 
####################################################### 
#                                                     # 
#                        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: 20 , MODEL 20 , TARGET 71 
#          The number of residues possible to evaluate: 20 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    55     V     E     C             1.00 
 SSP    56     A     E     E             1.00 
 SSP    57     Q     E     C             1.00 
 SSP    58     L     E     C             1.00 
 SSP    59     E     E     C             1.00 
 SSP    60     Q     E     C             1.00 
 SSP    61     V     E     C             1.00 
 SSP    62     Y     E     C             1.00 
 SSP    63     I     E     C             1.00 
 SSP    64     R     C     C             1.00 
 SSP    65     G     H     C             1.00 
 SSP    66     S     H     C             1.00 
 SSP    67     K     H     C             1.00 
 SSP    68     I     E     C             1.00 
 SSP    69     R     E     C             1.00 
 SSP    70     F     E     C             1.00 
 SSP    71     L     E     E             1.00 
 SSP    72     I     E     C             1.00 
 SSP    73     L     C     C             1.00 
 SSP    74     P     C     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              25.0       0.0     14.3    100.0     28.2 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        20.4       0.0     14.3     69.0     28.2 
 
           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      20    100.0     25.0 
 
 BIN  0.00 - 1.00      1.00      20    100.0     25.0 
 
 
 
 
              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          20              20            20             71 
 ALL CONTACTS (< 8.0A)      62              40            62            319 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        62         33   53.23   82.50   10.34       0     0.00          40       319  |   1-9999 
 RES CONTACTS        40         33   82.50   84.62   20.75       0     0.00          39       159  |   1-4    
 RES CONTACTS         6          0    0.00    0.00    0.00       0     0.00           1        23  |   5-8    
 RES CONTACTS        16          0    0.00    0.00    0.00       0     0.00           0       137  |   9-9999 
 
 
 
# WARNING! TARGET 563 atoms, MODEL 623 atoms, 557 common with TARGET 
           Number of atoms possible to evaluate: 166 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    71.26           48.7    39    27.9   140     ARMSMC  
     SECONDARY STRUCTURE . .    69.18           48.1    27    30.7    88     ARMSMC  
     SURFACE . . . . . . . .    67.54           55.2    29    30.9    94     ARMSMC  
     BURIED  . . . . . . . .    81.08           30.0    10    21.7    46     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    69.21           47.1    17    27.4    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    66.50           53.3    15    27.3    55     ARMSSC1 
     SECONDARY STRUCTURE . .    78.37           38.5    13    31.7    41     ARMSSC1 
     SURFACE . . . . . . . .    63.34           50.0    14    31.8    44     ARMSSC1 
     BURIED  . . . . . . . .    91.76           33.3     3    16.7    18     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.15           40.0    15    31.9    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.02           41.7    12    33.3    36     ARMSSC2 
     SECONDARY STRUCTURE . .    80.41           36.4    11    39.3    28     ARMSSC2 
     SURFACE . . . . . . . .    68.26           46.2    13    35.1    37     ARMSSC2 
     BURIED  . . . . . . . .   119.82            0.0     2    20.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    88.85           33.3     6    30.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .    76.87           25.0     4    23.5    17     ARMSSC3 
     SECONDARY STRUCTURE . .   107.34           25.0     4    36.4    11     ARMSSC3 
     SURFACE . . . . . . . .    88.85           33.3     6    33.3    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   109.46            0.0     3    37.5     8     ARMSSC4 
     RELIABLE SIDE CHAINS  .   109.46            0.0     3    37.5     8     ARMSSC4 
     SECONDARY STRUCTURE . .    47.86            0.0     1    25.0     4     ARMSSC4 
     SURFACE . . . . . . . .   109.46            0.0     3    37.5     8     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   55 - 75   21   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    15     61 - 75       4.66    10.24 
  LCS LOCAL_SCORE:             68.93 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   55 - 75   21   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8     68 - 75       1.77    12.44 
  LCS LOCAL_SCORE:             32.88 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   55 - 75   21   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6     55 - 60       1.00    15.61 
  LONGEST_CONTINUOUS_SEGMENT     6     69 - 74       0.97    16.25 
  LONGEST_CONTINUOUS_SEGMENT     6     70 - 75       0.92    14.67 
  LCS LOCAL_SCORE:             24.94 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      55       V     6    6   13       E        0   4   8   8   8   8   9  11  11  12  14  15  18  18  18  19  19  21  22  22  
 LCS      56       A     6    6   13       E        4   5   8   8   8   8   9  11  11  12  14  15  18  18  18  19  19  21  22  22  
 LCS      57       Q     6    6   13       E        4   5   8   8   8   8   9  11  11  12  14  15  18  18  18  19  19  21  26  26  
 LCS      58       L     6    6   13       E        4   5   8   8   8   8   9  11  11  12  14  15  18  18  18  19  19  21  26  26  
 LCS      59       E     6    6   13       E        4   5   8   8   8   8   9  11  11  12  14  15  18  18  18  19  19  21  26  26  
 LCS      60       Q     6    6   14       E        4   5   8   8   8   8   9  11  11  12  14  15  18  18  18  19  21  22  26  26  
 LCS      61       V     4    5   15       E        4   5   5   7   7   8   9  11  12  14  16  18  19  19  21  21  21  22  26  26  
 LCS      62       Y     4    5   15       E        4   5   5   7   7   8  11  12  12  14  16  18  19  19  21  21  21  22  26  26  
 LCS      63       I     4    7   15       E        4   5   5   5   8   9   9  12  12  12  14  16  18  19  21  21  21  22  26  26  
 LCS      64       R     4    7   15       C        4   5   5   7   8   9  11  12  12  14  16  18  19  19  21  21  21  22  26  26  
 LCS      65       G     4    7   15       H        4   5   5   7   8   9  11  12  12  14  16  18  19  19  21  21  21  22  26  26  
 LCS      66       S     4    7   15       H        4   5   5   7   9  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      67       K     4    7   15       H        4   5   5   8  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      68       I     4    8   15       E        4   5   5   8  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      69       R     6    8   15       E        4   8   8   9   9  12  12  14  14  14  15  18  19  19  21  21  21  22  26  26  
 LCS      70       F     6    8   15       E        5   8   8   9  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      71       L     6    8   15       E        5   8   8   9  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      72       I     6    8   15       E        5   5   8   9  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      73       L     6    8   15       C        5   8   8   9  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS      74       P     6    8   15       C        5   8   8   9  11  11  12  14  14  14  15  18  19  19  21  21  21  22  26  26  
 LCS      75       D     6    8   15       C        5   8   8   9  11  12  12  14  14  14  16  18  19  19  21  21  21  22  26  26  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   2.18 
 
 NUMBER_OF_CA_Tg:   71      NUMBER_OF_CA_Pr:   21      PERCENT_OF_CA:  29.58  
 
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       6       7       8       9       9      10      10      10      12      13      14      14      15      15      15      16      19      19  
 GDT PERCENT_OF_CA_Pr   19.05   28.57   28.57   33.33   38.10   42.86   42.86   47.62   47.62   47.62   57.14   61.90   66.67   66.67   71.43   71.43   71.43   76.19   90.48   90.48 
 GDT PERCENT_OF_CA_Tg    5.63    8.45    8.45    9.86   11.27   12.68   12.68   14.08   14.08   14.08   16.90   18.31   19.72   19.72   21.13   21.13   21.13   22.54   26.76   26.76 
 GDT FRAGMENT: Beg-End  72-75   69-75   69-75   69-75   67-75   66-75   67-75   66-75   66-75   66-75   61-75   61-75   61-75   61-75   61-75   61-75   61-75   60-75   57-75   57-75  
 GDT RMS_LOCAL           0.21    0.71    0.71    1.01    1.75    2.23    2.17    2.44    2.44    2.44    3.98    4.06    4.34    4.34    4.66    4.66    4.66    5.21    7.00    7.00 
 GDT RMS_ALL_CA         14.03   14.98   14.98   15.24   12.65    9.93   11.72   10.19   10.19   10.19   10.27   10.08   10.23   10.23   10.24   10.24   10.24    9.96    8.78    8.78 
 
 
 TEST (CA)  RMS =   8.43               (Number of atoms:   21) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    8.43         21    29.6    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4015                            CRMSCA  
     SECONDARY STRUCTURE . .    9.02         14    31.8    44     CRMSCA  
     SURFACE . . . . . . . .    8.26         16    33.3    48     CRMSCA  
     BURIED  . . . . . . . .    8.97          5    21.7    23     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    8.51        101    28.9   350     CRMSMC  
     SECONDARY STRUCTURE . .    9.05         70    32.0   219     CRMSMC  
     SURFACE . . . . . . . .    8.35         77    32.5   237     CRMSMC  
     BURIED  . . . . . . . .    8.99         24    21.2   113     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    9.28         84    30.1   279     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.83         70    30.0   233     CRMSSC  
     SECONDARY STRUCTURE . .    9.66         64    36.4   176     CRMSSC  
     SURFACE . . . . . . . .    9.19         72    34.3   210     CRMSSC  
     BURIED  . . . . . . . .    9.82         12    17.4    69     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    8.85        166    29.5   563     CRMSALL 
     SECONDARY STRUCTURE . .    9.33        120    34.1   352     CRMSALL 
     SURFACE . . . . . . . .    8.78        134    33.3   402     CRMSALL 
     BURIED  . . . . . . . .    9.15         32    19.9   161     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 . . . . . . . . . .    7.884      1.000       0.500     21    29.6    71     ERRCA  
     SECONDARY STRUCTURE . .    8.400      1.000       0.500     14    31.8    44     ERRCA  
     SURFACE . . . . . . . .    7.679      1.000       0.500     16    33.3    48     ERRCA  
     BURIED  . . . . . . . .    8.538      1.000       0.500      5    21.7    23     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.891      1.000       0.500    101    28.9   350     ERRMC  
     SECONDARY STRUCTURE . .    8.388      1.000       0.500     70    32.0   219     ERRMC  
     SURFACE . . . . . . . .    7.685      1.000       0.500     77    32.5   237     ERRMC  
     BURIED  . . . . . . . .    8.553      1.000       0.500     24    21.2   113     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.579      1.000       0.500     84    30.1   279     ERRSC  
     RELIABLE SIDE CHAINS  .    8.147      1.000       0.500     70    30.0   233     ERRSC  
     SECONDARY STRUCTURE . .    9.111      1.000       0.500     64    36.4   176     ERRSC  
     SURFACE . . . . . . . .    8.476      1.000       0.500     72    34.3   210     ERRSC  
     BURIED  . . . . . . . .    9.196      1.000       0.500     12    17.4    69     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.205      1.000       0.500    166    29.5   563     ERRALL 
     SECONDARY STRUCTURE . .    8.731      1.000       0.500    120    34.1   352     ERRALL 
     SURFACE . . . . . . . .    8.096      1.000       0.500    134    33.3   402     ERRALL 
     BURIED  . . . . . . . .    8.662      1.000       0.500     32    19.9   161     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         2        19      21      71   DISTCA 
CA  (P)      0.00      0.00      0.00      2.82     26.76              71   DISTCA 
CA  (RMS)    0.00      0.00      0.00      3.54      7.39                   DISTCA 
 
ALL (N)         1         3         8        21       126     166     563   DISTALL 
ALL (P)      0.18      0.53      1.42      3.73     22.38             563   DISTALL 
ALL (RMS)    0.86      1.49      2.19      3.44      7.10                   DISTALL 
 
 
 
 
END of the results output 
