 
####################################################### 
#                                                     # 
#                        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: 30 , MODEL 30 , TARGET 257 
#          The number of residues possible to evaluate: 30 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP    12     T     C     C             1.00 
 SSP    13     S     C     C             1.00 
 SSP    14     Y     C     C             1.00 
 SSP    15     H     H     C             1.00 
 SSP    16     D     H     C             1.00 
 SSP    17     T     H     C             1.00 
 SSP    18     C     H     C             1.00 
 SSP    19     E     H     C             1.00 
 SSP    20     K     H     H             1.00 
 SSP    21     N     C     H             1.00 
 SSP    22     I     H     H             1.00 
 SSP    23     V     H     H             1.00 
 SSP    24     A     H     H             1.00 
 SSP    25     C     H     H             1.00 
 SSP  BREAK 
 SSP    29     L     H     H             1.00 
 SSP    30     A     H     H             1.00 
 SSP    31     A     H     H             1.00 
 SSP    32     S     C     H             1.00 
 SSP    33     C     C     C             1.00 
 SSP    34     P     C     H             1.00 
 SSP    35     D     C     H             1.00 
 SSP    36     R     C     H             1.00 
 SSP    37     D     E     C             1.00 
 SSP    38     L     E     C             1.00 
 SSP    39     F     E     C             1.00 
 SSP    40     R     E     C             1.00 
 SSP    41     A     E     C             1.00 
 SSP    42     F     E     C             1.00 
 SSP    43     T     C     C             1.00 
 SSP    44     S     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              46.7      61.5      0.0     54.5     11.7 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        37.8      62.2      0.0     29.5     11.7 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            3              66.7               0.0 
 
         Number of wrong    Number of wrong 
             breaks             joins 
 B/J            0                 1 
 
  CONFIDENCE (P)     Average     NP    PP/BIN     Q3 
 BIN  0.90 - 1.00      1.00      30    100.0     46.7 
 
 BIN  0.00 - 1.00      1.00      30    100.0     46.7 
 
 
 
 
              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 241 
 
 ERROR! Check the common set of atoms between TARGET and MODEL 1888 1907 
# WARNING! TARGET 2018 atoms, MODEL 1936 atoms, 1888 common with TARGET 
           Number of atoms possible to evaluate: 120 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.20           46.4    56    10.9   512     ARMSMC  
     SECONDARY STRUCTURE . .    76.53           55.6    36    11.2   320     ARMSMC  
     SURFACE . . . . . . . .    74.62           46.4    28    10.9   256     ARMSMC  
     BURIED  . . . . . . . .    83.52           46.4    28    10.9   256     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   213     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   196     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   133     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   112     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   101     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   168     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   121     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   110     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    93     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    75     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    60     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    46     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    44     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    44     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    16     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    24     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    24     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    20     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    20     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   12 - 25   14   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    14     12 - 25       3.94     3.94 
  LCS LOCAL_SCORE:            100.00 
 
 FRAGMENT  2   29 - 44   16   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    16     29 - 44       2.25     2.25 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1   12 - 25   14   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     8     18 - 25       1.24     9.02 
  LCS LOCAL_SCORE:             47.96 
 
 FRAGMENT  2   29 - 44   16   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    15     29 - 43       1.78     2.35 
  LCS LOCAL_SCORE:             89.06 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1   12 - 25   14   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     6     20 - 25       0.62    10.60 
  LCS LOCAL_SCORE:             34.69 
 
 FRAGMENT  2   29 - 44   16   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     7     29 - 35       0.67     5.69 
  LCS LOCAL_SCORE:             38.28 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS      12       T     4    5   14       C        1   1   1   1   1   3   3   4   5   5   5   6   7   7   7   7   8   8   8   9  
 LCS      13       S     4    5   14       C        1   1   1   1   1   3   3   4   5   5   5   6   7   7   7   7   8   8   8   9  
 LCS      14       Y     4    5   14       C        1   1   1   1   1   3   3   4   5   5   5   6   7   7   7   7   8   8   8   9  
 LCS      15       H     4    5   14       H        1   1   1   1   1   3   3   4   5   5   5   6   7   7   7   8   8   8   8   9  
 LCS      16       D     3    5   14       H        1   1   1   1   1   3   3   4   5   5   5   6   7   9   9   9   9  10  10  10  
 LCS      17       T     3    5   14       H        1   1   1   1   1   3   3   5   6   7   8   9   9   9   9   9   9  10  10  10  
 LCS      18       C     5    8   14       H        0   2   2   3   3   6   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      19       E     5    8   14       H        1   1   2   3   3   6   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      20       K     6    8   14       H        1   2   2   3   3   3   3   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      21       N     6    8   14       C        1   2   2   3   4   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      22       I     6    8   14       H        1   2   2   3   4   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      23       V     6    8   14       H        1   2   2   3   4   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      24       A     6    8   14       H        1   2   2   3   3   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      25       C     6    8   14       H        1   2   2   3   3   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      26       E     0    0    0       H        0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
 LCS      27       R     0    0    0       H        0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
 LCS      28       D     0    0    0       H        0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0  
 LCS      29       L     7   15   16       H        1   1   2   3   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      30       A     7   15   16       H        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      31       A     7   15   16       H        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      32       S     7   15   16       C        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      33       C     7   15   16       C        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      34       P     7   15   16       C        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      35       D     7   15   16       C        1   2   2   3   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      36       R     5   15   16       C        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      37       D     5   15   16       E        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      38       L     6   15   16       E        1   1   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      39       F     6   15   16       E        1   1   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      40       R     6   15   16       E        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      41       A     6   15   16       E        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      42       F     6   15   16       E        1   2   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      43       T     6   15   16       C        1   1   2   4   5   7   7   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS      44       S     3    3   16       C        1   1   1   1   1   1   1   8   8   9   9   9   9   9   9   9   9  10  10  10  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.25 
 
 NUMBER_OF_CA_Tg:  257      NUMBER_OF_CA_Pr:   30      PERCENT_OF_CA:  11.67  
 
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       5       6       7      12      14      19      20      22      23      24      24      24      25      25      25      25      25      26      26      26  
 GDT PERCENT_OF_CA_Pr   16.67   20.00   23.33   40.00   46.67   63.33   66.67   73.33   76.67   80.00   80.00   80.00   83.33   83.33   83.33   83.33   83.33   86.67   86.67   86.67 
 GDT PERCENT_OF_CA_Tg    1.95    2.33    2.72    4.67    5.45    7.39    7.78    8.56    8.95    9.34    9.34    9.34    9.73    9.73    9.73    9.73    9.73   10.12   10.12   10.12 
 GDT FRAGMENT: Beg-End  21-25   30-35   29-35   30-43   29-43   21-43   21-43   19-43   18-44   18-44   18-44   18-44   17-44   17-44   17-44   17-44   17-44   16-44   16-44   16-44  
 GDT RMS_LOCAL           0.22    0.53    0.67    1.52    1.64    2.26    2.31    2.58    2.76    2.85    2.85    2.85    3.25    3.25    3.25    3.25    3.25    3.95    3.95    3.95 
 GDT RMS_ALL_CA          8.77   10.72   10.68    9.75    9.99    8.93    8.95    8.88    8.42    8.55    8.55    8.55    8.20    8.20    8.20    8.20    8.20    7.76    7.76    7.76 
 
 
 TEST (CA)  RMS =   6.93               (Number of atoms:   30) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.93         30    11.7   257     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2310                            CRMSCA  
     SECONDARY STRUCTURE . .    5.20         19    11.9   160     CRMSCA  
     SURFACE . . . . . . . .    6.74         14    10.9   129     CRMSCA  
     BURIED  . . . . . . . .    7.10         16    12.5   128     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.71        120     9.5  1269     CRMSMC  
     SECONDARY STRUCTURE . .    5.05         76     9.5   796     CRMSMC  
     SURFACE . . . . . . . .    6.45         56     8.8   639     CRMSMC  
     BURIED  . . . . . . . .    6.93         64    10.2   630     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   990     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   802     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   651     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   542     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   448     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.71        120     5.9  2018     CRMSALL 
     SECONDARY STRUCTURE . .    5.05         76     5.9  1291     CRMSALL 
     SURFACE . . . . . . . .    6.45         56     5.3  1058     CRMSALL 
     BURIED  . . . . . . . .    6.93         64     6.7   960     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 . . . . . . . . . .    5.980      1.000       0.500     30    11.7   257     ERRCA  
     SECONDARY STRUCTURE . .    4.691      1.000       0.500     19    11.9   160     ERRCA  
     SURFACE . . . . . . . .    5.949      1.000       0.500     14    10.9   129     ERRCA  
     BURIED  . . . . . . . .    6.007      1.000       0.500     16    12.5   128     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.804      1.000       0.500    120     9.5  1269     ERRMC  
     SECONDARY STRUCTURE . .    4.576      1.000       0.500     76     9.5   796     ERRMC  
     SURFACE . . . . . . . .    5.714      1.000       0.500     56     8.8   639     ERRMC  
     BURIED  . . . . . . . .    5.883      1.000       0.500     64    10.2   630     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   990     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   802     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   651     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   542     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   448     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.804      1.000       0.500    120     5.9  2018     ERRALL 
     SECONDARY STRUCTURE . .    4.576      1.000       0.500     76     5.9  1291     ERRALL 
     SURFACE . . . . . . . .    5.714      1.000       0.500     56     5.3  1058     ERRALL 
     BURIED  . . . . . . . .    5.883      1.000       0.500     64     6.7   960     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         3        15        26      30     257   DISTCA 
CA  (P)      0.00      0.39      1.17      5.84     10.12             257   DISTCA 
CA  (RMS)    0.00      1.07      2.15      3.70      5.12                   DISTCA 
 
ALL (N)         0         6        14        64       106     120    2018   DISTALL 
ALL (P)      0.00      0.30      0.69      3.17      5.25            2018   DISTALL 
ALL (RMS)    0.00      1.48      2.17      3.78      5.07                   DISTALL 
 
 
 
 
END of the results output 
