 
####################################################### 
#                                                     # 
#                        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_1.1cfd.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0076_1.1ncx.rot 
ALIGNMENT-DALI(3)      ../PARENTS/casp3.T0076_1.1a2x_A.rot 
ALIGNMENT-DALI(4)      ../PARENTS/casp3.T0076_1.5icb.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 1087 atoms, MODEL 1210 atoms, 634 common with TARGET 
           Number of atoms possible to evaluate: 634 
 
 
 CA-RMS TARGET<->PARENT(1cfd)	 2.655663 
 
 CA-RMS TARGET<->PARENT(1ncx)	 2.782501 
 
 CA-RMS TARGET<->PARENT(1a2x-A)	 3.224615 
 
 CA-RMS TARGET<->PARENT(5icb)	 2.843657 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    49.02           69.3   140   100.0   140     ARMSMC  
     WELL ORDERED  . . . . .    49.02           69.3   140   100.0   140     ARMSMC  
     NO INTER CONTACTS . . .    49.02           69.3   140   100.0   140     ARMSMC  
     SHIFTED CHAIN . . . . .    50.37           69.5   128   100.0   128     ARMSMC  
     ALTERNATIVE PARENT  . .    74.24           53.3    15   100.0    15     ARMSMC  
     SECONDARY STRUCTURE . .    16.27           93.8    64   100.0    64     ARMSMC  
     LARGE SHIFTS/INSERTIONS    68.45           47.9    48   100.0    48     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    49.64           67.3   110   100.0   110     ARMSMC  
     BURIED  . . . . . . . .    46.65           76.7    30   100.0    30     ARMSMC  
     CORE  . . . . . . . . .    34.81           80.4    92   100.0    92     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    86.36           36.1    61    98.4    62     ARMSSC1 
     WELL ORDERED  . . . . .    86.36           36.1    61    98.4    62     ARMSSC1 
     NO INTER CONTACTS . . .    86.36           36.1    61    98.4    62     ARMSSC1 
     RELIABLE SIDE CHAINS  .    86.16           35.6    59    98.3    60     ARMSSC1 
     CHANGED ANGLES  . . . .    97.51           24.3    37    97.4    38     ARMSSC1 
     SHIFTED CHAIN . . . . .    87.89           33.9    56    98.2    57     ARMSSC1 
     ALTERNATIVE PARENT  . .    76.38           20.0     5    83.3     6     ARMSSC1 
     SECONDARY STRUCTURE . .    83.38           46.4    28   100.0    28     ARMSSC1 
     LARGE SHIFTS/INSERTIONS    96.57           36.8    19    95.0    20     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .    80.35           41.7    48    98.0    49     ARMSSC1 
     BURIED  . . . . . . . .   105.65           15.4    13   100.0    13     ARMSSC1 
     CORE  . . . . . . . . .    81.32           35.7    42   100.0    42     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    80.61           37.5    48   100.0    48     ARMSSC2 
     WELL ORDERED  . . . . .    80.61           37.5    48   100.0    48     ARMSSC2 
     NO INTER CONTACTS . . .    80.61           37.5    48   100.0    48     ARMSSC2 
     RELIABLE SIDE CHAINS  .    76.48           40.5    37   100.0    37     ARMSSC2 
     CHANGED ANGLES  . . . .    83.18           34.2    38   100.0    38     ARMSSC2 
     SHIFTED CHAIN . . . . .    81.03           37.0    46   100.0    46     ARMSSC2 
     ALTERNATIVE PARENT  . .    87.64           25.0     4   100.0     4     ARMSSC2 
     SECONDARY STRUCTURE . .    76.77           52.2    23   100.0    23     ARMSSC2 
     LARGE SHIFTS/INSERTIONS    80.42           35.7    14   100.0    14     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .    77.54           37.8    37   100.0    37     ARMSSC2 
     BURIED  . . . . . . . .    90.19           36.4    11   100.0    11     ARMSSC2 
     CORE  . . . . . . . . .    80.69           38.2    34   100.0    34     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    73.23           35.3    17   100.0    17     ARMSSC3 
     WELL ORDERED  . . . . .    73.23           35.3    17   100.0    17     ARMSSC3 
     NO INTER CONTACTS . . .    73.23           35.3    17   100.0    17     ARMSSC3 
     RELIABLE SIDE CHAINS  .    57.78           46.2    13   100.0    13     ARMSSC3 
     CHANGED ANGLES  . . . .    73.33           37.5    16   100.0    16     ARMSSC3 
     SHIFTED CHAIN . . . . .    73.23           35.3    17   100.0    17     ARMSSC3 
     ALTERNATIVE PARENT  . .    74.60           50.0     2   100.0     2     ARMSSC3 
     SECONDARY STRUCTURE . .    71.02           27.3    11   100.0    11     ARMSSC3 
     LARGE SHIFTS/INSERTIONS   112.03            0.0     3   100.0     3     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .    72.75           37.5    16   100.0    16     ARMSSC3 
     BURIED  . . . . . . . .    80.57            0.0     1   100.0     1     ARMSSC3 
     CORE  . . . . . . . . .    61.83           42.9    14   100.0    14     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    63.74           33.3     6   100.0     6     ARMSSC4 
     WELL ORDERED  . . . . .    63.74           33.3     6   100.0     6     ARMSSC4 
     NO INTER CONTACTS . . .    63.74           33.3     6   100.0     6     ARMSSC4 
     RELIABLE SIDE CHAINS  .    63.74           33.3     6   100.0     6     ARMSSC4 
     CHANGED ANGLES  . . . .    69.71           20.0     5   100.0     5     ARMSSC4 
     SHIFTED CHAIN . . . . .    63.74           33.3     6   100.0     6     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .    70.18           33.3     3   100.0     3     ARMSSC4 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     0     ARMSSC4 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SURFACE . . . . . . . .    63.74           33.3     6   100.0     6     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     0     ARMSSC4 
     CORE  . . . . . . . . .    63.74           33.3     6   100.0     6     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.04800     r(1,2) =  -0.96702     r(1,3) =   0.25014 
 r(2,1) =   0.63523     r(2,2) =   0.16371     r(2,3) =   0.75477 
 r(3,1) =  -0.77083     r(3,2) =   0.19512     r(3,3) =   0.60642 
THE OFFSET VECTOR: 
 v(1) =  20.09723     v(2) = -45.75203     v(3) =  52.10732 
 
 Number of iteration  6                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   1.49           (Number of atoms:   31) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    4.88         71   100.0    71     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0688                            CRMSCA  
     WELL ORDERED  . . . . .    4.88         71   100.0    71     CRMSCA  
     NO INTER CONTACTS . . .    4.88         71   100.0    71     CRMSCA  
     SHIFTED CHAIN . . . . .    4.96         65   100.0    65     CRMSCA  
     ALTERNATIVE PARENT  . .    6.48          8   100.0     8     CRMSCA  
     SECONDARY STRUCTURE . .    3.96         32   100.0    32     CRMSCA  
     SHIFTED SS UNITS  . . .    2.72         16   100.0    16     CRMSCA  
     LARGE SHIFTS/INSERTIONS    6.71         25   100.0    25     CRMSCA  
     SURFACE . . . . . . . .    5.26         56   100.0    56     CRMSCA  
     BURIED  . . . . . . . .    3.10         15   100.0    15     CRMSCA  
     CORE  . . . . . . . . .    3.52         46   100.0    46     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    4.93        350   100.0   350     CRMSMC  
     WELL ORDERED  . . . . .    4.93        350   100.0   350     CRMSMC  
     NO INTER CONTACTS . . .    4.93        350   100.0   350     CRMSMC  
     SHIFTED CHAIN . . . . .    5.00        321   100.0   321     CRMSMC  
     ALTERNATIVE PARENT  . .    6.10         39   100.0    39     CRMSMC  
     SECONDARY STRUCTURE . .    4.10        159   100.0   159     CRMSMC  
     SHIFTED SS UNITS  . . .    2.83         80   100.0    80     CRMSMC  
     LARGE SHIFTS/INSERTIONS    6.64        123   100.0   123     CRMSMC  
     SURFACE . . . . . . . .    5.29        276   100.0   276     CRMSMC  
     BURIED  . . . . . . . .    3.28         74   100.0    74     CRMSMC  
     CORE  . . . . . . . . .    3.69        227   100.0   227     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    5.47        350    43.6   803     CRMSSC  
     WELL ORDERED  . . . . .    5.47        350    43.6   803     CRMSSC  
     NO INTER CONTACTS . . .    5.47        350    43.6   803     CRMSSC  
     RELIABLE SIDE CHAINS  .    5.46        314    40.9   767     CRMSSC  
     CHANGED ANGLES  . . . .    6.05        156   100.0   156     CRMSSC  
     SECONDARY STRUCTURE . .    4.43        163    41.4   394     CRMSSC  
     LARGE SHIFTS/INSERTIONS    6.90        102    43.6   234     CRMSSC  
     SURFACE . . . . . . . .    5.82        277    44.4   624     CRMSSC  
     BURIED  . . . . . . . .    3.88         73    40.8   179     CRMSSC  
     CORE  . . . . . . . . .    4.76        248    43.6   569     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    5.24        634    58.3  1087     CRMSALL 
     WELL ORDERED  . . . . .    5.24        634    58.3  1087     CRMSALL 
     NO INTER CONTACTS . . .    5.24        634    58.3  1087     CRMSALL 
     SHIFTED CHAIN . . . . .    5.27        578    57.6  1003     CRMSALL 
     ALTERNATIVE PARENT  . .    5.92         63    57.8   109     CRMSALL 
     SECONDARY STRUCTURE . .    4.32        291    55.7   522     CRMSALL 
     LARGE SHIFTS/INSERTIONS    6.79        202    60.5   334     CRMSALL 
     SURFACE . . . . . . . .    5.59        501    59.1   848     CRMSALL 
     BURIED  . . . . . . . .    3.61        133    55.6   239     CRMSALL 
     CORE  . . . . . . . . .    4.32        432    57.4   753     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     4.42      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     6.65     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     8.81      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     4.53     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     6.42     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     8.94     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     5.65     42    67.7    62       1-STDDS-5    
 ALL LOOP  2     6.13     96    58.5   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     9.03     51    60.7    84      66-PNGFDM-71   
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     2.16      5   100.0     5       1-STDDS-5    
 CA  LOOP  2     2.00     12   100.0    12      33-ACGQNPTLAEIT-44   
 CA  LOOP  3     2.91      6   100.0     6      66-PNGFDM-71   
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     2.71     25   100.0    25       1-STDDS-5    
 MC  LOOP  2     2.02     59   100.0    59      33-ACGQNPTLAEIT-44   
 MC  LOOP  3     3.03     29   100.0    29      66-PNGFDM-71   
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.77     42    67.7    62       1-STDDS-5    
 ALL LOOP  2     2.76     96    58.5   164      33-ACGQNPTLAEIT-44   
 ALL LOOP  3     3.96     51    60.7    84      66-PNGFDM-71   
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.388      0.649       0.325     71   100.0    71     ERRCA  
     WELL ORDERED  . . . . .    3.388      0.649       0.325     71   100.0    71     ERRCA  
     NO INTER CONTACTS . . .    3.388      0.649       0.325     71   100.0    71     ERRCA  
     SHIFTED CHAIN . . . . .    3.434      0.654       0.327     65   100.0    65     ERRCA  
     ALTERNATIVE PARENT  . .    4.560      0.645       0.323      8   100.0     8     ERRCA  
     SECONDARY STRUCTURE . .    2.677      0.614       0.307     32   100.0    32     ERRCA  
     LARGE SHIFTS/INSERTIONS    5.235      0.762       0.381     25   100.0    25     ERRCA  
     SURFACE . . . . . . . .    3.711      0.664       0.332     56   100.0    56     ERRCA  
     BURIED  . . . . . . . .    2.184      0.592       0.296     15   100.0    15     ERRCA  
     CORE  . . . . . . . . .    2.385      0.587       0.294     46   100.0    46     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.421      0.650       0.325    350   100.0   350     ERRMC  
     WELL ORDERED  . . . . .    3.421      0.650       0.325    350   100.0   350     ERRMC  
     NO INTER CONTACTS . . .    3.421      0.650       0.325    350   100.0   350     ERRMC  
     SHIFTED CHAIN . . . . .    3.469      0.654       0.327    321   100.0   321     ERRMC  
     ALTERNATIVE PARENT  . .    4.303      0.657       0.329     39   100.0    39     ERRMC  
     SECONDARY STRUCTURE . .    2.777      0.621       0.311    159   100.0   159     ERRMC  
     LARGE SHIFTS/INSERTIONS    5.145      0.756       0.378    123   100.0   123     ERRMC  
     SURFACE . . . . . . . .    3.726      0.664       0.332    276   100.0   276     ERRMC  
     BURIED  . . . . . . . .    2.283      0.595       0.298     74   100.0    74     ERRMC  
     CORE  . . . . . . . . .    2.486      0.592       0.297    227   100.0   227     ERRMC  
 (SC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    4.031      0.714       0.357    350    43.6   803     ERRSC  
     WELL ORDERED  . . . . .    4.031      0.714       0.357    350    43.6   803     ERRSC  
     NO INTER CONTACTS . . .    4.031      0.714       0.357    350    43.6   803     ERRSC  
     RELIABLE SIDE CHAINS  .    4.010      0.710       0.355    314    40.9   767     ERRSC  
     CHANGED ANGLES  . . . .    4.624      0.755       0.378    156   100.0   156     ERRSC  
     SHIFTED CHAIN . . . . .    4.046      0.721       0.360    318    42.8   743     ERRSC  
     ALTERNATIVE PARENT  . .    4.224      0.720       0.360     31    40.3    77     ERRSC  
     SECONDARY STRUCTURE . .    3.215      0.680       0.340    163    41.4   394     ERRSC  
     LARGE SHIFTS/INSERTIONS    5.523      0.791       0.396    102    43.6   234     ERRSC  
     SURFACE . . . . . . . .    4.362      0.733       0.367    277    44.4   624     ERRSC  
     BURIED  . . . . . . . .    2.777      0.639       0.320     73    40.8   179     ERRSC  
     CORE  . . . . . . . . .    3.418      0.682       0.341    248    43.6   569     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.749      0.682       0.341    634    58.3  1087     ERRALL 
     WELL ORDERED  . . . . .    3.749      0.682       0.341    634    58.3  1087     ERRALL 
     NO INTER CONTACTS . . .    3.749      0.682       0.341    634    58.3  1087     ERRALL 
     SHIFTED CHAIN . . . . .    3.784      0.688       0.344    578    57.6  1003     ERRALL 
     ALTERNATIVE PARENT  . .    4.273      0.687       0.344     63    57.8   109     ERRALL 
     SECONDARY STRUCTURE . .    3.035      0.653       0.327    291    55.7   522     ERRALL 
     LARGE SHIFTS/INSERTIONS    5.340      0.773       0.386    202    60.5   334     ERRALL 
     SURFACE . . . . . . . .    4.067      0.700       0.350    501    59.1   848     ERRALL 
     BURIED  . . . . . . . .    2.548      0.617       0.309    133    55.6   239     ERRALL 
     CORE  . . . . . . . . .    3.004      0.640       0.320    432    57.4   753     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)         8        27        34        51        66      71      71   DISTCA 
CA  (P)     11.27     38.03     47.89     71.83     92.96              71   DISTCA 
CA  (RMS)    0.74      1.35      1.66      2.68      4.03                   DISTCA 
 
ALL (N)        56       179       272       437       588     634    1087   DISTALL 
ALL (P)      5.15     16.47     25.02     40.20     54.09            1087   DISTALL 
ALL (RMS)    0.78      1.32      1.83      2.85      4.35                   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)          46            46            25          RMSLSI 
CA  (P)       64.79         64.79         35.21          RMSLSI 
CA  (RMS)      1.65          3.52          6.71          RMSLSI 
 
 
 
END of the results output 
