 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
# 
CONANA-INTER           ../CONANA/T0064.inter 
CONANA-PAIR            ../CONANA/T0064.pair 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0064.1r69.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0064.2cro.rot 
# 
ITER-CUTOFF            2.5       #    DISTANCE cutoff (for CA (iter))  
# 
# 
# 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 
SS-OUTPUT           0         #    1 - ON, 0 - OFF  
PHI-PSI             0         #    1 - SEPARATELY, 0 - NO  
ALIGNMENT-OUTPUT    0         #    1 - ON, 0 - OFF 
# 
# Calculation parameters 
# 
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)  
ROTAMERS-LIMIT      30.0      #    target-parent (diff > 30.0) 
SC-SWAPPING         1         #    1 - ON, 0 - OFF  
DSSP-HELIX          6         #    Secondary Structure subset: helix cutoff  
DSSP-STRAND         3         #    Secondary Structure subset: strand cutoff 
LIGAND-DIST1        4.0       #    Ligand contact: contact with ligand cutoff 
LIGAND-DIST2        6.0       #    Ligand contact: protein neighborhood cutoff 
PARENT-DIST3        2.5       #    target-parent (dist > 2.5) 
# 
CRMS-METHOD         3         #    0 - ALL, 1 - CA, 2 - MC+CB, 3 - CA (iter)  
# 
########################## 
#                        # 
#      ACE results:      # 
#                        # 
########################## 
 
# Reading the coordinates set (1) 
 
 
# Evaluating the coordinates set (1) 
 
# WARNING! TARGET 845 atoms, MODEL 914 atoms, 845 common with TARGET 
           Number of atoms possible to evaluate: 526 
 
 
 CA-RMS TARGET<->PARENT(1r69)	 1.473148 
 
 CA-RMS TARGET<->PARENT(2cro)	 1.394009 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    43.69           81.5   130    64.7   201     ARMSMC  
     WELL ORDERED  . . . . .    36.05           85.2   108    67.1   161     ARMSMC  
     NO INTER CONTACTS . . .    27.29           87.1    85    81.0   105     ARMSMC  
     SHIFTED CHAIN . . . . .    55.26           70.0    70    49.6   141     ARMSMC  
     ALTERNATIVE PARENT  . .    60.72           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .    16.90           93.2    74    58.3   127     ARMSMC  
     LARGE SHIFTS/INSERTIONS    76.18           47.4    19    21.3    89     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    50.39           81.5    81    53.6   151     ARMSMC  
     BURIED  . . . . . . . .    29.44           81.6    49    98.0    50     ARMSMC  
     CORE  . . . . . . . . .    35.24           87.4   111    99.1   112     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.15           50.8    59    64.8    91     ARMSSC1 
     WELL ORDERED  . . . . .    63.69           62.2    37    68.5    54     ARMSSC1 
     NO INTER CONTACTS . . .    79.57           48.6    37    82.2    45     ARMSSC1 
     RELIABLE SIDE CHAINS  .    83.73           46.3    54    64.3    84     ARMSSC1 
     CHANGED ANGLES  . . . .    98.64           26.5    34    51.5    66     ARMSSC1 
     SHIFTED CHAIN . . . . .    83.45           50.0    32    50.0    64     ARMSSC1 
     ALTERNATIVE PARENT  . .     3.54          100.0     2   100.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .    80.95           45.5    33    57.9    57     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    92.20           40.0    10    23.8    42     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    83.33           51.4    37    53.6    69     ARMSSC1 
     BURIED  . . . . . . . .    74.50           50.0    22   100.0    22     ARMSSC1 
     CORE  . . . . . . . . .    77.46           53.1    49   100.0    49     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.95           52.3    44    68.8    64     ARMSSC2 
     WELL ORDERED  . . . . .    45.80           81.0    21    75.0    28     ARMSSC2 
     NO INTER CONTACTS . . .    67.79           50.0    26    78.8    33     ARMSSC2 
     RELIABLE SIDE CHAINS  .    69.18           53.1    32    65.3    49     ARMSSC2 
     CHANGED ANGLES  . . . .    80.37           33.3    27    57.4    47     ARMSSC2 
     SHIFTED CHAIN . . . . .    66.93           45.8    24    54.5    44     ARMSSC2 
     ALTERNATIVE PARENT  . .    18.04          100.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    67.50           53.8    26    61.9    42     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    67.90           37.5     8    28.6    28     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    72.36           44.8    29    59.2    49     ARMSSC2 
     BURIED  . . . . . . . .    47.43           66.7    15   100.0    15     ARMSSC2 
     CORE  . . . . . . . . .    64.27           55.6    36   100.0    36     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    64.66           52.4    21    67.7    31     ARMSSC3 
     WELL ORDERED  . . . . .    39.46           66.7     6    60.0    10     ARMSSC3 
     NO INTER CONTACTS . . .    74.10           45.5    11    73.3    15     ARMSSC3 
     RELIABLE SIDE CHAINS  .    61.15           58.8    17    65.4    26     ARMSSC3 
     CHANGED ANGLES  . . . .    71.47           41.2    17    70.8    24     ARMSSC3 
     SHIFTED CHAIN . . . . .    66.13           50.0    10    50.0    20     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    60.12           53.3    15    65.2    23     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    77.23           25.0     4    28.6    14     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    58.80           55.6    18    64.3    28     ARMSSC3 
     BURIED  . . . . . . . .    92.31           33.3     3   100.0     3     ARMSSC3 
     CORE  . . . . . . . . .    61.32           58.8    17   100.0    17     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   106.74           10.0    10    83.3    12     ARMSSC4 
     WELL ORDERED  . . . . .    98.67            0.0     3   100.0     3     ARMSSC4 
     NO INTER CONTACTS . . .   116.27            0.0     5    83.3     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .   106.74           10.0    10    83.3    12     ARMSSC4 
     CHANGED ANGLES  . . . .   112.00           11.1     9    81.8    11     ARMSSC4 
     SHIFTED CHAIN . . . . .    91.22           25.0     4    66.7     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   111.44            0.0     7    77.8     9     ARMSSC4 
     LARGE SHIFTS/INSERTIONS   120.26            0.0     1    33.3     3     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .   102.29           12.5     8    80.0    10     ARMSSC4 
     BURIED  . . . . . . . .   122.92            0.0     2   100.0     2     ARMSSC4 
     CORE  . . . . . . . . .   105.13           11.1     9   100.0     9     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =   0.12969     r(1,2) =   0.96839     r(1,3) =  -0.21307 
 r(2,1) =  -0.27307     r(2,2) =  -0.17169     r(2,3) =  -0.94655 
 r(3,1) =  -0.95321     r(3,2) =   0.18094     r(3,3) =   0.24217 
THE OFFSET VECTOR: 
 v(1) =  19.02013     v(2) =  64.23855     v(3) =  32.44991 
 
 Number of iteration 24                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.86           (Number of atoms:   58) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    2.68         66    64.1   103     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0407                            CRMSCA  
     WELL ORDERED  . . . . .    1.43         56    65.9    85     CRMSCA  
     NO INTER CONTACTS . . .    1.43         43    79.6    54     CRMSCA  
     SHIFTED CHAIN . . . . .    3.59         36    49.3    73     CRMSCA  
     ALTERNATIVE PARENT  . .    3.42          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    1.03         37    56.9    65     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.50         10    21.3    47     CRMSCA  
     SURFACE . . . . . . . .    3.34         41    52.6    78     CRMSCA  
     BURIED  . . . . . . . .    0.81         25   100.0    25     CRMSCA  
     CORE  . . . . . . . . .    0.97         56   100.0    56     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    2.89        327    64.0   511     CRMSMC  
     WELL ORDERED  . . . . .    1.39        277    66.0   420     CRMSMC  
     NO INTER CONTACTS . . .    1.54        213    79.8   267     CRMSMC  
     SHIFTED CHAIN . . . . .    3.86        179    49.3   363     CRMSMC  
     ALTERNATIVE PARENT  . .    3.96         10   100.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    1.06        184    56.8   324     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.98         50    21.4   234     CRMSMC  
     SURFACE . . . . . . . .    3.60        203    52.5   387     CRMSMC  
     BURIED  . . . . . . . .    0.95        124   100.0   124     CRMSMC  
     CORE  . . . . . . . . .    1.04        277   100.0   277     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    4.06        262    60.5   433     CRMSSC  
     WELL ORDERED  . . . . .    2.58        153    61.7   248     CRMSSC  
     NO INTER CONTACTS . . .    3.14        156    74.3   210     CRMSSC  
     RELIABLE SIDE CHAINS  .    4.00        216    58.2   371     CRMSSC  
     CHANGED ANGLES  . . . .    4.98        146    52.0   281     CRMSSC  
     SECONDARY STRUCTURE . .    2.67        153    51.5   297     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.00         42    19.7   213     CRMSSC  
     SURFACE . . . . . . . .    4.76        173    50.3   344     CRMSSC  
     BURIED  . . . . . . . .    2.08         89   100.0    89     CRMSSC  
     CORE  . . . . . . . . .    2.71        220   100.0   220     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    3.50        526    62.2   845     CRMSALL 
     WELL ORDERED  . . . . .    1.89        381    64.2   593     CRMSALL 
     NO INTER CONTACTS . . .    2.39        328    77.0   426     CRMSALL 
     SHIFTED CHAIN . . . . .    4.54        282    46.9   601     CRMSALL 
     ALTERNATIVE PARENT  . .    4.81         14   100.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    2.02        301    54.0   557     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.52         82    20.4   401     CRMSALL 
     SURFACE . . . . . . . .    4.22        337    51.4   656     CRMSALL 
     BURIED  . . . . . . . .    1.56        189   100.0   189     CRMSALL 
     CORE  . . . . . . . . .    2.02        444   100.0   444     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.41      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     9.39      4    10.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.58     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2    10.13     20    10.1   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     4.66     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     9.95     37    10.6   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.09      6   100.0     6      40-TNPSIQ-45   
 CA  LOOP  2     2.12      4    10.0    40      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.47     30   100.0    30      40-TNPSIQ-45   
 MC  LOOP  2     2.57     20    10.1   199      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.11     45   100.0    45      40-TNPSIQ-45   
 ALL LOOP  2     4.26     37    10.6   348      64-EKHETLDSEWEKLVRDAMTSGVSKKQFREFLDYQKWRKSQ-108  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.743      0.783       0.799     66    64.1   103     ERRCA  
     WELL ORDERED  . . . . .    8.032      0.822       0.841     56    65.9    85     ERRCA  
     NO INTER CONTACTS . . .    8.004      0.816       0.838     43    79.6    54     ERRCA  
     SHIFTED CHAIN . . . . .    7.146      0.695       0.720     36    49.3    73     ERRCA  
     ALTERNATIVE PARENT  . .    6.129      0.554       0.614      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    8.257      0.855       0.869     37    56.9    65     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.811      0.374       0.422     10    21.3    47     ERRCA  
     SURFACE . . . . . . . .    7.419      0.740       0.759     41    52.6    78     ERRCA  
     BURIED  . . . . . . . .    8.273      0.853       0.865     25   100.0    25     ERRCA  
     CORE  . . . . . . . . .    8.266      0.855       0.867     56   100.0    56     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.710      0.775       0.791    327    64.0   511     ERRMC  
     WELL ORDERED  . . . . .    8.043      0.822       0.840    277    66.0   420     ERRMC  
     NO INTER CONTACTS . . .    7.939      0.806       0.827    213    79.8   267     ERRMC  
     SHIFTED CHAIN . . . . .    7.130      0.689       0.711    179    49.3   363     ERRMC  
     ALTERNATIVE PARENT  . .    5.553      0.479       0.536     10   100.0    10     ERRMC  
     SECONDARY STRUCTURE . .    8.238      0.852       0.865    184    56.8   324     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.893      0.372       0.403     50    21.4   234     ERRMC  
     SURFACE . . . . . . . .    7.406      0.733       0.750    203    52.5   387     ERRMC  
     BURIED  . . . . . . . .    8.209      0.843       0.858    124   100.0   124     ERRMC  
     CORE  . . . . . . . . .    8.219      0.848       0.861    277   100.0   277     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.578      0.620       0.647    262    60.5   433     ERRSC  
     WELL ORDERED  . . . . .    7.319      0.726       0.751    153    61.7   248     ERRSC  
     NO INTER CONTACTS . . .    6.688      0.639       0.673    156    74.3   210     ERRSC  
     RELIABLE SIDE CHAINS  .    6.720      0.634       0.662    216    58.2   371     ERRSC  
     CHANGED ANGLES  . . . .    5.680      0.496       0.532    146    52.0   281     ERRSC  
     SHIFTED CHAIN . . . . .    5.833      0.523       0.546    138    44.7   309     ERRSC  
     ALTERNATIVE PARENT  . .    3.448      0.282       0.320      6   100.0     6     ERRSC  
     SECONDARY STRUCTURE . .    7.041      0.680       0.714    153    51.5   297     ERRSC  
     LARGE SHIFTS/INSERTIONS    3.806      0.251       0.258     42    19.7   213     ERRSC  
     SURFACE . . . . . . . .    6.141      0.564       0.589    173    50.3   344     ERRSC  
     BURIED  . . . . . . . .    7.427      0.727       0.761     89   100.0    89     ERRSC  
     CORE  . . . . . . . . .    7.107      0.690       0.722    220   100.0   220     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    7.177      0.701       0.723    526    62.2   845     ERRALL 
     WELL ORDERED  . . . . .    7.792      0.789       0.810    381    64.2   593     ERRALL 
     NO INTER CONTACTS . . .    7.375      0.731       0.758    328    77.0   426     ERRALL 
     SHIFTED CHAIN . . . . .    6.547      0.614       0.637    282    46.9   601     ERRALL 
     ALTERNATIVE PARENT  . .    4.827      0.409       0.465     14   100.0    14     ERRALL 
     SECONDARY STRUCTURE . .    7.644      0.767       0.791    301    54.0   557     ERRALL 
     LARGE SHIFTS/INSERTIONS    4.409      0.317       0.339     82    20.4   401     ERRALL 
     SURFACE . . . . . . . .    6.794      0.651       0.673    337    51.4   656     ERRALL 
     BURIED  . . . . . . . .    7.861      0.792       0.814    189   100.0   189     ERRALL 
     CORE  . . . . . . . . .    7.689      0.772       0.795    444   100.0   444     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)        46        56        58        63        65      66     103   DISTCA 
CA  (P)     44.66     54.37     56.31     61.17     63.11             103   DISTCA 
CA  (RMS)    0.58      0.74      0.86      1.52      2.00                   DISTCA 
 
ALL (N)       290       363       413       463       513     526     845   DISTALL 
ALL (P)     34.32     42.96     48.88     54.79     60.71             845   DISTALL 
ALL (RMS)    0.61      0.84      1.15      1.68      2.65                   DISTALL 
 
CA RMS: P<->T (parent <-> target), and T<->M (target <-> model) calculated using 
        CA positions for which there exists an alignment with principal parent, 
        and for which does not (LARGE SHIFTS/INSERTIONS): 
              P<->T         T<->M         T<->M (LSI) 
CA  (N)          56            56            10          RMSLSI 
CA  (P)       54.37         54.37          9.71          RMSLSI 
CA  (RMS)      1.04          0.97          6.50          RMSLSI 
 
 
 
END of the results output 
