 
####################################################### 
#                                                     # 
#                        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: 21 , MODEL 21 , TARGET 248 
#          The number of residues possible to evaluate: 21 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   225     I     C     C             1.00 
 SSP   226     I     E     C             1.00 
 SSP   227     W     E     C             1.00 
 SSP   228     A     C     C             1.00 
 SSP   229     T     C     C             1.00 
 SSP   230     W     C     C             1.00 
 SSP   231     K     C     C             1.00 
 SSP   232     T     C     C             1.00 
 SSP   233     R     C     C             1.00 
 SSP   234     W     C     C             1.00 
 SSP   235     Y     E     C             1.00 
 SSP   236     S     C     C             1.00 
 SSP   237     M     C     C             1.00 
 SSP   238     K     C     C             1.00 
 SSP   239     K     E     C             1.00 
 SSP   240     T     E     C             1.00 
 SSP   241     T     E     C             1.00 
 SSP   242     M     E     C             1.00 
 SSP   243     K     E     C             1.00 
 SSP   244     I     E     C             1.00 
 SSP   245     I     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              52.4       0.0      0.0    100.0      8.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        18.8     100.0      0.0     35.9      8.5 
 
           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      21    100.0     52.4 
 
 BIN  0.00 - 1.00      1.00      21    100.0     52.4 
 
 
 
 
              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          21              21            21            249 
 ALL CONTACTS (< 8.0A)      53              51            53           1264 
 
               in PREDICTION      Predicted correctly          Submitted as        in TARGET 
                CONSIDERED     NPC   PC(P)   PC(T)   PC(TT)    NOT  predicted   CONSIDERED  TOTAL  |   SEP 
 RES CONTACTS        53         34   64.15   66.67    2.69       0     0.00          51      1264  |   1-9999 
 RES CONTACTS        39         32   82.05   80.00    5.61       0     0.00          40       570  |   1-4    
 RES CONTACTS         4          0    0.00    0.00    0.00       0     0.00           4        81  |   5-8    
 RES CONTACTS        10          2   20.00   28.57    0.33       0     0.00           7       613  |   9-9999 
 
 
 
# WARNING! TARGET 1995 atoms, MODEL 2136 atoms, 1995 common with TARGET 
           Number of atoms possible to evaluate: 188 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    74.18           50.0    40     8.1   496     ARMSMC  
     SECONDARY STRUCTURE . .    33.43           53.8    13     8.4   154     ARMSMC  
     SURFACE . . . . . . . .   100.16           42.9    14     5.6   251     ARMSMC  
     BURIED  . . . . . . . .    55.36           53.8    26    10.6   245     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   106.79           25.0    20     9.8   205     ARMSSC1 
     RELIABLE SIDE CHAINS  .   106.79           25.0    20    10.1   199     ARMSSC1 
     SECONDARY STRUCTURE . .   131.43            0.0     7    10.4    67     ARMSSC1 
     SURFACE . . . . . . . .    96.18           42.9     7     6.6   106     ARMSSC1 
     BURIED  . . . . . . . .   112.08           15.4    13    13.1    99     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.85           33.3    15     9.1   164     ARMSSC2 
     RELIABLE SIDE CHAINS  .    80.85           33.3    15    11.5   131     ARMSSC2 
     SECONDARY STRUCTURE . .    54.14           40.0     5     9.6    52     ARMSSC2 
     SURFACE . . . . . . . .    67.36           40.0     5     5.8    86     ARMSSC2 
     BURIED  . . . . . . . .    86.82           30.0    10    12.8    78     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    92.95           28.6     7    13.7    51     ARMSSC3 
     RELIABLE SIDE CHAINS  .    92.95           28.6     7    17.5    40     ARMSSC3 
     SECONDARY STRUCTURE . .    45.23           33.3     3    17.6    17     ARMSSC3 
     SURFACE . . . . . . . .    95.94            0.0     3     7.7    39     ARMSSC3 
     BURIED  . . . . . . . .    90.65           50.0     4    33.3    12     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    77.63            0.0     5    19.2    26     ARMSSC4 
     RELIABLE SIDE CHAINS  .    77.63            0.0     5    19.2    26     ARMSSC4 
     SECONDARY STRUCTURE . .    85.77            0.0     2    28.6     7     ARMSSC4 
     SURFACE . . . . . . . .    87.41            0.0     3    13.6    22     ARMSSC4 
     BURIED  . . . . . . . .    60.05            0.0     2    50.0     4     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  225 - 245  21   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    18    225 - 242      4.97     6.01 
  LONGEST_CONTINUOUS_SEGMENT    18    226 - 243      4.92     5.70 
  LCS LOCAL_SCORE:             83.90 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  225 - 245  21   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8    238 - 245      1.59    14.63 
  LCS LOCAL_SCORE:             31.52 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  225 - 245  21   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6    234 - 239      0.69     8.84 
  LONGEST_CONTINUOUS_SEGMENT     6    238 - 243      0.71    15.96 
  LCS LOCAL_SCORE:             24.26 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     225       I     5    5   18       C        1   1   2   2   3   4   4   4   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     226       I     5    5   18       E        1   1   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     227       W     5    5   18       E        1   1   2   2   3   3   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     228       A     5    5   18       C        0   1   2   2   3   3   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     229       T     5    5   18       C        1   1   2   2   2   2   2   2   4   4   5   5   6   6   7   8   8   8   8   8  
 LCS     230       W     3    5   18       C        1   1   1   1   2   2   2   3   3   4   5   5   6   6   7   8   8   8   8   8  
 LCS     231       K     3    5   18       C        1   1   1   1   2   2   2   2   3   4   4   4   6   6   6   7   8   8   8   8  
 LCS     232       T     3    5   18       C        1   1   1   1   2   2   2   3   3   4   5   5   6   6   7   8   8   8   8   8  
 LCS     233       R     3    7   18       C        1   1   1   2   2   2   2   3   3   4   5   5   6   6   7   8   8   8   8   8  
 LCS     234       W     6    7   18       C        1   2   2   2   3   3   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     235       Y     6    7   18       E        1   2   2   2   3   3   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     236       S     6    7   18       C        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     237       M     6    7   18       C        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     238       K     6    8   18       C        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     239       K     6    8   18       E        1   2   2   2   3   3   4   4   5   6   6   6   6   6   7   8   8   8   8   8  
 LCS     240       T     6    8   18       E        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     241       T     6    8   18       E        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     242       M     6    8   18       E        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     243       K     6    8   18       E        1   2   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     244       I     5    8   14       E        1   1   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS     245       I     5    8   14       E        1   1   2   2   3   4   4   5   6   6   6   6   6   6   7   8   8   8   8   8  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.17 
 
 NUMBER_OF_CA_Tg:  249      NUMBER_OF_CA_Pr:   21      PERCENT_OF_CA:   8.43  
 
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       9      10      12      13      15      16      16      16      16      17      18      20      21      21      21      21  
 GDT PERCENT_OF_CA_Pr   19.05   28.57   28.57   33.33   42.86   47.62   57.14   61.90   71.43   76.19   76.19   76.19   76.19   80.95   85.71   95.24  100.00  100.00  100.00  100.00 
 GDT PERCENT_OF_CA_Tg    1.61    2.41    2.41    2.81    3.61    4.02    4.82    5.22    6.02    6.43    6.43    6.43    6.43    6.83    7.23    8.03    8.43    8.43    8.43    8.43 
 GDT FRAGMENT: Beg-End 234-237 238-243 234-239 227-241 225-245 225-245 226-245 226-245 225-245 225-245 225-245 225-245 225-245 225-245 225-245 225-245 225-245 225-245 225-245 225-245 
 GDT RMS_LOCAL           0.24    0.71    0.69    1.41    1.82    1.99    2.62    2.75    3.08    3.24    3.24    3.24    3.24    3.87    4.40    5.05    5.36    5.36    5.36    5.36 
 GDT RMS_ALL_CA          7.13   15.96    8.84    5.73    7.99    7.72    5.84    5.92    6.07    6.07    6.07    6.07    6.07    5.95    5.54    5.39    5.36    5.36    5.36    5.36 
 
 
 TEST (CA)  RMS =   5.36               (Number of atoms:   21) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.36         21     8.4   249     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2553                            CRMSCA  
     SECONDARY STRUCTURE . .    4.73          7     9.1    77     CRMSCA  
     SURFACE . . . . . . . .    6.56          7     5.6   126     CRMSCA  
     BURIED  . . . . . . . .    4.65         14    11.4   123     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.70        105     8.6  1216     CRMSMC  
     SECONDARY STRUCTURE . .    5.38         35     9.2   381     CRMSMC  
     SURFACE . . . . . . . .    6.66         35     5.7   615     CRMSMC  
     BURIED  . . . . . . . .    5.15         70    11.6   601     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    8.36        104    10.4  1000     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.36        104    11.7   888     CRMSSC  
     SECONDARY STRUCTURE . .    8.77         28     8.6   325     CRMSSC  
     SURFACE . . . . . . . .    9.05         43     8.6   498     CRMSSC  
     BURIED  . . . . . . . .    7.84         61    12.2   502     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.22        188     9.4  1995     CRMSALL 
     SECONDARY STRUCTURE . .    7.18         56     8.8   633     CRMSALL 
     SURFACE . . . . . . . .    8.11         71     7.1  1002     CRMSALL 
     BURIED  . . . . . . . .    6.62        117    11.8   993     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 . . . . . . . . . .    2.275      0.268       0.224     21     8.4   249     ERRCA  
     SECONDARY STRUCTURE . .    1.205      0.135       0.077      7     9.1    77     ERRCA  
     SURFACE . . . . . . . .    2.683      0.250       0.137      7     5.6   126     ERRCA  
     BURIED  . . . . . . . .    2.071      0.277       0.267     14    11.4   123     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    2.318      0.253       0.196    105     8.6  1216     ERRMC  
     SECONDARY STRUCTURE . .    1.542      0.153       0.082     35     9.2   381     ERRMC  
     SURFACE . . . . . . . .    2.784      0.260       0.162     35     5.7   615     ERRMC  
     BURIED  . . . . . . . .    2.085      0.250       0.213     70    11.6   601     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.117      0.327       0.202    104    10.4  1000     ERRSC  
     RELIABLE SIDE CHAINS  .    4.117      0.327       0.202    104    11.7   888     ERRSC  
     SECONDARY STRUCTURE . .    4.367      0.324       0.162     28     8.6   325     ERRSC  
     SURFACE . . . . . . . .    4.745      0.356       0.203     43     8.6   498     ERRSC  
     BURIED  . . . . . . . .    3.675      0.307       0.201     61    12.2   502     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.259      0.291       0.200    188     9.4  1995     ERRALL 
     SECONDARY STRUCTURE . .    2.869      0.232       0.120     56     8.8   633     ERRALL 
     SURFACE . . . . . . . .    3.866      0.309       0.180     71     7.1  1002     ERRALL 
     BURIED  . . . . . . . .    2.890      0.281       0.211    117    11.8   993     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         5         8        10        21      21     249   DISTCA 
CA  (P)      0.00      2.01      3.21      4.02      8.43             249   DISTCA 
CA  (RMS)    0.00      1.56      2.13      2.66      5.36                   DISTCA 
 
ALL (N)         1        25        42        74       165     188    1995   DISTALL 
ALL (P)      0.05      1.25      2.11      3.71      8.27            1995   DISTALL 
ALL (RMS)    0.88      1.54      2.09      3.09      5.92                   DISTALL 
 
 
 
 
END of the results output 
