 
####################################################### 
#                                                     # 
#                        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 185 
#          The number of residues possible to evaluate: 25 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   160     L     C     C             1.00 
 SSP   161     R     C     C             1.00 
 SSP   162     A     C     C             1.00 
 SSP   163     P     C     C             1.00 
 SSP   164     V     C     C             1.00 
 SSP   165     A     E     C             1.00 
 SSP   166     G     E     C             1.00 
 SSP   167     T     E     C             1.00 
 SSP   168     C     E     C             1.00 
 SSP   169     Y     E     C             1.00 
 SSP   170     Q     E     C             1.00 
 SSP   171     A     E     C             1.00 
 SSP   172     E     C     C             1.00 
 SSP   173     W     C     C             1.00 
 SSP   174     D     C     C             1.00 
 SSP   175     D     C     C             1.00 
 SSP   176     Y     C     C             1.00 
 SSP   177     V     H     C             1.00 
 SSP   178     P     H     C             1.00 
 SSP   179     K     H     C             1.00 
 SSP   180     L     H     C             1.00 
 SSP   181     Y     H     C             1.00 
 SSP   182     E     H     C             1.00 
 SSP   183     Q     H     C             1.00 
 SSP   184     L     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              44.0       0.0      0.0    100.0     13.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        11.4       0.0      0.0     25.8     13.5 
 
           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      25    100.0     44.0 
 
 BIN  0.00 - 1.00      1.00      25    100.0     44.0 
 
 
 
 
              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 170 
 
# WARNING! TARGET 1470 atoms, MODEL 1381 atoms, 1364 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 . . . . . . . . . .    90.30           41.7    48    13.0   368     ARMSMC  
     SECONDARY STRUCTURE . .   101.52           28.6    28    23.7   118     ARMSMC  
     SURFACE . . . . . . . .    95.18           45.0    20    10.6   188     ARMSMC  
     BURIED  . . . . . . . .    86.64           39.3    28    15.6   180     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   162     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   146     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    55     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    83     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    79     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   120     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    91     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    36     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    63     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    57     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    40     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    33     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    11     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    23     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    23     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    20     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  160 - 184  25   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    16    166 - 181      4.88    12.92 
  LONGEST_CONTINUOUS_SEGMENT    16    167 - 182      4.98    12.99 
  LCS LOCAL_SCORE:             58.24 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  160 - 184  25   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9    167 - 175      1.97    15.37 
  LONGEST_CONTINUOUS_SEGMENT     9    168 - 176      1.64    15.09 
  LCS LOCAL_SCORE:             25.12 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  160 - 184  25   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     5    168 - 172      0.68    15.48 
  LCS LOCAL_SCORE:             14.88 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     160       L     3    4   11       C        1   1   1   2   3   3   3   4   4   4   4   4   4   5   5   5   5   5   5   6  
 LCS     161       R     3    6   11       C        1   1   1   2   3   3   3   4   4   4   4   4   4   5   5   5   5   5   5   6  
 LCS     162       A     4    6   11       C        1   2   2   2   3   3   3   4   4   4   4   4   4   5   5   5   5   5   5   6  
 LCS     163       P     4    6   11       C        1   2   2   2   3   3   3   4   4   4   4   4   4   5   5   5   5   5   5   6  
 LCS     164       V     4    6   11       C        1   2   2   2   3   3   3   4   4   4   4   4   4   5   5   5   5   5   5   6  
 LCS     165       A     4    6   15       E        1   2   2   2   3   3   3   4   4   4   4   4   4   5   5   7   9   9   9  10  
 LCS     166       G     3    6   16       E        1   1   2   2   3   3   3   4   4   4   7   7   8   8   9   9   9   9   9  10  
 LCS     167       T     3    9   16       E        0   1   2   2   3   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     168       C     5    9   16       E        2   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     169       Y     5    9   16       E        2   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     170       Q     5    9   16       E        2   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     171       A     5    9   16       E        1   2   2   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     172       E     5    9   16       C        2   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     173       W     4    9   16       C        1   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     174       D     4    9   16       C        1   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     175       D     4    9   16       C        2   2   3   4   4   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     176       Y     4    9   16       C        1   2   2   2   3   4   5   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     177       V     3    4   16       H        1   1   1   2   2   2   3   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     178       P     3    4   16       H        1   1   1   2   2   2   2   3   5   7   7   7   8   8   9   9   9   9   9  10  
 LCS     179       K     3    4   16       H        1   1   1   2   2   2   4   5   6   7   7   7   8   8   9   9   9   9   9  10  
 LCS     180       L     3    3   16       H        0   1   1   1   1   2   2   3   4   4   4   5   8   8   9   9   9   9   9  10  
 LCS     181       Y     3    3   16       H        0   1   1   1   1   1   2   2   4   4   4   5   5   7   9   9   9   9   9  10  
 LCS     182       E     3    3   16       H        1   1   1   1   1   1   2   2   3   4   4   5   8   8   9   9   9   9   9  10  
 LCS     183       Q     3    3   11       H        1   1   1   1   1   1   2   2   3   3   4   4   4   5   5   7   7   8   9  10  
 LCS     184       L     3    3   11       C        1   1   1   1   1   1   2   2   3   3   4   4   5   5   5   7   7   8   9  10  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.27 
 
 NUMBER_OF_CA_Tg:  185      NUMBER_OF_CA_Pr:   25      PERCENT_OF_CA:  13.51  
 
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       5       7       8       8       9      10      10      12      13      13      14      16      16      17      17      17      18      18      19  
 GDT PERCENT_OF_CA_Pr   16.00   20.00   28.00   32.00   32.00   36.00   40.00   40.00   48.00   52.00   52.00   56.00   64.00   64.00   68.00   68.00   68.00   72.00   72.00   76.00 
 GDT PERCENT_OF_CA_Tg    2.16    2.70    3.78    4.32    4.32    4.86    5.41    5.41    6.49    7.03    7.03    7.57    8.65    8.65    9.19    9.19    9.19    9.73    9.73   10.27 
 GDT FRAGMENT: Beg-End 168-175 168-175 168-175 168-175 168-175 168-176 167-176 167-176 167-179 167-179 167-179 166-179 166-182 166-182 166-182 166-182 166-182 165-182 165-182 166-184 
 GDT RMS_LOCAL           0.20    0.54    0.93    1.15    1.15    1.64    2.13    2.13    3.13    3.47    3.47    3.89    4.77    4.77    5.12    5.12    5.12    5.68    5.68    6.13 
 GDT RMS_ALL_CA         14.91   14.96   15.24   15.29   15.29   15.09   15.26   15.26   13.95   13.73   13.73   13.49   13.04   13.04   12.83   12.83   12.83   12.56   12.56   12.61 
 
 
 TEST (CA)  RMS =  11.38               (Number of atoms:   25) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .   11.38         25    13.5   185     CRMSCA  
     CRN = ALL/NP  . . . . .    0.4552                            CRMSCA  
     SECONDARY STRUCTURE . .    7.28         14    23.7    59     CRMSCA  
     SURFACE . . . . . . . .   12.28         10    10.5    95     CRMSCA  
     BURIED  . . . . . . . .   10.74         15    16.7    90     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .   11.23        100    11.0   910     CRMSMC  
     SECONDARY STRUCTURE . .    7.12         56    19.0   294     CRMSMC  
     SURFACE . . . . . . . .   11.89         40     8.6   466     CRMSMC  
     BURIED  . . . . . . . .   10.77         60    13.5   444     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   730     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   614     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   262     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   361     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   369     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .   11.23        100     6.8  1470     CRMSALL 
     SECONDARY STRUCTURE . .    7.12         56    11.2   498     CRMSALL 
     SURFACE . . . . . . . .   11.89         40     5.4   741     CRMSALL 
     BURIED  . . . . . . . .   10.77         60     8.2   729     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 . . . . . . . . . .   10.001      1.000       0.500     25    13.5   185     ERRCA  
     SECONDARY STRUCTURE . .    6.963      1.000       0.500     14    23.7    59     ERRCA  
     SURFACE . . . . . . . .   10.617      1.000       0.500     10    10.5    95     ERRCA  
     BURIED  . . . . . . . .    9.590      1.000       0.500     15    16.7    90     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.789      1.000       0.500    100    11.0   910     ERRMC  
     SECONDARY STRUCTURE . .    6.725      1.000       0.500     56    19.0   294     ERRMC  
     SURFACE . . . . . . . .   10.279      1.000       0.500     40     8.6   466     ERRMC  
     BURIED  . . . . . . . .    9.463      1.000       0.500     60    13.5   444     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   730     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   614     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   262     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   361     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   369     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    9.789      1.000       0.500    100     6.8  1470     ERRALL 
     SECONDARY STRUCTURE . .    6.725      1.000       0.500     56    11.2   498     ERRALL 
     SURFACE . . . . . . . .   10.279      1.000       0.500     40     5.4   741     ERRALL 
     BURIED  . . . . . . . .    9.463      1.000       0.500     60     8.2   729     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        16      25     185   DISTCA 
CA  (P)      0.00      0.00      0.00      1.62      8.65             185   DISTCA 
CA  (RMS)    0.00      0.00      0.00      4.17      7.41                   DISTCA 
 
ALL (N)         0         1         3        16        67     100    1470   DISTALL 
ALL (P)      0.00      0.07      0.20      1.09      4.56            1470   DISTALL 
ALL (RMS)    0.00      1.21      2.22      3.98      7.40                   DISTALL 
 
 
 
 
END of the results output 
