 
####################################################### 
#                                                     # 
#                        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:     # 
#                        # 
########################## 
NUMBER-OF-PARENTS      4 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0076_2.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_2.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_2.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_2.1aj4.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 1062 atoms, MODEL 1089 atoms, 537 common with TARGET 
           Number of atoms possible to evaluate: 537 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 3.538625 
 
 CA-RMS TARGET<->PARENT(1ncx)	 3.287245 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.396291 
 
 CA-RMS TARGET<->PARENT(1aj4)	 5.635736 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    59.83           65.4   136   100.0   136     ARMSMC  
     WELL ORDERED  . . . . .    59.83           65.4   136   100.0   136     ARMSMC  
     NO INTER CONTACTS . . .    59.83           65.4   136   100.0   136     ARMSMC  
     SHIFTED CHAIN . . . . .    59.83           65.4   136   100.0   136     ARMSMC  
     ALTERNATIVE PARENT  . .    34.38            0.0     1   100.0     1     ARMSMC  
     SECONDARY STRUCTURE . .    20.48           93.1    72   100.0    72     ARMSMC  
     LARGE SHIFTS/INSERTIONS    63.97           62.3   114   100.0   114     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    59.86           64.7   116   100.0   116     ARMSMC  
     BURIED  . . . . . . . .    59.68           70.0    20   100.0    20     ARMSMC  
     CORE  . . . . . . . . .    30.38           81.8    22   100.0    22     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .   100.67           27.1    59   100.0    59     ARMSSC1 
     WELL ORDERED  . . . . .   100.67           27.1    59   100.0    59     ARMSSC1 
     NO INTER CONTACTS . . .   100.67           27.1    59   100.0    59     ARMSSC1 
     RELIABLE SIDE CHAINS  .   103.92           21.6    51   100.0    51     ARMSSC1 
     CHANGED ANGLES  . . . .   101.65           30.0    40   100.0    40     ARMSSC1 
     SHIFTED CHAIN . . . . .   100.67           27.1    59   100.0    59     ARMSSC1 
     ALTERNATIVE PARENT  . .    48.33            0.0     1   100.0     1     ARMSSC1 
     SECONDARY STRUCTURE . .    98.56           21.9    32   100.0    32     ARMSSC1 
     LARGE SHIFTS/INSERTIONS   100.17           28.6    49   100.0    49     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    98.94           26.9    52   100.0    52     ARMSSC1 
     BURIED  . . . . . . . .   112.68           28.6     7   100.0     7     ARMSSC1 
     CORE  . . . . . . . . .   103.04           20.0    10   100.0    10     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    78.05           34.0    47   100.0    47     ARMSSC2 
     WELL ORDERED  . . . . .    78.05           34.0    47   100.0    47     ARMSSC2 
     NO INTER CONTACTS . . .    78.05           34.0    47   100.0    47     ARMSSC2 
     RELIABLE SIDE CHAINS  .    70.62           33.3    36   100.0    36     ARMSSC2 
     CHANGED ANGLES  . . . .    83.28           22.6    31   100.0    31     ARMSSC2 
     SHIFTED CHAIN . . . . .    78.05           34.0    47   100.0    47     ARMSSC2 
     ALTERNATIVE PARENT  . .    60.18            0.0     1   100.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .    75.08           34.6    26   100.0    26     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    79.68           35.1    37   100.0    37     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    77.62           34.9    43   100.0    43     ARMSSC2 
     BURIED  . . . . . . . .    82.52           25.0     4   100.0     4     ARMSSC2 
     CORE  . . . . . . . . .    71.67           30.0    10   100.0    10     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    76.50           21.1    19   100.0    19     ARMSSC3 
     WELL ORDERED  . . . . .    76.50           21.1    19   100.0    19     ARMSSC3 
     NO INTER CONTACTS . . .    76.50           21.1    19   100.0    19     ARMSSC3 
     RELIABLE SIDE CHAINS  .    74.87           23.5    17   100.0    17     ARMSSC3 
     CHANGED ANGLES  . . . .    70.81           20.0    15   100.0    15     ARMSSC3 
     SHIFTED CHAIN . . . . .    76.50           21.1    19   100.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .    74.59           25.0    12   100.0    12     ARMSSC3 
     LARGE SHIFTS/INSERTIONS    77.59           23.1    13   100.0    13     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    77.53           23.5    17   100.0    17     ARMSSC3 
     BURIED  . . . . . . . .    67.18            0.0     2   100.0     2     ARMSSC3 
     CORE  . . . . . . . . .    74.09           16.7     6   100.0     6     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.59           16.7     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    80.59           16.7     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    80.59           16.7     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    80.59           16.7     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    80.59           16.7     6   100.0     6     ARMSSC4 
     SHIFTED CHAIN . . . . .    80.59           16.7     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .   108.16            0.0     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS    86.82           20.0     5   100.0     5     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    80.59           16.7     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    35.85            0.0     1   100.0     1     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.29495     r(1,2) =  -0.32648     r(1,3) =  -0.89801 
 r(2,1) =  -0.95359     r(2,2) =   0.04102     r(2,3) =   0.29829 
 r(3,1) =  -0.06055     r(3,2) =   0.94432     r(3,3) =  -0.32342 
THE OFFSET VECTOR: 
 v(1) =  31.16245     v(2) =  44.10937     v(3) =  -4.62237 
 
 Number of iteration  3                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.75           (Number of atoms:   27) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    6.08         69   100.0    69     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0881                            CRMSCA  
     WELL ORDERED  . . . . .    6.08         69   100.0    69     CRMSCA  
     NO INTER CONTACTS . . .    6.08         69   100.0    69     CRMSCA  
     SHIFTED CHAIN . . . . .    6.08         69   100.0    69     CRMSCA  
     ALTERNATIVE PARENT  . .   18.71          1   100.0     1     CRMSCA  
     SECONDARY STRUCTURE . .    5.31         36   100.0    36     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.24         58   100.0    58     CRMSCA  
     SURFACE . . . . . . . .    6.42         59   100.0    59     CRMSCA  
     BURIED  . . . . . . . .    3.43         10   100.0    10     CRMSCA  
     CORE  . . . . . . . . .    5.14         11   100.0    11     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    6.05        337   100.0   337     CRMSMC  
     WELL ORDERED  . . . . .    6.05        337   100.0   337     CRMSMC  
     NO INTER CONTACTS . . .    6.05        337   100.0   337     CRMSMC  
     SHIFTED CHAIN . . . . .    6.05        337   100.0   337     CRMSMC  
     ALTERNATIVE PARENT  . .   17.98          5   100.0     5     CRMSMC  
     SECONDARY STRUCTURE . .    5.30        176   100.0   176     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.23        283   100.0   283     CRMSMC  
     SURFACE . . . . . . . .    6.38        290   100.0   290     CRMSMC  
     BURIED  . . . . . . . .    3.30         47   100.0    47     CRMSMC  
     CORE  . . . . . . . . .    4.97         54   100.0    54     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    7.76        261    33.2   786     CRMSSC  
     WELL ORDERED  . . . . .    7.76        261    33.2   786     CRMSSC  
     NO INTER CONTACTS . . .    7.76        261    33.2   786     CRMSSC  
     RELIABLE SIDE CHAINS  .    8.13        217    29.2   742     CRMSSC  
     CHANGED ANGLES  . . . .    8.07        158   100.0   158     CRMSSC  
     SECONDARY STRUCTURE . .    6.58        145    33.8   429     CRMSSC  
     LARGE SHIFTS/INSERTIONS    8.06        213    32.0   666     CRMSSC  
     SURFACE . . . . . . . .    8.10        235    34.1   689     CRMSSC  
     BURIED  . . . . . . . .    3.25         26    26.8    97     CRMSSC  
     CORE  . . . . . . . . .    6.22         48    40.0   120     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    6.86        537    50.6  1062     CRMSALL 
     WELL ORDERED  . . . . .    6.86        537    50.6  1062     CRMSALL 
     NO INTER CONTACTS . . .    6.86        537    50.6  1062     CRMSALL 
     SHIFTED CHAIN . . . . .    6.86        537    50.6  1062     CRMSALL 
     ALTERNATIVE PARENT  . .   19.14          7    50.0    14     CRMSALL 
     SECONDARY STRUCTURE . .    5.92        289    50.4   573     CRMSALL 
     LARGE SHIFTS/INSERTIONS    7.09        445    49.6   898     CRMSALL 
     SURFACE . . . . . . . .    7.22        471    50.9   925     CRMSALL 
     BURIED  . . . . . . . .    3.32         66    48.2   137     CRMSALL 
     CORE  . . . . . . . . .    5.64         92    56.1   164     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1    12.51      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.84     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     4.71     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1    12.31     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.93    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     4.81    118   100.0   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1    12.96     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.78    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     5.64    189    49.2   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.95      9   100.0     9      72-PGDPEEFVK-80   
 CA  LOOP  2     2.43     23   100.0    23      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 CA  LOOP  3     4.01     24   100.0    24     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.99     44   100.0    44      72-PGDPEEFVK-80   
 MC  LOOP  2     2.55    111   100.0   111      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 MC  LOOP  3     4.21    118   100.0   118     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.90     71    52.6   135      72-PGDPEEFVK-80   
 ALL LOOP  2     3.46    167    48.7   343      89-ATGMIGVGELRYVLTSLGEKLSN-111  
 ALL LOOP  3     5.10    189    49.2   384     117-LLKGVPVKDGMVNYHDFVQMILAN-140  
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.408      0.774       0.387     69   100.0    69     ERRCA  
     WELL ORDERED  . . . . .    4.408      0.774       0.387     69   100.0    69     ERRCA  
     NO INTER CONTACTS . . .    4.408      0.774       0.387     69   100.0    69     ERRCA  
     SHIFTED CHAIN . . . . .    4.408      0.774       0.387     69   100.0    69     ERRCA  
     ALTERNATIVE PARENT  . .   18.351      0.962       0.481      1   100.0     1     ERRCA  
     SECONDARY STRUCTURE . .    3.639      0.729       0.364     36   100.0    36     ERRCA  
     LARGE SHIFTS/INSERTIONS    4.426      0.763       0.381     58   100.0    58     ERRCA  
     SURFACE . . . . . . . .    4.746      0.790       0.395     59   100.0    59     ERRCA  
     BURIED  . . . . . . . .    2.410      0.682       0.341     10   100.0    10     ERRCA  
     CORE  . . . . . . . . .    4.315      0.834       0.417     11   100.0    11     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.401      0.770       0.385    337   100.0   337     ERRMC  
     WELL ORDERED  . . . . .    4.401      0.770       0.385    337   100.0   337     ERRMC  
     NO INTER CONTACTS . . .    4.401      0.770       0.385    337   100.0   337     ERRMC  
     SHIFTED CHAIN . . . . .    4.401      0.770       0.385    337   100.0   337     ERRMC  
     ALTERNATIVE PARENT  . .   17.500      0.960       0.480      5   100.0     5     ERRMC  
     SECONDARY STRUCTURE . .    3.626      0.718       0.359    176   100.0   176     ERRMC  
     LARGE SHIFTS/INSERTIONS    4.451      0.759       0.380    283   100.0   283     ERRMC  
     SURFACE . . . . . . . .    4.733      0.785       0.392    290   100.0   290     ERRMC  
     BURIED  . . . . . . . .    2.355      0.677       0.339     47   100.0    47     ERRMC  
     CORE  . . . . . . . . .    4.144      0.825       0.412     54   100.0    54     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    6.062      0.825       0.413    261    33.2   786     ERRSC  
     WELL ORDERED  . . . . .    6.062      0.825       0.413    261    33.2   786     ERRSC  
     NO INTER CONTACTS . . .    6.062      0.825       0.413    261    33.2   786     ERRSC  
     RELIABLE SIDE CHAINS  .    6.327      0.824       0.412    217    29.2   742     ERRSC  
     CHANGED ANGLES  . . . .    6.288      0.822       0.411    158   100.0   158     ERRSC  
     SHIFTED CHAIN . . . . .    6.062      0.825       0.413    261    33.2   786     ERRSC  
     ALTERNATIVE PARENT  . .   20.748      0.966       0.483      3    30.0    10     ERRSC  
     SECONDARY STRUCTURE . .    5.050      0.798       0.399    145    33.8   429     ERRSC  
     LARGE SHIFTS/INSERTIONS    6.245      0.816       0.408    213    32.0   666     ERRSC  
     SURFACE . . . . . . . .    6.461      0.843       0.422    235    34.1   689     ERRSC  
     BURIED  . . . . . . . .    2.456      0.658       0.330     26    26.8    97     ERRSC  
     CORE  . . . . . . . . .    5.250      0.865       0.432     48    40.0   120     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    5.143      0.794       0.397    537    50.6  1062     ERRALL 
     WELL ORDERED  . . . . .    5.143      0.794       0.397    537    50.6  1062     ERRALL 
     NO INTER CONTACTS . . .    5.143      0.794       0.397    537    50.6  1062     ERRALL 
     SHIFTED CHAIN . . . . .    5.143      0.794       0.397    537    50.6  1062     ERRALL 
     ALTERNATIVE PARENT  . .   18.617      0.962       0.481      7    50.0    14     ERRALL 
     SECONDARY STRUCTURE . .    4.281      0.753       0.377    289    50.4   573     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.235      0.783       0.392    445    49.6   898     ERRALL 
     SURFACE . . . . . . . .    5.527      0.811       0.406    471    50.9   925     ERRALL 
     BURIED  . . . . . . . .    2.397      0.667       0.334     66    48.2   137     ERRALL 
     CORE  . . . . . . . . .    4.697      0.844       0.422     92    56.1   164     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)         1        18        31        44        63      69      69   DISTCA 
CA  (P)      1.45     26.09     44.93     63.77     91.30              69   DISTCA 
CA  (RMS)    0.82      1.46      1.94      2.67      4.71                   DISTCA 
 
ALL (N)        18       108       184       292       464     537    1062   DISTALL 
ALL (P)      1.69     10.17     17.33     27.50     43.69            1062   DISTALL 
ALL (RMS)    0.78      1.48      1.98      2.84      4.97                   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)          11            11            58          RMSLSI 
CA  (P)       15.94         15.94         84.06          RMSLSI 
CA  (RMS)      1.81          5.14          6.24          RMSLSI 
 
 
 
END of the results output 
