M    18_C      M    18_C     0.485     0    0.041   0.620     1.503   95.238   93.036
LGA    E    19_C      E    19_C     0.647     4    0.039   0.038     0.767   90.476   50.265
LGA    T    20_C      T    20_C     0.747     0    0.089   0.102     0.991   90.476   90.476
LGA    K    21_C      K    21_C     0.473     0    0.024   0.450     2.822   97.619   88.148
LGA    F    22_C      F    22_C     0.503     0    0.014   0.040     0.610   97.619   93.074
LGA    C    23_C      C    23_C     0.478     0    0.052   0.068     0.567  100.000   98.413
LGA    Y    24_C      Y    24_C     0.521     0    0.019   0.075     0.839   92.857   91.270
LGA    Y    25_C      Y    25_C     0.411     0    0.070   0.082     0.480  100.000  100.000
LGA    N    26_C      N    26_C     0.874     0    0.056   0.249     2.192   90.476   83.929
LGA    N    27_C      N    27_C     1.285     0    0.024   0.321     2.568   81.429   76.250
LGA    Y    28_C      Y    28_C     1.016     0    0.077   0.089     2.407   83.690   75.159
LGA    N    29_C      N    29_C     0.540     0    0.060   0.175     0.691   95.238   96.429
LGA    V    30_C      V    30_C     0.269     0    0.045   1.140     2.648  100.000   88.844
LGA    N    31_C      N    31_C     0.282     0    0.024   0.410     1.681  100.000   93.095
LGA    Q    32_C      Q    32_C     0.288     0    0.019   0.296     1.116   97.619   92.646
LGA    P    33_C      P    33_C     0.543     0    0.037   0.069     0.677   92.857   93.197
LGA    R    34_C      R    34_C     0.603     0    0.030   0.990     3.872   95.238   80.909
LGA    H    35_C      H    35_C     0.465     0    0.075   1.059     2.571   95.238   87.429
LGA    F    36_C      F    36_C     0.827     0    0.017   0.121     1.417   90.476   87.186
LGA    C    37_C      C    37_C     0.741     0    0.067   0.125     1.024   88.214   88.968
LGA    K    38_C      K    38_C     0.588     0    0.089   0.486     1.521   92.857   88.571
LGA    A    39_C      A    39_C     0.507     0    0.095   0.093     0.576   92.857   92.381
LGA    C    40_C      C    40_C     0.859     0    0.030   0.041     0.882   90.476   90.476
LGA    Q    41_C      Q    41_C     1.002     0    0.032   0.101     1.143   85.952   83.439
LGA    R    42_C      R    42_C     0.988     0    0.020   1.251     6.102   85.952   69.610
LGA    Y    43_C      Y    43_C     0.817     0    0.064   0.144     1.031   90.476   88.968
LGA    W    44_C      W    44_C     0.598     0    0.037   0.171     0.933   90.476   90.476
LGA    T    45_C      T    45_C     0.416     0    0.062   0.137     0.792   97.619   94.558
LGA    S    46_C      S    46_C     0.609     0    0.039   0.166     1.015   90.595   90.556
LGA    G    47_C      G    47_C     0.723     0    0.037   0.037     1.055   88.214   88.214
LGA    G    48_C      G    48_C     0.935     0    0.086   0.086     0.935   90.476   90.476
LGA    T    49_C      T    49_C     0.728     0    0.093   0.273     1.179   88.214   87.891
LGA    M    50_C      M    50_C     0.818     0    0.100   0.661     4.433   92.857   73.036
LGA    R    51_C      R    51_C     0.458     0    0.127   0.546     4.122   95.238   71.861
LGA    S    52_C      S    52_C     1.500     0    0.077   0.088     2.438   77.262   74.444
LGA    V    53_C      V    53_C     2.139     0    0.144   1.138     3.812   68.810   60.952
LGA    P    54_C      P    54_C     4.205     0    0.104   0.194     5.629   41.786   35.306
LGA    I    55_C      I    55_C     3.241     0    0.106   1.362     4.392   45.119   49.464
LGA    G    56_C      G    56_C     4.967     0    0.648   0.648     5.767   27.857   27.857

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       51     204    204  100.00     404    404  100.00                51
SUMMARY(RMSD_GDC):     1.563          1.602                  1.749           85.847   80.332

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   65   51    4.0     49    1.24    92.157    95.132     3.669

LGA_LOCAL      RMSD:   1.235  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.572  Number of assigned atoms:   51 
Std_ASGN_ATOMS RMSD:   1.563  Standard rmsd on all 51 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.109734 * X  +   0.188911 * Y  +  -0.975844 * Z  + -29.415968
  Y_new =  -0.826515 * X  +  -0.528003 * Y  +  -0.195156 * Z  +  -9.083002
  Z_new =  -0.552116 * X  +   0.827965 * Y  +   0.098198 * Z  +   5.872898 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.438802  0.584899  1.452746   [DEG:  -82.4373   33.5123   83.2362 ]
ZXZ: -1.373413  1.472440 -0.588119   [DEG:  -78.6908   84.3646  -33.6967 ]
 
# END of job
