 
####################################################### 
#                                                     # 
#                        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: 18 , MODEL 18 , TARGET 248 
#          The number of residues possible to evaluate: 18 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   182     G     C     C             1.00 
 SSP   183     N     C     C             1.00 
 SSP   184     C     H     E             1.00 
 SSP   185     A     H     E             1.00 
 SSP   186     E     H     E             1.00 
 SSP   187     Q     H     E             1.00 
 SSP   188     D     H     E             1.00 
 SSP   189     G     C     C             1.00 
 SSP   190     S     C     C             1.00 
 SSP   191     G     C     E             1.00 
 SSP   192     W     E     E             1.00 
 SSP   193     W     C     E             1.00 
 SSP   194     M     C     E             1.00 
 SSP   195     N     C     E             1.00 
 SSP   196     K     C     C             1.00 
 SSP   197     C     C     C             1.00 
 SSP   198     H     C     C             1.00 
 SSP   199     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              50.0       0.0    100.0     66.7      7.3 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        62.2       0.0     20.0     91.7      7.3 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            1               0.0             100.0 
 
         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      18    100.0     50.0 
 
 BIN  0.00 - 1.00      1.00      18    100.0     50.0 
 
 
 
 
              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 221 
 
# WARNING! TARGET 1995 atoms, MODEL 2136 atoms, 1995 common with TARGET 
           Number of atoms possible to evaluate: 72 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    95.87           20.6    34     6.9   496     ARMSMC  
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   154     ARMSMC  
     SURFACE . . . . . . . .   118.78           14.3     7     2.8   251     ARMSMC  
     BURIED  . . . . . . . .    88.97           22.2    27    11.0   245     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   205     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   199     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    67     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   106     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    99     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   164     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   131     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    52     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    86     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    78     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    51     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    40     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    12     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    26     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    26     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     7     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    22     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     4     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  182 - 199  18   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    16    182 - 197      4.68     6.44 
  LONGEST_CONTINUOUS_SEGMENT    16    183 - 198      4.79     5.99 
  LCS LOCAL_SCORE:             88.27 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  182 - 199  18   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8    188 - 195      1.99     8.34 
  LONGEST_CONTINUOUS_SEGMENT     8    189 - 196      1.89     8.22 
  LCS LOCAL_SCORE:             34.57 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  182 - 199  18   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     4    182 - 185      0.83     7.99 
  LONGEST_CONTINUOUS_SEGMENT     4    190 - 193      0.92    12.16 
  LONGEST_CONTINUOUS_SEGMENT     4    193 - 196      0.55    11.36 
  LCS LOCAL_SCORE:             20.06 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     182       G     4    4   16       C        1   1   1   2   2   3   4   4   4   4   4   5   6   6   6   6   7   7   7   7  
 LCS     183       N     4    4   16       C        1   1   1   1   1   1   4   4   4   4   4   5   6   6   6   6   7   7   7   7  
 LCS     184       C     4    4   16       H        1   1   2   2   2   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     185       A     4    4   16       H        1   1   2   2   2   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     186       E     3    3   16       H        1   1   1   1   1   1   2   2   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     187       Q     3    5   16       H        1   1   1   1   1   1   2   2   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     188       D     3    8   16       H        1   1   1   2   3   3   3   3   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     189       G     3    8   16       C        1   1   2   2   3   3   3   3   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     190       S     4    8   16       C        1   1   2   2   3   3   3   3   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     191       G     4    8   16       C        1   1   1   2   3   3   3   3   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     192       W     4    8   16       E        1   1   2   2   3   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     193       W     4    8   16       C        1   1   2   2   3   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     194       M     4    8   16       C        1   1   1   2   3   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     195       N     4    8   16       C        1   1   2   2   3   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     196       K     4    8   16       C        1   1   2   2   3   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     197       C     3    6   16       C        1   1   2   2   2   3   4   4   4   5   5   5   6   6   6   6   7   7   7   7  
 LCS     198       H     3    5   16       C        1   1   2   2   2   2   3   4   4   4   5   5   6   6   6   6   7   7   7   7  
 LCS     199       A     3    5   14       C        0   1   1   1   2   2   2   3   4   4   4   5   5   6   6   6   7   7   7   7  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.10 
 
 NUMBER_OF_CA_Tg:  249      NUMBER_OF_CA_Pr:   18      PERCENT_OF_CA:   7.23  
 
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       4       5       6       8       9      10      10      12      13      14      14      15      16      17      17      18      18      18      18  
 GDT PERCENT_OF_CA_Pr   16.67   22.22   27.78   33.33   44.44   50.00   55.56   55.56   66.67   72.22   77.78   77.78   83.33   88.89   94.44   94.44  100.00  100.00  100.00  100.00 
 GDT PERCENT_OF_CA_Tg    1.20    1.61    2.01    2.41    3.21    3.61    4.02    4.02    4.82    5.22    5.62    5.62    6.02    6.43    6.83    6.83    7.23    7.23    7.23    7.23 
 GDT FRAGMENT: Beg-End 185-198 184-198 184-198 184-196 189-196 188-196 182-197 182-197 185-196 184-196 184-197 184-197 183-197 182-197 182-198 182-198 182-199 182-199 182-199 182-199 
 GDT RMS_LOCAL           0.06    0.32    0.95    1.40    1.89    2.02    2.40    2.40    3.34    3.60    3.84    3.84    4.34    4.68    5.06    5.06    5.51    5.51    5.51    5.51 
 GDT RMS_ALL_CA          6.90    6.96    8.10    7.60    8.22    8.10    7.82    7.82    7.28    7.01    6.69    6.69    6.57    6.44    5.82    5.82    5.51    5.51    5.51    5.51 
 
 
 TEST (CA)  RMS =   5.51               (Number of atoms:   18) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    5.51         18     7.2   249     CRMSCA  
     CRN = ALL/NP  . . . . .    0.3064                            CRMSCA  
     SECONDARY STRUCTURE . .    0.00          0     0.0    77     CRMSCA  
     SURFACE . . . . . . . .    5.66          4     3.2   126     CRMSCA  
     BURIED  . . . . . . . .    5.47         14    11.4   123     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    5.41         72     5.9  1216     CRMSMC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   381     CRMSMC  
     SURFACE . . . . . . . .    5.45         16     2.6   615     CRMSMC  
     BURIED  . . . . . . . .    5.40         56     9.3   601     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0  1000     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   888     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   325     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   498     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   502     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.41         72     3.6  1995     CRMSALL 
     SECONDARY STRUCTURE . .    0.00          0     0.0   633     CRMSALL 
     SURFACE . . . . . . . .    5.45         16     1.6  1002     CRMSALL 
     BURIED  . . . . . . . .    5.40         56     5.6   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 . . . . . . . . . .    3.234      0.412       0.206     18     7.2   249     ERRCA  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0    77     ERRCA  
     SURFACE . . . . . . . .    3.425      0.427       0.214      4     3.2   126     ERRCA  
     BURIED  . . . . . . . .    3.179      0.408       0.204     14    11.4   123     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.128      0.402       0.202     72     5.9  1216     ERRMC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   381     ERRMC  
     SURFACE . . . . . . . .    3.191      0.404       0.203     16     2.6   615     ERRMC  
     BURIED  . . . . . . . .    3.110      0.402       0.202     56     9.3   601     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  1000     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   888     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   325     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   498     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   502     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.128      0.402       0.202     72     3.6  1995     ERRALL 
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   633     ERRALL 
     SURFACE . . . . . . . .    3.191      0.404       0.203     16     1.6  1002     ERRALL 
     BURIED  . . . . . . . .    3.110      0.402       0.202     56     5.6   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         0         1         9        18      18     249   DISTCA 
CA  (P)      0.00      0.00      0.40      3.61      7.23             249   DISTCA 
CA  (RMS)    0.00      0.00      2.73      3.70      5.51                   DISTCA 
 
ALL (N)         0         4         9        34        72      72    1995   DISTALL 
ALL (P)      0.00      0.20      0.45      1.70      3.61            1995   DISTALL 
ALL (RMS)    0.00      1.63      2.25      3.56      5.41                   DISTALL 
 
 
 
 
END of the results output 
