 
####################################################### 
#                                                     # 
#                        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: 24 , MODEL 24 , TARGET 119 
#          The number of residues possible to evaluate: 24 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    24     N     C     C             1.00 
 SSP    25     P     C     C             1.00 
 SSP    26     S     C     C             1.00 
 SSP    27     V     E     C             1.00 
 SSP    28     T     E     C             1.00 
 SSP    29     V     E     C             1.00 
 SSP    30     I     E     C             1.00 
 SSP    31     T     E     C             1.00 
 SSP    32     I     E     C             1.00 
 SSP    33     Q     E     C             1.00 
 SSP    34     A     E     C             1.00 
 SSP    35     S     E     C             1.00 
 SSP    36     N     E     C             1.00 
 SSP    37     S     C     C             1.00 
 SSP    38     T     C     C             1.00 
 SSP    39     E     C     C             1.00 
 SSP    40     L     C     C             1.00 
 SSP    41     D     C     C             1.00 
 SSP    42     M     E     C             1.00 
 SSP    43     T     E     C             1.00 
 SSP    44     D     E     C             1.00 
 SSP    45     F     E     C             1.00 
 SSP    46     V     E     C             1.00 
 SSP    47     F     E     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              33.3       0.0      0.0    100.0     20.2 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed         8.2     100.0      0.0     24.5     20.2 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            2               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      24    100.0     33.3 
 
 BIN  0.00 - 1.00      1.00      24    100.0     33.3 
 
 
 
 
              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 
 
 
 
 CONSIDERED - explicitly provided contacts (with positive confidence) or 
              non contacts (with negative confidence) possible to evaluate 
 SEP      - Minimum separation between residues considered 
 NPC      - Number of contacts predicted correctly 
 PC(P)    - Percent of contacts predicted correctly from CONSIDERED in PREDICTION 
 PC(T)    - Percent of contacts predicted correctly from CONSIDERED in TARGET with SEP limit 
 PC(TT)   - Percent of contacts predicted correctly from TOTAL in TARGET with SEP limit 
 
                        CONSIDERED     CONSIDERED       TOTAL          TOTAL 
                      in PREDICTION    in TARGET    in PREDICTION    in TARGET 
 ALL RESIDUES USED          24              24            24            119 
 ALL CONTACTS (< 8.0A)      64              49            64            554 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        64         40   62.50   81.63    7.22       0     0.00          49       554  |   1-9999 
 RES CONTACTS        47         40   85.11   90.91   16.81       0     0.00          44       238  |   1-4    
 RES CONTACTS         5          0    0.00    0.00    0.00       0     0.00           2        34  |   5-8    
 RES CONTACTS        12          0    0.00    0.00    0.00       0     0.00           3       282  |   9-9999 
 
 
 
# WARNING! TARGET 914 atoms, MODEL 970 atoms, 914 common with TARGET 
           Number of atoms possible to evaluate: 183 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    68.24           50.0    46    19.5   236     ARMSMC  
     SECONDARY STRUCTURE . .    66.39           51.6    31    24.2   128     ARMSMC  
     SURFACE . . . . . . . .    75.91           38.1    21    14.4   146     ARMSMC  
     BURIED  . . . . . . . .    61.06           60.0    25    27.8    90     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    84.21           43.5    23    21.3   108     ARMSSC1 
     RELIABLE SIDE CHAINS  .    88.07           40.0    20    20.2    99     ARMSSC1 
     SECONDARY STRUCTURE . .    82.74           46.7    15    26.3    57     ARMSSC1 
     SURFACE . . . . . . . .    81.25           45.5    11    16.2    68     ARMSSC1 
     BURIED  . . . . . . . .    86.83           41.7    12    30.0    40     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    61.30           61.5    13    18.3    71     ARMSSC2 
     RELIABLE SIDE CHAINS  .    57.01           70.0    10    19.2    52     ARMSSC2 
     SECONDARY STRUCTURE . .    67.18           50.0     8    19.5    41     ARMSSC2 
     SURFACE . . . . . . . .    57.68           71.4     7    15.9    44     ARMSSC2 
     BURIED  . . . . . . . .    65.28           50.0     6    22.2    27     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   114.69            0.0     3    13.6    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .    80.59            0.0     2    18.2    11     ARMSSC3 
     SECONDARY STRUCTURE . .   128.98            0.0     2    12.5    16     ARMSSC3 
     SURFACE . . . . . . . .   127.79            0.0     2    10.5    19     ARMSSC3 
     BURIED  . . . . . . . .    82.46            0.0     1    33.3     3     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     5     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     5     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1   24 - 47   24   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    15     24 - 38       4.10    13.35 
  LCS LOCAL_SCORE:             60.59 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   24 - 47   24   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    12     25 - 36       1.91    14.64 
  LCS LOCAL_SCORE:             36.46 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   24 - 47   24   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7     27 - 33       0.92    15.01 
  LONGEST_CONTINUOUS_SEGMENT     7     29 - 35       0.98    14.38 
  LCS LOCAL_SCORE:             22.22 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      24       N     3    7   15       C        0   2   2   3   4   4   6  10  10  11  11  11  11  11  11  12  12  13  15  16  
 LCS      25       P     3   12   15       C        0   2   5   7   9  10  10  10  10  11  11  11  11  11  11  12  12  12  13  14  
 LCS      26       S     6   12   15       C        3   4   6   8   9  10  10  10  10  11  11  11  11  11  11  12  12  12  13  14  
 LCS      27       V     7   12   15       E        3   5   6   8   9  10  10  10  10  11  11  11  11  11  11  12  12  13  15  16  
 LCS      28       T     7   12   15       E        3   5   6   8   9  10  10  10  10  11  11  11  11  11  11  12  12  13  14  16  
 LCS      29       V     7   12   15       E        3   5   6   8   9  10  10  10  10  11  11  11  11  11  11  12  12  13  15  16  
 LCS      30       I     7   12   15       E        3   5   6   8   9  10  10  10  10  11  11  11  11  11  11  12  12  14  15  16  
 LCS      31       T     7   12   15       E        2   5   6   8   9  10  10  10  10  11  11  11  11  11  11  12  12  14  15  16  
 LCS      32       I     7   12   15       E        2   4   6   8   9  10  10  10  10  11  11  11  11  11  12  12  12  14  15  16  
 LCS      33       Q     7   12   15       E        3   5   6   8   9  10  10  10  10  11  11  11  11  11  12  12  12  14  15  16  
 LCS      34       A     7   12   15       E        2   3   6   8   9  10  10  10  10  11  11  11  11  11  12  12  12  14  15  16  
 LCS      35       S     7   12   15       E        3   5   6   8   9  10  10  10  10  11  11  11  11  11  12  12  12  14  15  16  
 LCS      36       N     4   12   15       E        3   3   5   5   8  10  10  10  10  11  11  11  11  11  12  12  12  14  15  16  
 LCS      37       S     4    6   15       C        3   3   3   4   5   7   7   8   9  11  11  11  11  11  12  12  12  14  15  16  
 LCS      38       T     4    6   15       C        3   3   3   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  16  
 LCS      39       E     4    6   14       C        3   3   3   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  16  
 LCS      40       L     4    6   14       C        2   2   3   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  16  
 LCS      41       D     4    5   14       C        2   3   3   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  16  
 LCS      42       M     4    5   14       E        2   3   3   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  16  
 LCS      43       T     5    5   14       E        2   3   4   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  16  
 LCS      44       D     5    5   14       E        3   3   4   4   5   7   7   8   8   9   9   9  11  11  12  12  12  14  15  15  
 LCS      45       F     5    5   14       E        3   3   4   4   5   7   7   8   8   8   9   9  11  11  12  12  12  14  15  16  
 LCS      46       V     5    5   13       E        3   3   4   4   4   5   5   8   8   8   9   9  10  11  12  12  12  14  15  16  
 LCS      47       F     5    5   13       E        3   3   4   4   4   4   4   5   7   8   9   9   9   9   9   9  10  14  15  16  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.90 
 
 NUMBER_OF_CA_Tg:  119      NUMBER_OF_CA_Pr:   24      PERCENT_OF_CA:  20.17  
 
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       4       6       8      10      11      12      12      13      13      14      14      14      14      14      15      15      15      17      18      20  
 GDT PERCENT_OF_CA_Pr   16.67   25.00   33.33   41.67   45.83   50.00   50.00   54.17   54.17   58.33   58.33   58.33   58.33   58.33   62.50   62.50   62.50   70.83   75.00   83.33 
 GDT PERCENT_OF_CA_Tg    3.36    5.04    6.72    8.40    9.24   10.08   10.08   10.92   10.92   11.76   11.76   11.76   11.76   11.76   12.61   12.61   12.61   14.29   15.13   16.81 
 GDT FRAGMENT: Beg-End  26-30   28-35   27-35   26-35   25-35   25-36   25-36   24-36   24-36   24-37   24-37   24-37   24-37   24-37   32-46   32-46   32-46   30-46   30-47   24-47  
 GDT RMS_LOCAL           0.25    0.63    0.90    1.35    1.55    1.91    1.91    2.24    2.24    2.92    2.92    2.92    2.92    2.92    5.24    5.24    5.24    6.58    6.78    7.95 
 GDT RMS_ALL_CA         15.87   14.92   14.90   14.84   14.92   14.64   14.64   14.46   14.46   13.93   13.93   13.93   13.93   13.93   14.99   14.99   14.99   12.72   12.18    8.82 
 
 
 TEST (CA)  RMS =   8.73               (Number of atoms:   24) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.73         24    20.2   119     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3636                            CRMSCA  
     SECONDARY STRUCTURE . .    8.88         16    25.0    64     CRMSCA  
     SURFACE . . . . . . . .    9.31         11    14.9    74     CRMSCA  
     BURIED  . . . . . . . .    8.20         13    28.9    45     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.89        120    20.3   592     CRMSMC  
     SECONDARY STRUCTURE . .    9.02         80    25.0   320     CRMSMC  
     SURFACE . . . . . . . .    9.48         55    15.0   367     CRMSMC  
     BURIED  . . . . . . . .    8.35         65    28.9   225     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .   10.13         87    19.9   438     CRMSSC  
     RELIABLE SIDE CHAINS  .   10.25         73    20.4   358     CRMSSC  
     SECONDARY STRUCTURE . .    9.93         60    23.6   254     CRMSSC  
     SURFACE . . . . . . . .   11.04         39    15.2   257     CRMSSC  
     BURIED  . . . . . . . .    9.33         48    26.5   181     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.40        183    20.0   914     CRMSALL 
     SECONDARY STRUCTURE . .    9.38        124    24.3   510     CRMSALL 
     SURFACE . . . . . . . .   10.14         83    15.0   553     CRMSALL 
     BURIED  . . . . . . . .    8.75        100    27.7   361     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 . . . . . . . . . .    8.468      1.000       0.500     24    20.2   119     ERRCA  
     SECONDARY STRUCTURE . .    8.706      1.000       0.500     16    25.0    64     ERRCA  
     SURFACE . . . . . . . .    8.957      1.000       0.500     11    14.9    74     ERRCA  
     BURIED  . . . . . . . .    8.054      1.000       0.500     13    28.9    45     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.598      1.000       0.500    120    20.3   592     ERRMC  
     SECONDARY STRUCTURE . .    8.818      1.000       0.500     80    25.0   320     ERRMC  
     SURFACE . . . . . . . .    9.123      1.000       0.500     55    15.0   367     ERRMC  
     BURIED  . . . . . . . .    8.154      1.000       0.500     65    28.9   225     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.708      1.000       0.500     87    19.9   438     ERRSC  
     RELIABLE SIDE CHAINS  .    9.861      1.000       0.500     73    20.4   358     ERRSC  
     SECONDARY STRUCTURE . .    9.742      1.000       0.500     60    23.6   254     ERRSC  
     SURFACE . . . . . . . .   10.334      1.000       0.500     39    15.2   257     ERRSC  
     BURIED  . . . . . . . .    9.199      1.000       0.500     48    26.5   181     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.033      1.000       0.500    183    20.0   914     ERRALL 
     SECONDARY STRUCTURE . .    9.175      1.000       0.500    124    24.3   510     ERRALL 
     SURFACE . . . . . . . .    9.607      1.000       0.500     83    15.0   553     ERRALL 
     BURIED  . . . . . . . .    8.557      1.000       0.500    100    27.7   361     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)         0         0         0         1        17      24     119   DISTCA 
CA  (P)      0.00      0.00      0.00      0.84     14.29             119   DISTCA 
CA  (RMS)    0.00      0.00      0.00      3.57      7.50                   DISTCA 
 
ALL (N)         0         0         4        11       116     183     914   DISTALL 
ALL (P)      0.00      0.00      0.44      1.20     12.69             914   DISTALL 
ALL (RMS)    0.00      0.00      2.50      3.47      7.69                   DISTALL 
 
 
 
 
END of the results output 
