 
####################################################### 
#                                                     # 
#                        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: 32 , MODEL 32 , TARGET 104 
#          The number of residues possible to evaluate: 32 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    63     S     H     C             1.00 
 SSP    64     K     C     E             1.00 
 SSP    65     T     C     E             1.00 
 SSP    66     K     C     E             1.00 
 SSP    67     V     E     E             1.00 
 SSP    68     Y     E     E             1.00 
 SSP    69     Y     E     E             1.00 
 SSP    70     F     E     E             1.00 
 SSP    71     Q     C     C             1.00 
 SSP    72     G     C     C             1.00 
 SSP    73     G     C     E             1.00 
 SSP    74     N     C     E             1.00 
 SSP    75     N     C     E             1.00 
 SSP    76     E     C     E             1.00 
 SSP    77     L     H     E             1.00 
 SSP    78     G     H     E             1.00 
 SSP    79     T     H     C             1.00 
 SSP    80     A     H     E             1.00 
 SSP    81     V     C     C             1.00 
 SSP    82     G     C     C             1.00 
 SSP    83     K     C     E             1.00 
 SSP    84     L     C     C             1.00 
 SSP    85     F     C     C             1.00 
 SSP    86     R     C     E             1.00 
 SSP  BREAK 
 SSP    88     G     C     E             1.00 
 SSP    89     V     E     E             1.00 
 SSP    90     V     E     E             1.00 
 SSP    91     S     E     C             1.00 
 SSP    92     I     E     H             1.00 
 SSP    93     L     C     H             1.00 
 SSP    94     E     C     H             1.00 
 SSP    95     A     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              40.6       0.0     75.0     36.8     30.8 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        41.7       0.0     72.9     40.0     30.8 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            4              41.7              33.3 
 
         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      32    100.0     40.6 
 
 BIN  0.00 - 1.00      1.00      32    100.0     40.6 
 
 
 
 
              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 95 
 
# WARNING! TARGET 1647 atoms, MODEL 687 atoms, 679 common with TARGET 
           Number of atoms possible to evaluate: 128 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    91.08           23.3    60    29.1   206     ARMSMC  
     SECONDARY STRUCTURE . .    66.77           35.3    17    17.3    98     ARMSMC  
     SURFACE . . . . . . . .    89.27           25.0    32    25.4   126     ARMSMC  
     BURIED  . . . . . . . .    93.10           21.4    28    35.0    80     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    87     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    78     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    45     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    57     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    30     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    61     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    44     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    32     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    43     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    25     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    21     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    11     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     1     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    15     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    15     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   63 - 86   24   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    14     73 - 86       4.52    13.04 
  LCS LOCAL_SCORE:             56.60 
 
 FRAGMENT  2   88 - 95   8    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8     88 - 95       3.04     3.04 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   63 - 86   24   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    10     63 - 72       1.79    15.54 
  LCS LOCAL_SCORE:             30.73 
 
 FRAGMENT  2   88 - 95   8    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6     88 - 93       1.13     3.88 
  LCS LOCAL_SCORE:             68.75 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   63 - 86   24   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     5     81 - 85       0.80    19.11 
  LCS LOCAL_SCORE:             14.93 
 
 FRAGMENT  2   88 - 95   8    Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     5     88 - 92       0.85     4.18 
  LCS LOCAL_SCORE:             57.81 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      63       S     3   10   13       H        2   4   7   8   9   9  10  11  11  12  12  12  12  12  13  13  14  14  14  15  
 LCS      64       K     3   10   13       C        2   2   3   3   5   9  10  10  11  12  12  12  12  12  13  13  14  14  14  15  
 LCS      65       T     4   10   13       C        2   5   7   8   9   9  10  11  11  12  12  12  12  12  13  13  14  14  15  17  
 LCS      66       K     4   10   13       C        2   5   7   8   9   9  10  11  11  12  12  12  12  12  13  13  14  16  19  20  
 LCS      67       V     4   10   13       E        2   5   7   8   9   9  10  11  11  12  12  12  12  13  15  16  17  18  19  20  
 LCS      68       Y     4   10   13       E        2   3   4   6   9   9  10  11  11  12  12  13  17  17  17  20  20  21  21  22  
 LCS      69       Y     3   10   13       E        2   4   7   8   9   9  10  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      70       F     3   10   13       E        2   5   7   8   9   9  10  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      71       Q     3   10   13       C        2   5   7   8   9   9  10  11  11  12  13  16  17  18  18  20  20  21  21  22  
 LCS      72       G     3   10   13       C        2   5   7   8   9   9  10  11  11  12  12  12  12  12  13  15  15  19  20  20  
 LCS      73       G     3    4   14       C        2   2   2   3   3   6   9  11  11  12  12  13  14  14  15  16  17  17  20  21  
 LCS      74       N     3    4   14       C        2   2   2   3   3   3   5   6   8   8   9  10  13  13  15  16  17  17  19  21  
 LCS      75       N     3    4   14       C        2   2   2   3   3   3   5   6   8  10  11  13  17  18  18  20  20  21  21  22  
 LCS      76       E     3    4   14       C        2   2   2   6   6   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      77       L     3    3   14       H        2   2   2   3   7   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      78       G     3    3   14       H        2   2   2   4   5   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      79       T     3    7   14       H        2   2   3   4   5   7   8   8   9  13  16  16  17  18  18  20  20  21  21  22  
 LCS      80       A     3    7   14       H        2   2   3   4   4   6   8   8   8  10  11  12  13  13  14  16  16  18  21  22  
 LCS      81       V     5    7   14       C        2   3   4   4   5   7   8   8   8  10  11  12  13  13  14  16  17  17  19  20  
 LCS      82       G     5    7   14       C        2   3   4   4   5   7   8   8   8  10  11  13  14  14  15  16  17  21  21  22  
 LCS      83       K     5    7   14       C        2   3   4   4   5   7   8   8   8  10  11  13  14  14  15  20  20  21  21  22  
 LCS      84       L     5    7   14       C        2   3   4   4   7   7   8   9  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      85       F     5    7   14       C        2   3   4   4   7   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      86       R     3    6   14       C        2   3   4   6   7   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      87       V     0    0    0       C        0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
 LCS      88       G     5    6    8       C        0   3   4   5   7   7   7  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      89       V     5    6    8       E        2   3   4   5   7   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      90       V     5    6    8       E        2   4   7   8   9   9  10  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      91       S     5    6    8       E        2   3   4   6   6   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      92       I     5    6    8       E        2   3   4   6   6   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      93       L     4    6    8       C        2   3   4   6   6   7   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      94       E     4    4    8       C        2   2   3   3   3   3   9  12  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS      95       A     4    4    8       C        2   2   3   3   3   3   4  11  13  14  16  16  17  18  18  20  20  21  21  22  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   1.14 
 
 NUMBER_OF_CA_Tg:  104      NUMBER_OF_CA_Pr:   32      PERCENT_OF_CA:  30.77  
 
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       3       6       8       9      10      10      11      13      14      15      17      17      18      19      19      21      21      22      22      23  
 GDT PERCENT_OF_CA_Pr    9.38   18.75   25.00   28.12   31.25   31.25   34.38   40.62   43.75   46.88   53.12   53.12   56.25   59.38   59.38   65.62   65.62   68.75   68.75   71.88 
 GDT PERCENT_OF_CA_Tg    2.88    5.77    7.69    8.65    9.62    9.62   10.58   12.50   13.46   14.42   16.35   16.35   17.31   18.27   18.27   20.19   20.19   21.15   21.15   22.12 
 GDT FRAGMENT: Beg-End  70-72   65-72   63-90   63-90   63-90   63-90   63-90   69-93   69-95   69-95   69-95   69-95   68-95   69-95   69-95   68-95   68-95   68-95   68-95   68-95  
 GDT RMS_LOCAL           0.00    0.67    1.05    1.14    1.42    1.42    1.73    2.99    3.24    3.36    3.83    3.83    4.06    4.44    4.44    5.09    5.09    5.52    5.52    5.87 
 GDT RMS_ALL_CA         15.49   14.97   15.10   15.05   15.01   15.01   15.20   12.20   12.05   12.08   11.78   11.78   11.66   12.02   12.02   11.63   11.63   11.39   11.39   11.25 
 
 
 TEST (CA)  RMS =  10.33               (Number of atoms:   32) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   10.33         32    30.8   104     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3229                            CRMSCA  
     SECONDARY STRUCTURE . .    9.59          9    18.4    49     CRMSCA  
     SURFACE . . . . . . . .   11.03         17    26.6    64     CRMSCA  
     BURIED  . . . . . . . .    9.49         15    37.5    40     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   10.26        128    25.0   511     CRMSMC  
     SECONDARY STRUCTURE . .    9.71         36    14.8   244     CRMSMC  
     SURFACE . . . . . . . .   10.92         68    21.5   317     CRMSMC  
     BURIED  . . . . . . . .    9.45         60    30.9   194     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0  1231     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0  1171     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   642     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   798     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   433     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   10.26        128     7.8  1647     CRMSALL 
     SECONDARY STRUCTURE . .    9.71         36     4.3   838     CRMSALL 
     SURFACE . . . . . . . .   10.92         68     6.5  1054     CRMSALL 
     BURIED  . . . . . . . .    9.45         60    10.1   593     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 . . . . . . . . . .    9.010      1.000       0.500     32    30.8   104     ERRCA  
     SECONDARY STRUCTURE . .    7.494      1.000       0.500      9    18.4    49     ERRCA  
     SURFACE . . . . . . . .    9.501      1.000       0.500     17    26.6    64     ERRCA  
     BURIED  . . . . . . . .    8.454      1.000       0.500     15    37.5    40     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.916      1.000       0.500    128    25.0   511     ERRMC  
     SECONDARY STRUCTURE . .    7.649      1.000       0.500     36    14.8   244     ERRMC  
     SURFACE . . . . . . . .    9.380      1.000       0.500     68    21.5   317     ERRMC  
     BURIED  . . . . . . . .    8.390      1.000       0.500     60    30.9   194     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  1231     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0  1171     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   642     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   798     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   433     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    8.916      1.000       0.500    128     7.8  1647     ERRALL 
     SECONDARY STRUCTURE . .    7.649      1.000       0.500     36     4.3   838     ERRALL 
     SURFACE . . . . . . . .    9.380      1.000       0.500     68     6.5  1054     ERRALL 
     BURIED  . . . . . . . .    8.390      1.000       0.500     60    10.1   593     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         2         3         7        21      32     104   DISTCA 
CA  (P)      0.96      1.92      2.88      6.73     20.19             104   DISTCA 
CA  (RMS)    0.83      1.26      1.74      3.66      6.40                   DISTCA 
 
ALL (N)         1         4        12        28        79     128    1647   DISTALL 
ALL (P)      0.06      0.24      0.73      1.70      4.80            1647   DISTALL 
ALL (RMS)    0.83      1.56      2.23      3.45      5.99                   DISTALL 
 
 
 
 
END of the results output 
