 
####################################################### 
#                                                     # 
#                        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: 42 , MODEL 42 , TARGET 378 
#          The number of residues possible to evaluate: 42 
 
 
 SECONDARY STRUCTURE PREDICTION: 
       NUM    RES   SS   Prediction   Probability 
 SSP   349     G     E     C             1.00 
 SSP   350     G     E     C             1.00 
 SSP   351     V     C     C             1.00 
 SSP   352     Y     C     C             1.00 
 SSP   353     G     C     E             1.00 
 SSP   354     H     E     E             1.00 
 SSP   355     S     E     E             1.00 
 SSP   356     W     E     E             1.00 
 SSP   357     F     E     E             1.00 
 SSP   358     V     E     E             1.00 
 SSP   359     D     E     E             1.00 
 SSP   360     R     C     H             1.00 
 SSP   361     A     C     H             1.00 
 SSP   362     L     C     H             1.00 
 SSP   363     G     C     C             1.00 
 SSP   364     L     E     E             1.00 
 SSP   365     S     E     E             1.00 
 SSP   366     V     E     E             1.00 
 SSP   367     L     E     E             1.00 
 SSP   368     L     E     E             1.00 
 SSP   369     L     E     E             1.00 
 SSP   370     T     E     E             1.00 
 SSP   371     N     C     C             1.00 
 SSP   372     T     E     C             1.00 
 SSP   373     A     E     C             1.00 
 SSP   374     Y     C     C             1.00 
 SSP   375     E     H     C             1.00 
 SSP   376     G     H     C             1.00 
 SSP   377     M     H     C             1.00 
 SSP   378     S     H     H             1.00 
 SSP   379     G     C     H             1.00 
 SSP   380     P     H     H             1.00 
 SSP   381     L     H     H             1.00 
 SSP   382     T     H     H             1.00 
 SSP   383     I     H     H             1.00 
 SSP   384     A     H     H             1.00 
 SSP   385     L     H     H             1.00 
 SSP   386     R     H     H             1.00 
 SSP   387     D     H     H             1.00 
 SSP   388     A     H     H             1.00 
 SSP   389     V     H     C             1.00 
 SSP   390     Y     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              69.0      71.4     76.5     54.5     11.1 
 
                     ALL      HELIX    STRAND    COIL      PP 
 SOV observed        64.7      75.5     76.5     32.6     11.1 
 
           Considered    Percent predicted   Percent predicted 
            segments        correctly         as wrong type 
 SEG            6              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      42    100.0     69.0 
 
 BIN  0.00 - 1.00      1.00      42    100.0     69.0 
 
 
 
 
              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 336 
 
# WARNING! TARGET 2840 atoms, MODEL 2797 atoms, 2692 common with TARGET 
           Number of atoms possible to evaluate: 168 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    49.59           75.6    82    10.9   754     ARMSMC  
     SECONDARY STRUCTURE . .    35.48           85.7    49    15.8   310     ARMSMC  
     SURFACE . . . . . . . .    18.48           93.8    16     4.8   330     ARMSMC  
     BURIED  . . . . . . . .    54.52           71.2    66    15.6   424     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   278     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   249     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0   116     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   119     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   159     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   216     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   157     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    88     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0   106     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0   110     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    69     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    60     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    25     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    51     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    35     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    35     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    16     ARMSSC4 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    28     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     7     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   5.00): 
 FRAGMENT  1  349 - 390  42   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    42    349 - 390      4.02     4.02 
  LCS LOCAL_SCORE:            100.00 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   2.00): 
 FRAGMENT  1  349 - 390  42   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    25    351 - 375      1.87     4.32 
  LONGEST_CONTINUOUS_SEGMENT    25    352 - 376      1.73     4.35 
  LCS LOCAL_SCORE:             47.28 
 
 
LONGEST_CONTINUOUS_SEGMENT (Longest continuous sequence under CA RMS cutoff   1.00): 
 FRAGMENT  1  349 - 390  42   Length     Seq        L_RMS   ALL_CA_RMS 
  LONGEST_CONTINUOUS_SEGMENT    23    352 - 374      1.00     4.27 
  LCS LOCAL_SCORE:             39.57 
 
 
 LCS                   LENGTH_OF_THE 
 LCS  RESIDUE  RESIDUE    CONTINUOUS  SECONDARY 
 LCS   NUMBER     NAME       SEGMENT  STRUCTURE   GDT_DATA_COLUMNS (PERCENT OF THE TARGET) 
 LCS     349       G     3    5   42       E        0   0   0   0   1   1   2   2   2   3   5   5   7   8  10  10  11  11  11  11  
 LCS     350       G     3    5   42       E        0   0   0   1   1   1   2   2   2   3   5   5   7   8  10  10  11  11  11  11  
 LCS     351       V     3   25   42       C        0   0   0   1   1   2   3   5   6   7   7   8   9  10  10  10  11  11  11  11  
 LCS     352       Y    23   25   42       C        0   3   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     353       G    23   25   42       C        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     354       H    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     355       S    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     356       W    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     357       F    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     358       V    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     359       D    23   25   42       E        1   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     360       R    23   25   42       C        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     361       A    23   25   42       C        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     362       L    23   25   42       C        1   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     363       G    23   25   42       C        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     364       L    23   25   42       E        1   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     365       S    23   25   42       E        1   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     366       V    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     367       L    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     368       L    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     369       L    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     370       T    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     371       N    23   25   42       C        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     372       T    23   25   42       E        1   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     373       A    23   25   42       E        2   4   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     374       Y    23   25   42       C        2   3   5   6   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     375       E     4   25   42       H        1   1   1   5   6   6   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     376       G     4   25   42       H        1   1   1   1   1   1   5   6   6   8   8  10  10  10  10  10  11  11  11  11  
 LCS     377       M     4    5   42       H        1   1   1   1   2   3   4   5   6   7   9  10  10  10  10  10  11  11  11  11  
 LCS     378       S     4   13   42       H        1   1   1   2   5   7   7   7   8   9   9  10  10  10  10  10  11  11  11  11  
 LCS     379       G    12   13   42       C        1   2   3   3   3   3   3   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     380       P    12   13   42       H        2   2   3   3   3   3   3   5   6   9   9  10  10  10  10  10  11  11  11  11  
 LCS     381       L    12   13   42       H        2   2   3   3   3   4   6   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     382       T    12   13   42       H        2   2   3   3   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     383       I    12   13   42       H        2   2   3   3   3   3   3   7   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     384       A    12   13   42       H        2   2   3   3   3   3   5   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     385       L    12   13   42       H        2   2   3   3   4   6   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     386       R    12   13   42       H        2   2   3   3   3   7   7   7   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     387       D    12   13   42       H        2   2   3   3   3   4   6   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     388       A    12   13   42       H        2   2   3   3   3   3   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     389       V    12   13   42       H        1   2   3   3   3   3   6   7   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS     390       Y    12   13   42       C        0   1   3   4   6   7   7   8   9   9   9  10  10  10  10  10  11  11  11  11  
 LCS TOTAL_SCORE (RMS CUTOFF   1.00):   0.49 
 
 NUMBER_OF_CA_Tg:  378      NUMBER_OF_CA_Pr:   42      PERCENT_OF_CA:  11.11  
 
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      11      18      22      23      25      27      27      31      35      36      37      38      39      39      40      41      42      42      42      42  
 GDT PERCENT_OF_CA_Pr   26.19   42.86   52.38   54.76   59.52   64.29   64.29   73.81   83.33   85.71   88.10   90.48   92.86   92.86   95.24   97.62  100.00  100.00  100.00  100.00 
 GDT PERCENT_OF_CA_Tg    2.91    4.76    5.82    6.08    6.61    7.14    7.14    8.20    9.26    9.52    9.79   10.05   10.32   10.32   10.58   10.85   11.11   11.11   11.11   11.11 
 GDT FRAGMENT: Beg-End 353-371 353-373 352-373 352-374 352-390 352-390 352-390 352-390 352-390 352-390 352-390 352-390 352-390 352-390 351-390 349-390 349-390 349-390 349-390 349-390 
 GDT RMS_LOCAL           0.32    0.61    0.88    1.00    1.34    1.54    1.54    2.40    2.74    2.81    2.94    3.09    3.24    3.24    3.45    3.92    4.02    4.02    4.02    4.02 
 GDT RMS_ALL_CA          4.40    4.28    4.33    4.27    4.27    4.43    4.43    4.09    4.11    4.11    4.11    4.12    4.13    4.13    4.07    4.03    4.02    4.02    4.02    4.02 
 
 
 TEST (CA)  RMS =   4.02               (Number of atoms:   42) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    4.02         42    11.1   378     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0958                            CRMSCA  
     SECONDARY STRUCTURE . .    4.15         25    16.1   155     CRMSCA  
     SURFACE . . . . . . . .    4.22          8     4.8   166     CRMSCA  
     BURIED  . . . . . . . .    3.98         34    16.0   212     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    3.77        168     9.1  1848     CRMSMC  
     SECONDARY STRUCTURE . .    3.84        100    13.0   769     CRMSMC  
     SURFACE . . . . . . . .    3.79         32     4.0   809     CRMSMC  
     BURIED  . . . . . . . .    3.76        136    13.1  1039     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0  1328     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0  1118     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   560     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   583     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   745     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.77        168     5.9  2840     CRMSALL 
     SECONDARY STRUCTURE . .    3.84        100     8.5  1180     CRMSALL 
     SURFACE . . . . . . . .    3.79         32     2.6  1247     CRMSALL 
     BURIED  . . . . . . . .    3.76        136     8.5  1593     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 . . . . . . . . . .    3.286      1.000       0.500     42    11.1   378     ERRCA  
     SECONDARY STRUCTURE . .    3.276      1.000       0.500     25    16.1   155     ERRCA  
     SURFACE . . . . . . . .    3.841      1.000       0.500      8     4.8   166     ERRCA  
     BURIED  . . . . . . . .    3.155      1.000       0.500     34    16.0   212     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.092      1.000       0.500    168     9.1  1848     ERRMC  
     SECONDARY STRUCTURE . .    3.009      1.000       0.500    100    13.0   769     ERRMC  
     SURFACE . . . . . . . .    3.488      1.000       0.500     32     4.0   809     ERRMC  
     BURIED  . . . . . . . .    2.999      1.000       0.500    136    13.1  1039     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  1328     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0  1118     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   560     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   583     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   745     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.092      1.000       0.500    168     5.9  2840     ERRALL 
     SECONDARY STRUCTURE . .    3.009      1.000       0.500    100     8.5  1180     ERRALL 
     SURFACE . . . . . . . .    3.488      1.000       0.500     32     2.6  1247     ERRALL 
     BURIED  . . . . . . . .    2.999      1.000       0.500    136     8.5  1593     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)         5        17        22        35        42      42     378   DISTCA 
CA  (P)      1.32      4.50      5.82      9.26     11.11             378   DISTCA 
CA  (RMS)    0.64      1.36      1.64      2.83      4.02                   DISTCA 
 
ALL (N)        24        63        96       142       168     168    2840   DISTALL 
ALL (P)      0.85      2.22      3.38      5.00      5.92            2840   DISTALL 
ALL (RMS)    0.69      1.31      1.78      2.69      3.77                   DISTALL 
 
 
 
 
END of the results output 
