 
####################################################### 
#                                                     # 
#                        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: 35 , MODEL 35 , TARGET 332 
#          The number of residues possible to evaluate: 35 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   118     F     C     C             1.00 
 SSP   119     R     C     C             1.00 
 SSP   120     N     C     C             1.00 
 SSP   121     W     C     C             1.00 
 SSP   122     A     C     C             1.00 
 SSP   123     A     C     C             1.00 
 SSP   124     G     C     C             1.00 
 SSP   125     Q     C     C             1.00 
 SSP   126     G     C     C             1.00 
 SSP   127     A     C     C             1.00 
 SSP   128     D     C     C             1.00 
 SSP   129     D     C     C             1.00 
 SSP   130     N     C     C             1.00 
 SSP   131     G     C     C             1.00 
 SSP   132     I     C     C             1.00 
 SSP   133     R     C     E             1.00 
 SSP   134     A     E     C             1.00 
 SSP   135     N     C     C             1.00 
 SSP   136     N     C     E             1.00 
 SSP   137     L     E     C             1.00 
 SSP   138     I     E     C             1.00 
 SSP   139     S     E     C             1.00 
 SSP   140     Y     E     C             1.00 
 SSP   141     Y     E     C             1.00 
 SSP   142     T     C     C             1.00 
 SSP   143     P     C     C             1.00 
 SSP   144     N     C     E             1.00 
 SSP   145     F     E     E             1.00 
 SSP   146     G     C     C             1.00 
 SSP   147     G     C     C             1.00 
 SSP   148     F     E     E             1.00 
 SSP   149     N     E     E             1.00 
 SSP   150     A     E     C             1.00 
 SSP   151     G     E     C             1.00 
 SSP   152     F     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              65.7       0.0     25.0     87.0     10.5 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        68.5     100.0     29.2     88.9     10.5 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            2              50.0               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      35    100.0     65.7 
 
 BIN  0.00 - 1.00      1.00      35    100.0     65.7 
 
 
 
 
              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 278 
 
# WARNING! TARGET 2461 atoms, MODEL 2331 atoms, 2331 common with TARGET 
           Number of atoms possible to evaluate: 140 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    79.42           50.0    68    10.3   662     ARMSMC  
     SECONDARY STRUCTURE . .    17.67           89.5    19     5.5   348     ARMSMC  
     SURFACE . . . . . . . .    79.41           42.9    35     9.4   372     ARMSMC  
     BURIED  . . . . . . . .    79.43           57.6    33    11.4   290     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   245     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   226     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   135     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   145     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   100     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   180     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   129     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    97     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   115     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    65     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    56     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    41     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    33     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    23     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    31     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    31     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    20     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  118 - 152  35   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    26    127 - 152      4.83     8.57 
  LCS LOCAL_SCORE:             67.59 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  118 - 152  35   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    15    138 - 152      1.80     9.18 
  LCS LOCAL_SCORE:             30.37 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  118 - 152  35   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT     9    144 - 152      0.82     9.40 
  LCS LOCAL_SCORE:             18.94 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     118       F     4    5   13       C        1   1   1   1   1   1   2   2   2   2   2   3   5   6   6   7   8   8   8   8  
 LCS     119       R     4    5   13       C        1   1   1   1   1   3   3   3   5   5   5   6   6   6   6   7   8   8   9   9  
 LCS     120       N     4    5   18       C        1   1   1   1   1   1   1   2   2   2   3   3   5   5   6   6   7   8   9   9  
 LCS     121       W     7    8   18       C        1   1   2   2   2   2   2   3   3   3   4   6   6   6   6   6   7   8   9   9  
 LCS     122       A     7    8   18       C        1   1   2   2   2   2   2   3   3   3   4   4   4   5   5   5   7   8   9   9  
 LCS     123       A     7    8   18       C        1   1   2   2   2   2   2   3   3   3   4   4   4   5   5   5   7   8   9   9  
 LCS     124       G     7    8   18       C        1   1   2   2   2   2   2   3   3   3   4   4   4   5   5   5   6   8   9   9  
 LCS     125       Q     7    8   18       C        0   1   2   2   2   2   2   3   3   3   4   4   4   5   5   5   6   7   7   9  
 LCS     126       G     7    8   18       C        0   0   2   2   2   2   2   3   3   3   4   4   4   5   5   5   6   8   9   9  
 LCS     127       A     7    8   26       C        0   1   2   2   2   2   2   2   3   3   4   4   4   5   5   5   7   8   9   9  
 LCS     128       D     5    8   26       C        0   1   2   2   2   2   2   2   4   5   5   6   6   6   7   7   8   8   9   9  
 LCS     129       D     3    5   26       C        0   0   1   1   1   1   2   3   3   3   4   6   6   7   7   7   8   8   9   9  
 LCS     130       N     4    5   26       C        1   1   1   1   1   1   2   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     131       G     4    5   26       C        1   1   1   1   1   2   3   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     132       I     4    5   26       C        1   1   1   1   1   1   2   2   3   6   6   6   6   7   7   7   8   8   9   9  
 LCS     133       R     4    5   26       C        1   1   1   1   1   2   2   3   4   6   6   6   6   7   7   7   8   8   9   9  
 LCS     134       A     3    7   26       E        0   0   1   1   1   2   2   3   3   4   6   6   6   7   7   7   8   8   8   9  
 LCS     135       N     6   12   26       C        0   1   1   2   3   3   4   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     136       N     7   12   26       C        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     137       L     7   12   26       E        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     138       I     7   15   26       E        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     139       S     7   15   26       E        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     140       Y     7   15   26       E        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     141       Y     7   15   26       E        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     142       T     7   15   26       C        1   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     143       P     8   15   26       C        0   1   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     144       N     9   15   26       C        0   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     145       F     9   15   26       E        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     146       G     9   15   26       C        0   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     147       G     9   15   26       C        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     148       F     9   15   26       E        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     149       N     9   15   26       E        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     150       A     9   15   26       E        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     151       G     9   15   26       E        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS     152       F     9   15   26       E        1   2   2   3   4   5   5   5   5   6   6   6   6   7   7   7   8   8   9   9  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.21 
 
 NUMBER_OF_CA_Tg:  332      NUMBER_OF_CA_Pr:   35      PERCENT_OF_CA:  10.54  
 
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       8       9      11      15      17      17      17      19      20      22      23      23      24      24      25      27      28      31      32  
 GDT PERCENT_OF_CA_Pr   14.29   22.86   25.71   31.43   42.86   48.57   48.57   48.57   54.29   57.14   62.86   65.71   65.71   68.57   68.57   71.43   77.14   80.00   88.57   91.43 
 GDT PERCENT_OF_CA_Tg    1.51    2.41    2.71    3.31    4.52    5.12    5.12    5.12    5.72    6.02    6.63    6.93    6.93    7.23    7.23    7.53    8.13    8.43    9.34    9.64 
 GDT FRAGMENT: Beg-End 136-142 145-152 144-152 140-152 138-152 136-152 136-152 136-152 130-152 130-152 130-152 130-152 130-152 129-152 129-152 128-152 118-152 119-152 119-152 119-152 
 GDT RMS_LOCAL           0.10    0.61    0.82    1.21    1.80    2.09    2.09    2.09    2.99    3.09    3.51    3.73    3.73    3.92    3.92    4.23    4.87    6.20    6.58    6.73 
 GDT RMS_ALL_CA         18.35    9.99    9.40   10.82    9.18    8.27    8.27    8.27    9.01    8.92    9.37    9.50    9.50    9.17    9.17    8.86    8.29    7.33    7.22    7.20 
 
 
 TEST (CA)  RMS =   7.19               (Number of atoms:   35) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    7.19         35    10.5   332     CRMSCA  
     CRN = ALL/NP  . . . . .    0.2055                            CRMSCA  
     SECONDARY STRUCTURE . .    3.68         10     5.7   174     CRMSCA  
     SURFACE . . . . . . . .    6.93         18     9.6   187     CRMSCA  
     BURIED  . . . . . . . .    7.47         17    11.7   145     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    7.13        140     8.7  1606     CRMSMC  
     SECONDARY STRUCTURE . .    3.75         40     4.7   848     CRMSMC  
     SURFACE . . . . . . . .    6.86         72     7.9   910     CRMSMC  
     BURIED  . . . . . . . .    7.41         68     9.8   696     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0  1133     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   957     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   626     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   682     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   451     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    7.13        140     5.7  2461     CRMSALL 
     SECONDARY STRUCTURE . .    3.75         40     3.0  1322     CRMSALL 
     SURFACE . . . . . . . .    6.86         72     5.0  1430     CRMSALL 
     BURIED  . . . . . . . .    7.41         68     6.6  1031     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 . . . . . . . . . .    6.503      1.000       0.500     35    10.5   332     ERRCA  
     SECONDARY STRUCTURE . .    3.450      1.000       0.500     10     5.7   174     ERRCA  
     SURFACE . . . . . . . .    6.259      1.000       0.500     18     9.6   187     ERRCA  
     BURIED  . . . . . . . .    6.762      1.000       0.500     17    11.7   145     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.444      1.000       0.500    140     8.7  1606     ERRMC  
     SECONDARY STRUCTURE . .    3.514      1.000       0.500     40     4.7   848     ERRMC  
     SURFACE . . . . . . . .    6.191      1.000       0.500     72     7.9   910     ERRMC  
     BURIED  . . . . . . . .    6.711      1.000       0.500     68     9.8   696     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  1133     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   957     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   626     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   682     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   451     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.444      1.000       0.500    140     5.7  2461     ERRALL 
     SECONDARY STRUCTURE . .    3.514      1.000       0.500     40     3.0  1322     ERRALL 
     SURFACE . . . . . . . .    6.191      1.000       0.500     72     5.0  1430     ERRALL 
     BURIED  . . . . . . . .    6.711      1.000       0.500     68     6.6  1031     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        15        27      35     332   DISTCA 
CA  (P)      0.00      0.30      1.20      4.52      8.13             332   DISTCA 
CA  (RMS)    0.00      1.09      2.22      3.71      5.80                   DISTCA 
 
ALL (N)         1         6        14        60       113     140    2461   DISTALL 
ALL (P)      0.04      0.24      0.57      2.44      4.59            2461   DISTALL 
ALL (RMS)    0.92      1.40      2.05      3.66      5.92                   DISTALL 
 
 
 
 
END of the results output 
