 
####################################################### 
#                                                     # 
#                        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: 25 , MODEL 25 , TARGET 237 
#          The number of residues possible to evaluate: 25 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    70     T     E     C             1.00 
 SSP    71     K     C     C             1.00 
 SSP    72     P     C     C             1.00 
 SSP    73     V     C     C             1.00 
 SSP    74     D     C     C             1.00 
 SSP    75     P     C     C             1.00 
 SSP    76     T     C     C             1.00 
 SSP    77     V     E     C             1.00 
 SSP    78     D     C     C             1.00 
 SSP    79     G     C     C             1.00 
 SSP    80     G     C     H             1.00 
 SSP    81     A     C     H             1.00 
 SSP    82     Q     E     H             1.00 
 SSP    83     V     E     H             1.00 
 SSP    84     Q     E     H             1.00 
 SSP    85     Q     E     C             1.00 
 SSP    86     V     E     C             1.00 
 SSP    87     I     E     C             1.00 
 SSP    88     N     E     H             1.00 
 SSP    89     I     E     H             1.00 
 SSP    90     E     E     H             1.00 
 SSP    91     C     E     H             1.00 
 SSP    92     I     C     H             1.00 
 SSP    93     S     C     H             1.00 
 SSP    94     D     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              36.0       0.0      0.0     69.2     10.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        30.9     100.0      0.0     59.5     10.5 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            2               0.0              50.0 
 
         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      25    100.0     36.0 
 
 BIN  0.00 - 1.00      1.00      25    100.0     36.0 
 
 
 
 
              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 
 
 
# WARNING! The number of residues with CB atom coordinates: MODEL 0 , TARGET 224 
 
# WARNING! TARGET 1874 atoms, MODEL 1817 atoms, 1795 common with TARGET 
           Number of atoms possible to evaluate: 100 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   100.39           31.2    48    10.2   472     ARMSMC  
     SECONDARY STRUCTURE . .   112.91            9.5    21     7.4   284     ARMSMC  
     SURFACE . . . . . . . .   102.71           31.0    29    10.9   267     ARMSMC  
     BURIED  . . . . . . . .    96.75           31.6    19     9.3   205     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   211     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   198     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   131     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   116     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    95     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   161     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   116     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   103     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    91     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    70     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    57     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    35     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    35     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    48     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     9     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    20     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    20     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    13     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    17     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1   70 - 94   25   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    15     74 - 88       4.78    12.80 
  LONGEST_CONTINUOUS_SEGMENT    15     75 - 89       4.85    12.32 
  LCS LOCAL_SCORE:             55.36 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   70 - 94   25   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8     75 - 82       1.79    14.68 
  LCS LOCAL_SCORE:             22.56 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   70 - 94   25   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     5     85 - 89       0.99    17.29 
  LCS LOCAL_SCORE:             14.72 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      70       T     3    4   14       E        1   1   1   1   2   2   3   4   4   5   5   5   5   5   5   5   5   5   5   6  
 LCS      71       K     3    4   14       C        1   1   1   1   2   2   3   4   4   5   5   5   5   5   5   5   5   6   8   8  
 LCS      72       P     3    4   14       C        1   1   1   1   2   2   3   4   4   5   5   5   5   5   5   6   7   7   8   8  
 LCS      73       V     4    7   14       C        1   1   1   2   2   2   3   4   4   5   5   5   5   5   5   5   7   7   8   8  
 LCS      74       D     4    7   15       C        1   1   1   2   2   2   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      75       P     4    8   15       C        1   1   2   2   3   3   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      76       T     4    8   15       C        1   1   2   2   3   3   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      77       V     4    8   15       E        1   1   2   2   3   3   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      78       D     4    8   15       C        1   1   2   2   3   3   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      79       G     4    8   15       C        1   1   2   2   3   3   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      80       G     3    8   15       C        1   1   2   2   3   3   3   4   4   5   5   5   5   6   6   6   7   7   8   8  
 LCS      81       A     3    8   15       C        1   1   1   2   3   3   3   3   3   5   5   5   5   6   6   6   7   7   8   8  
 LCS      82       Q     3    8   15       E        0   1   1   2   3   3   3   3   3   4   5   5   5   6   6   6   7   7   8   8  
 LCS      83       V     3    3   15       E        0   1   2   2   2   2   3   3   3   4   5   5   5   6   6   6   7   7   8   8  
 LCS      84       Q     3    4   15       E        0   1   2   2   2   2   3   3   3   4   5   5   5   6   6   6   7   7   8   8  
 LCS      85       Q     5    5   15       E        1   1   2   2   2   2   2   2   2   4   5   5   5   6   6   6   7   7   8   8  
 LCS      86       V     5    5   15       E        1   1   2   2   2   2   2   2   3   4   5   5   5   6   6   6   7   7   8   8  
 LCS      87       I     5    5   15       E        1   1   2   2   2   2   2   3   3   4   5   5   5   6   6   6   7   7   8   8  
 LCS      88       N     5    5   15       E        1   1   2   2   2   2   2   2   2   3   4   5   5   6   6   6   7   7   8   8  
 LCS      89       I     5    5   15       E        1   1   2   2   2   2   2   2   2   3   3   5   5   6   6   6   7   7   8   8  
 LCS      90       E     3    3   10       E        1   1   1   1   1   1   2   2   2   3   3   3   3   4   4   4   4   4   5   8  
 LCS      91       C     3    4   10       E        1   1   1   1   1   1   2   2   2   3   3   3   3   4   4   4   4   4   4   5  
 LCS      92       I     3    4   10       C        1   1   1   1   1   1   2   2   2   3   3   3   3   4   4   4   4   4   4   5  
 LCS      93       S     3    4   10       C        1   1   1   1   1   1   2   2   2   3   3   3   3   4   4   4   4   4   4   5  
 LCS      94       D     3    4   10       C        0   1   1   1   1   1   2   2   2   3   3   3   3   4   4   4   4   4   4   4  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.16 
 
 NUMBER_OF_CA_Tg:  237      NUMBER_OF_CA_Pr:   25      PERCENT_OF_CA:  10.55  
 
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       4       5       6       8       8       9      11      11      12      13      13      14      16      16      16      18      18      19      19  
 GDT PERCENT_OF_CA_Pr   16.00   16.00   20.00   24.00   32.00   32.00   36.00   44.00   44.00   48.00   52.00   52.00   56.00   64.00   64.00   64.00   72.00   72.00   76.00   76.00 
 GDT PERCENT_OF_CA_Tg    1.69    1.69    2.11    2.53    3.38    3.38    3.80    4.64    4.64    5.06    5.49    5.49    5.91    6.75    6.75    6.75    7.59    7.59    8.02    8.02 
 GDT FRAGMENT: Beg-End  76-79   76-79   85-89   75-82   75-82   75-82   75-83   70-80   70-80   70-81   70-83   75-87   70-83   74-89   74-89   74-89   72-89   72-89   71-89   71-89  
 GDT RMS_LOCAL           0.34    0.34    0.99    1.37    1.79    1.79    2.33    3.01    3.01    3.47    4.26    3.95    4.38    5.09    5.09    5.09    6.24    6.24    6.75    6.75 
 GDT RMS_ALL_CA         16.09   16.09   17.29   16.03   14.68   14.68   13.48   20.67   20.67   19.97   17.31   13.71   17.94   12.20   12.20   12.20   11.16   11.16   10.77   10.77 
 
 
 TEST (CA)  RMS =   9.90               (Number of atoms:   25) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    9.90         25    10.5   237     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3959                            CRMSCA  
     SECONDARY STRUCTURE . .    8.43         11     7.7   142     CRMSCA  
     SURFACE . . . . . . . .    8.73         15    11.2   134     CRMSCA  
     BURIED  . . . . . . . .   11.43         10     9.7   103     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    9.81        100     8.5  1172     CRMSMC  
     SECONDARY STRUCTURE . .    8.34         44     6.3   702     CRMSMC  
     SURFACE . . . . . . . .    8.70         60     9.1   662     CRMSMC  
     BURIED  . . . . . . . .   11.27         40     7.8   510     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   926     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   762     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   598     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   507     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   419     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    9.81        100     5.3  1874     CRMSALL 
     SECONDARY STRUCTURE . .    8.34         44     3.8  1166     CRMSALL 
     SURFACE . . . . . . . .    8.70         60     5.8  1043     CRMSALL 
     BURIED  . . . . . . . .   11.27         40     4.8   831     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 . . . . . . . . . .    9.249      1.000       0.500     25    10.5   237     ERRCA  
     SECONDARY STRUCTURE . .    7.835      1.000       0.500     11     7.7   142     ERRCA  
     SURFACE . . . . . . . .    8.450      1.000       0.500     15    11.2   134     ERRCA  
     BURIED  . . . . . . . .   10.446      1.000       0.500     10     9.7   103     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.164      1.000       0.500    100     8.5  1172     ERRMC  
     SECONDARY STRUCTURE . .    7.786      1.000       0.500     44     6.3   702     ERRMC  
     SURFACE . . . . . . . .    8.468      1.000       0.500     60     9.1   662     ERRMC  
     BURIED  . . . . . . . .   10.209      1.000       0.500     40     7.8   510     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   926     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   762     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   598     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   507     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   419     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.164      1.000       0.500    100     5.3  1874     ERRALL 
     SECONDARY STRUCTURE . .    7.786      1.000       0.500     44     3.8  1166     ERRALL 
     SURFACE . . . . . . . .    8.468      1.000       0.500     60     5.8  1043     ERRALL 
     BURIED  . . . . . . . .   10.209      1.000       0.500     40     4.8   831     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         3        19      25     237   DISTCA 
CA  (P)      0.00      0.00      0.00      1.27      8.02             237   DISTCA 
CA  (RMS)    0.00      0.00      0.00      4.61      7.81                   DISTCA 
 
ALL (N)         0         0         0         5        72     100    1874   DISTALL 
ALL (P)      0.00      0.00      0.00      0.27      3.84            1874   DISTALL 
ALL (RMS)    0.00      0.00      0.00      4.58      7.53                   DISTALL 
 
 
 
 
END of the results output 
