 
####################################################### 
#                                                     # 
#                        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: 33 , MODEL 33 , TARGET 71 
#          The number of residues possible to evaluate: 33 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP     5     V     C     C             1.00 
 SSP     6     P     H     C             1.00 
 SSP     7     I     H     E             1.00 
 SSP     8     K     H     E             1.00 
 SSP     9     V     H     E             1.00 
 SSP    10     L     H     E             1.00 
 SSP    11     H     H     E             1.00 
 SSP    12     E     C     C             1.00 
 SSP    13     A     C     C             1.00 
 SSP    14     E     C     C             1.00 
 SSP    15     G     C     C             1.00 
 SSP    16     H     C     E             1.00 
 SSP    17     I     E     E             1.00 
 SSP    18     V     E     E             1.00 
 SSP    19     T     E     E             1.00 
 SSP    20     C     E     E             1.00 
 SSP    21     E     E     E             1.00 
 SSP    22     T     E     E             1.00 
 SSP    23     N     C     E             1.00 
 SSP    24     T     C     C             1.00 
 SSP    25     G     C     C             1.00 
 SSP    26     E     C     E             1.00 
 SSP    27     V     E     E             1.00 
 SSP    28     Y     E     E             1.00 
 SSP    29     R     E     E             1.00 
 SSP    30     G     E     E             1.00 
 SSP    31     K     E     E             1.00 
 SSP    32     L     E     E             1.00 
 SSP    33     I     E     E             1.00 
 SSP    34     E     E     C             1.00 
 SSP    35     A     E     C             1.00 
 SSP    36     E     C     C             1.00 
 SSP    37     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              66.7       0.0     86.7     75.0     46.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        75.8       0.0    100.0     83.3     46.5 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            3              66.7              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      33    100.0     66.7 
 
 BIN  0.00 - 1.00      1.00      33    100.0     66.7 
 
 
 
 
              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 66 
 
# WARNING! TARGET 563 atoms, MODEL 457 atoms, 440 common with TARGET 
           Number of atoms possible to evaluate: 132 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.20           48.4    64    45.7   140     ARMSMC  
     SECONDARY STRUCTURE . .    84.22           42.9    42    47.7    88     ARMSMC  
     SURFACE . . . . . . . .    84.27           50.0    40    42.6    94     ARMSMC  
     BURIED  . . . . . . . .    69.93           45.8    24    52.2    46     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    55     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    41     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    44     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    36     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    28     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    37     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    20     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    17     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    11     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     2     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0     8     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     4     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0     8     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    5 - 37   33   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    28      7 - 34       4.91     7.51 
  LCS LOCAL_SCORE:             78.42 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1    5 - 37   33   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    10     22 - 31       1.75     9.28 
  LCS LOCAL_SCORE:             21.67 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1    5 - 37   33   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8     16 - 23       0.81    13.76 
  LCS LOCAL_SCORE:             16.16 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS       5       V     3    3   12       C        4   4   4   4   4   4   7   8  11  11  12  14  16  18  21  21  23  29  29  29  
 LCS       6       P     3    3   12       H        4   4   4   4   4   4   7   9  11  12  14  16  18  25  25  33  36  39  40  40  
 LCS       7       I     3    3   28       H        4   4   4   4   4   4   7   9  12  14  15  23  32  33  36  38  39  39  40  40  
 LCS       8       K     3    3   28       H        0   4   4   4   4   4   7   9  12  14  15  16  29  33  36  38  39  39  40  40  
 LCS       9       V     3    3   28       H        0   4   4   4   9  12  16  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      10       L     3    3   28       H        1   4   5   8  11  15  19  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      11       H     4    5   28       H        5   5   5   5   8   9  16  21  25  29  30  32  33  35  36  38  40  40  40  40  
 LCS      12       E     4    5   28       C        5   5   5   5  11  14  19  22  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      13       A     4    5   28       C        5   5   5   5   5   7   7   9  11  15  22  23  26  35  35  36  40  40  40  40  
 LCS      14       E     4    7   28       C        5   5   5   7   8   9   9  12  15  15  28  30  33  35  36  38  40  40  40  40  
 LCS      15       G     4    9   28       C        5   5   5   7   9  11  19  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      16       H     8    9   28       C        5   8  11  11  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      17       I     8    9   28       E        5   8  11  11  11  18  21  22  23  26  29  32  32  35  35  38  40  40  40  40  
 LCS      18       V     8    9   28       E        8   8  11  11  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      19       T     8    9   28       E        8   8  11  11  11  18  19  22  23  26  30  32  33  35  36  38  40  40  40  40  
 LCS      20       C     8    9   28       E        8   8  11  11  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      21       E     8    9   28       E        8   8  11  11  12  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      22       T     8   10   28       E        8   8  11  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      23       N     8   10   28       C        8   8  11  11  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      24       T     7   10   28       C        4   7   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      25       G     7   10   28       C        5   8   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      26       E     7   10   28       C        7   8   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      27       V     7   10   28       E        7   8   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      28       Y     7   10   28       E        7   8   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      29       R     7   10   28       E        7   8   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      30       G     7   10   28       E        7   8   9  12  14  18  21  22  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      31       K     4   10   28       E        4   7   9  12  14  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      32       L     4    9   28       E        4   5   7   8  12  18  21  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      33       I     4    6   28       E        4   5   7   8  11  12  19  23  26  29  30  32  33  35  36  38  40  40  40  40  
 LCS      34       E     4    6   28       E        0   5   7   7   8   9  11  16  19  23  28  30  33  35  36  38  40  40  40  40  
 LCS      35       A     3    6   22       E        0   4   4   7   8   9  11  11  12  12  18  21  25  25  26  32  40  40  40  40  
 LCS      36       E     3    3   12       C        1   4   4   4   7   8  11  12  14  15  18  21  25  30  33  36  40  40  40  40  
 LCS      37       D     3    3   12       C        0   4   4   4   4   5   5  11  12  12  18  21  22  23  26  32  40  40  40  40  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   3.49 
 
 NUMBER_OF_CA_Tg:   71      NUMBER_OF_CA_Pr:   33      PERCENT_OF_CA:  46.48  
 
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       6       6       8       9      10      13      15      17      19      21      22      23      24      25      26      27      29      29      29      29  
 GDT PERCENT_OF_CA_Pr   18.18   18.18   24.24   27.27   30.30   39.39   45.45   51.52   57.58   63.64   66.67   69.70   72.73   75.76   78.79   81.82   87.88   87.88   87.88   87.88 
 GDT PERCENT_OF_CA_Tg    8.45    8.45   11.27   12.68   14.08   18.31   21.13   23.94   26.76   29.58   30.99   32.39   33.80   35.21   36.62   38.03   40.85   40.85   40.85   40.85 
 GDT FRAGMENT: Beg-End  18-23   25-30   16-23   22-31   20-31   16-31   16-32    9-32    9-33    9-33    9-33    9-33    9-34    9-34    7-34    7-34    9-37    9-37    6-34    6-34  
 GDT RMS_LOCAL           0.39    0.35    0.81    1.27    1.54    2.08    2.42    2.93    3.21    3.43    3.59    3.75    4.10    4.25    4.58    4.71    5.72    5.72    5.22    5.22 
 GDT RMS_ALL_CA         14.24   11.02   13.76    9.55    9.32    9.03    8.60    7.91    7.59    7.74    7.77    7.87    7.47    7.53    7.44    7.51    7.41    7.41    7.43    7.43 
 
 
 TEST (CA)  RMS =   6.97               (Number of atoms:   33) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.97         33    46.5    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2111                            CRMSCA  
     SECONDARY STRUCTURE . .    6.13         21    47.7    44     CRMSCA  
     SURFACE . . . . . . . .    7.25         21    43.8    48     CRMSCA  
     BURIED  . . . . . . . .    6.45         12    52.2    23     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.98        132    37.7   350     CRMSMC  
     SECONDARY STRUCTURE . .    6.02         84    38.4   219     CRMSMC  
     SURFACE . . . . . . . .    7.35         84    35.4   237     CRMSMC  
     BURIED  . . . . . . . .    6.27         48    42.5   113     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   279     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   233     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   176     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   210     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0    69     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.98        132    23.4   563     CRMSALL 
     SECONDARY STRUCTURE . .    6.02         84    23.9   352     CRMSALL 
     SURFACE . . . . . . . .    7.35         84    20.9   402     CRMSALL 
     BURIED  . . . . . . . .    6.27         48    29.8   161     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 . . . . . . . . . .    4.477      0.501       0.251     33    46.5    71     ERRCA  
     SECONDARY STRUCTURE . .    3.855      0.469       0.234     21    47.7    44     ERRCA  
     SURFACE . . . . . . . .    4.652      0.505       0.253     21    43.8    48     ERRCA  
     BURIED  . . . . . . . .    4.170      0.495       0.247     12    52.2    23     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.420      0.493       0.247    132    37.7   350     ERRMC  
     SECONDARY STRUCTURE . .    3.738      0.458       0.229     84    38.4   219     ERRMC  
     SURFACE . . . . . . . .    4.644      0.496       0.248     84    35.4   237     ERRMC  
     BURIED  . . . . . . . .    4.027      0.488       0.244     48    42.5   113     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   279     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   233     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   176     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   210     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0    69     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.420      0.493       0.247    132    23.4   563     ERRALL 
     SECONDARY STRUCTURE . .    3.738      0.458       0.229     84    23.9   352     ERRALL 
     SURFACE . . . . . . . .    4.644      0.496       0.248     84    20.9   402     ERRALL 
     BURIED  . . . . . . . .    4.027      0.488       0.244     48    29.8   161     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         1         4        16        29      33      71   DISTCA 
CA  (P)      0.00      1.41      5.63     22.54     40.85              71   DISTCA 
CA  (RMS)    0.00      1.77      2.49      3.86      5.68                   DISTCA 
 
ALL (N)         0         5        16        62       116     132     563   DISTALL 
ALL (P)      0.00      0.89      2.84     11.01     20.60             563   DISTALL 
ALL (RMS)    0.00      1.76      2.26      3.70      5.51                   DISTALL 
 
 
 
 
END of the results output 
