 
####################################################### 
#                                                     # 
#                        ACE                          # 
#                                                     # 
#        Ab-initio protein structure prediction       # 
#                         &                           # 
#               Comparative modeling                  # 
#                                                     # 
#                     Evaluator                       # 
#                                                     # 
#                ----------------- 11/1998            # 
#                                                     # 
#                         by                          # 
#           Adam Zemla & Ceslovas Venclovas           # 
#                                                     # 
#         Protein Structure Prediction Center         # 
#      Lawrence Livermore National Laboratory, CA     # 
#                                                     # 
####################################################### 
########################## 
#                        # 
#    ACE parameters:     # 
#                        # 
########################## 
# 
# MEASURES: 
# 
# For AB: 0 3 9 13 14 
# For CM: 0 1 2 3 6 7 8 9 10 11 12 13 14 18 
# 
ARMSMC  0 1 2     7 8 9    11 12 13 14 18 
ARMSSC  0 1 2 3 6 7 8 9    11 12 13 14 18 
# 
CRMSCA  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSMC  0 1 2     7 8 9 10 11 12 13 14 18 
CRMSSC  0 1 2 3 6     9    11 12 13 14 18 
CRMSALL 0 1 2     7 8 9    11 12 13 14 18 
# 
D-E_CA  0 1 2     7 8 9    11 12 13 14 18 
D-E_MC  0 1 2     7 8 9    11 12 13 14 18 
D-E_SC  0 1 2 3 6 7 8 9    11 12 13 14 18 
D-E_ALL 0 1 2     7 8 9    11 12 13 14 18 
# 
# Output parameters 
# 
DIHED-OUTPUT        0         #    1 - ON, 0 - OFF 
RES-CONTACTS        0         #    1 - ON, 0 - OFF 
SS-OUTPUT           1         #    1 - ON, 0 - OFF 
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
# 
# Calculation parameters 
# 
SOV-METHOD          1         #    0 - SOV 94,  1 - SOV 
# 
TEMP-FACTOR         30.0      #    Target structure temperature factor cutoff 
ACCESS-CUTOFF       0.20      #    Solvent accessibility cutoff   
ANGLES-CORRECT      30.0      #    target-model  (diff < 30.0)    
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
ROTATION-MATRIX     0         #    1 - ON, 0 - OFF   
SC-SWAPPING         1         #    1 - ON, 0 - OFF    
SEP-CONTACTS        1         #    Separation interval along the chain 
RESIDUE-CONTACTS    8.0       #    Contact definition between two C-beta atoms 
# 
CRMS-METHOD         1         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
ITER-CUTOFF         2.5       #    DISTANCE cutoff (for CA (iter))  
LCS_GDT             1         #    LCS and GDT calculations (1 - ON, 0 - OFF) 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
 
 
# WARNING! The number of residues in SS section: 31 , MODEL 31 , TARGET 226 
#          The number of residues possible to evaluate: 31 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    41     D     C     C             1.00 
 SSP    42     E     C     C             1.00 
 SSP    43     R     C     C             1.00 
 SSP    44     D     C     C             1.00 
 SSP    45     K     E     C             1.00 
 SSP    46     R     E     C             1.00 
 SSP    47     P     E     C             1.00 
 SSP    48     F     E     C             1.00 
 SSP    49     S     E     C             1.00 
 SSP    50     M     C     C             1.00 
 SSP    51     A     C     C             1.00 
 SSP    52     S     C     C             1.00 
 SSP    53     T     C     C             1.00 
 SSP    54     P     C     C             1.00 
 SSP    55     D     C     C             1.00 
 SSP    56     E     C     C             1.00 
 SSP    57     K     C     C             1.00 
 SSP    58     G     C     C             1.00 
 SSP    59     F     C     C             1.00 
 SSP    60     I     E     C             1.00 
 SSP    61     E     E     C             1.00 
 SSP    62     L     E     C             1.00 
 SSP    63     H     E     C             1.00 
 SSP    64     I     E     C             1.00 
 SSP    65     G     C     C             1.00 
 SSP  BREAK 
 SSP    72     Y     C     C             1.00 
 SSP    73     A     C     C             1.00 
 SSP    74     K     H     C             1.00 
 SSP    75     A     H     C             1.00 
 SSP    76     V     H     C             1.00 
 SSP    77     M     H     C             1.00 
 SSP  BREAK 
 
 NP      - Number of predicted residues 
 PP      - Percent of predicted residues 
 Q3      - Residues predicted correctly (H, E, C) 
 Qhelix  - Residues predicted correctly (HELIX) 
 Qstrand - Residues predicted correctly (STRAND) 
 Qcoil   - Residues predicted correctly (COIL) 
 SOV     - Segment overlap quantity 
 
                     Q3      Qhelix   Qstrand   Qcoil      PP 
 Qindex              54.8       0.0      0.0    100.0     13.7 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        25.8       0.0      0.0     47.1     13.7 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            3               0.0               0.0 
 
         Number of wrong    Number of wrong 
             breaks             joins 
 B/J            0                 0 
 
  CONFIDENCE (P)     Average     NP    PP/BIN     Q3 
 BIN  0.90 - 1.00      1.00      31    100.0     54.8 
 
 BIN  0.00 - 1.00      1.00      31    100.0     54.8 
 
 
 
 
              predicted        number of target      total number   total number 
                as a         contacts possible in         of             of 
               contact         predicted subset:       contacts       contacts 
            percent  number    percent    number       in target    in prediction 
 CONTACTS:     0.0      0         0.0        0             0              0 
 
 
# WARNING! The number of residues with CB atom coordinates: MODEL 0 , TARGET 210 
 
# WARNING! TARGET 1793 atoms, MODEL 1694 atoms, 1670 common with TARGET 
           Number of atoms possible to evaluate: 124 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.16           44.9    49    11.0   447     ARMSMC  
     SECONDARY STRUCTURE . .    43.68           60.0    20     8.2   244     ARMSMC  
     SURFACE . . . . . . . .    91.86           33.3    27    11.8   228     ARMSMC  
     BURIED  . . . . . . . .    43.52           59.1    22    10.0   219     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   163     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   150     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    95     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    89     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    74     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   114     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    92     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    62     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    52     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    32     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    27     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    16     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    13     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     9     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     9     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     5     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1   41 - 77   31   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    28     41 - 74       4.79     6.17 
  LCS LOCAL_SCORE:            101.25 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   41 - 77   31   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    23     43 - 65       2.00     7.02 
  LCS LOCAL_SCORE:             60.25 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   41 - 77   31   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    16     44 - 59       0.99     6.73 
  LCS LOCAL_SCORE:             34.13 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      41       D     3    3   28       C        0   1   1   1   1   1   1   1   3   5   9  11  11  11  11  11  11  11  12  12  
 LCS      42       E     3   19   28       C        1   1   1   1   2   7   7   9  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      43       R     8   23   28       C        1   1   3   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      44       D    16   23   28       C        2   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      45       K    16   23   28       E        1   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      46       R    16   23   28       E        2   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      47       P    16   23   28       E        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      48       F    16   23   28       E        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      49       S    16   23   28       E        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      50       M    16   23   28       C        1   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      51       A    16   23   28       C        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      52       S    16   23   28       C        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      53       T    16   23   28       C        1   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      54       P    16   23   28       C        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      55       D    16   23   28       C        1   2   5   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      56       E    16   23   28       C        2   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      57       K    16   23   28       C        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      58       G    16   23   28       C        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      59       F    16   23   28       C        3   5   6   7   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      60       I     6   23   28       E        1   1   2   5   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      61       E     6   23   28       E        1   1   2   3   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      62       L     6   23   28       E        1   1   2   2   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      63       H     6   23   28       E        1   1   2   5   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      64       I     6   23   28       E        1   1   2   2   6   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS      65       G     6   23   28       C        1   1   2   5   7   9  10  10  10  10  10  11  11  11  11  11  11  11  12  12  
 LCS    BREAK 
 LCS      72       Y     4    5   28       C        1   1   1   1   2   2   2   2   2   2   2   2   3   4   6   7   8  11  12  12  
 LCS      73       A     4    5   28       C        1   1   1   1   2   2   2   2   2   2   2   2   2   2   3   3   6   7   8  11  
 LCS      74       K     4    5   28       H        1   1   1   1   2   2   2   2   2   2   2   2   3   4   9  11  11  11  12  12  
 LCS      75       A     4    5    7       H        1   1   1   1   2   2   2   2   2   2   2   3   4   5   9   9  11  11  12  12  
 LCS      76       V     3    5    7       H        1   1   1   1   2   2   2   2   2   2   2   2   2   2   3   5   6   7   7   9  
 LCS      77       M     3    3    7       H        1   1   1   1   1   1   1   2   2   2   2   2   3   4   6   7   8  10  11  11  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.64 
 
 NUMBER_OF_CA_Tg:  226      NUMBER_OF_CA_Pr:   31      PERCENT_OF_CA:  13.72  
 
GLOBAL_DISTANCE_TEST (the largest set of residues under DISTANCE_CUTOFF (using LCS results)): 
 GDT DISTANCE_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_OF_CA_max       8      13      15      16      17      21      23      23      24      24      24      25      25      25      25      26      26      27      28      28  
 GDT PERCENT_OF_CA_Pr   25.81   41.94   48.39   51.61   54.84   67.74   74.19   74.19   77.42   77.42   77.42   80.65   80.65   80.65   80.65   83.87   83.87   87.10   90.32   90.32 
 GDT PERCENT_OF_CA_Tg    3.54    5.75    6.64    7.08    7.52    9.29   10.18   10.18   10.62   10.62   10.62   11.06   11.06   11.06   11.06   11.50   11.50   11.95   12.39   12.39 
 GDT FRAGMENT: Beg-End  47-59   45-59   44-59   44-59   43-59   43-65   43-65   43-65   42-65   42-65   42-65   41-65   41-65   41-65   41-65   41-74   41-74   41-75   41-75   41-75  
 GDT RMS_LOCAL           0.34    0.68    0.84    0.99    1.22    1.79    2.00    2.00    2.36    2.36    2.36    2.68    2.68    2.68    2.68    3.48    3.48    4.11    4.62    4.62 
 GDT RMS_ALL_CA          7.25    6.74    6.64    6.73    6.60    6.90    7.02    7.02    6.76    6.76    6.76    6.66    6.66    6.66    6.66    6.33    6.33    6.18    6.13    6.13 
 
 
 TEST (CA)  RMS =   5.98               (Number of atoms:   31) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.98         31    13.7   226     CRMSCA  
     CRN = ALL/NP  . . . . .    0.1928                            CRMSCA  
     SECONDARY STRUCTURE . .    6.86         14    11.5   122     CRMSCA  
     SURFACE . . . . . . . .    5.27         17    14.8   115     CRMSCA  
     BURIED  . . . . . . . .    6.73         14    12.6   111     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.95        124    11.1  1114     CRMSMC  
     SECONDARY STRUCTURE . .    6.74         56     9.2   607     CRMSMC  
     SURFACE . . . . . . . .    5.35         68    12.0   567     CRMSMC  
     BURIED  . . . . . . . .    6.60         56    10.2   547     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   889     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   771     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   477     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   465     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   424     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.95        124     6.9  1793     CRMSALL 
     SECONDARY STRUCTURE . .    6.74         56     5.8   965     CRMSALL 
     SURFACE . . . . . . . .    5.35         68     7.4   925     CRMSALL 
     BURIED  . . . . . . . .    6.60         56     6.5   868     CRMSALL 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.898      1.000       0.500     31    13.7   226     ERRCA  
     SECONDARY STRUCTURE . .    5.881      1.000       0.500     14    11.5   122     ERRCA  
     SURFACE . . . . . . . .    4.501      1.000       0.500     17    14.8   115     ERRCA  
     BURIED  . . . . . . . .    5.380      1.000       0.500     14    12.6   111     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.899      1.000       0.500    124    11.1  1114     ERRMC  
     SECONDARY STRUCTURE . .    5.810      1.000       0.500     56     9.2   607     ERRMC  
     SURFACE . . . . . . . .    4.524      1.000       0.500     68    12.0   567     ERRMC  
     BURIED  . . . . . . . .    5.355      1.000       0.500     56    10.2   547     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    0.000      0.000       0.000      0     0.0   889     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   771     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   477     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   465     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   424     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.899      1.000       0.500    124     6.9  1793     ERRALL 
     SECONDARY STRUCTURE . .    5.810      1.000       0.500     56     5.8   965     ERRALL 
     SURFACE . . . . . . . .    4.524      1.000       0.500     68     7.4   925     ERRALL 
     BURIED  . . . . . . . .    5.355      1.000       0.500     56     6.5   868     ERRALL 
 
 
 
DISTANCES: Percent of total atoms where distance (target <-> model) in global 
           superposition is less than: 1 , 2 , 3 , 5 , 10 Angstroms 
            D < 1     D < 2     D < 3     D < 5    D < 10      NP      TN 
CA  (N)         1         5        13        18        26      31     226   DISTCA 
CA  (P)      0.44      2.21      5.75      7.96     11.50             226   DISTCA 
CA  (RMS)    0.88      1.49      2.23      2.70      4.04                   DISTCA 
 
ALL (N)         1        23        48        74       107     124    1793   DISTALL 
ALL (P)      0.06      1.28      2.68      4.13      5.97            1793   DISTALL 
ALL (RMS)    0.88      1.54      2.12      2.81      4.38                   DISTALL 
 
 
 
 
END of the results output 
