 
####################################################### 
#                                                     # 
#                        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/T0058.inter 
# 
NUMBER-OF-PARENTS      2 
ALIGNMENT-DALI(1)      ../PARENTS/casp3.T0058.1akz.rot 
ALIGNMENT-DALI(2)      ../PARENTS/casp3.T0058.1udh.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 1784 atoms, MODEL 954 atoms, 924 common with TARGET 
           Number of atoms possible to evaluate: 868 
 
 
 CA-RMS TARGET<->PARENT(1akz)	 1.191923 
 
 CA-RMS TARGET<->PARENT(1udh)	 1.648171 
 
 
MEASURES: 
 
 
ANGLES RMS : model <-> target 
 
 (MC: PHI+PSI) DIHED RMS:      ARMSMC            PC     NP     PP     TN 
     ALL . . . . . . . . . .    30.91           94.9   430    96.0   448     ARMSMC  
     WELL ORDERED  . . . . .    30.91           94.9   430    96.6   445     ARMSMC  
     NO INTER CONTACTS . . .    29.83           95.1   309    98.1   315     ARMSMC  
     SHIFTED CHAIN . . . . .    43.20           88.0   117    87.3   134     ARMSMC  
     ALTERNATIVE PARENT  . .    89.94           50.0     4   100.0     4     ARMSMC  
     SECONDARY STRUCTURE . .     8.32           99.4   158   100.0   158     ARMSMC  
     LARGE SHIFTS/INSERTIONS    72.32           50.0     6    27.3    22     ARMSMC  
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSMC  
     SURFACE . . . . . . . .    38.36           92.4   210    92.1   228     ARMSMC  
     BURIED  . . . . . . . .    21.53           97.3   220   100.0   220     ARMSMC  
     CORE  . . . . . . . . .    29.92           95.5   424    99.5   426     ARMSMC  
 (SC: CHI1) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   190     ARMSSC1 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   176     ARMSSC1 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   135     ARMSSC1 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   173     ARMSSC1 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    58     ARMSSC1 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    58     ARMSSC1 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     2     ARMSSC1 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    74     ARMSSC1 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0    10     ARMSSC1 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC1 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    97     ARMSSC1 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    93     ARMSSC1 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   180     ARMSSC1 
 (SC: CHI2) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0   148     ARMSSC2 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0   132     ARMSSC2 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0   102     ARMSSC2 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0   102     ARMSSC2 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    74     ARMSSC2 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    44     ARMSSC2 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     1     ARMSSC2 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    57     ARMSSC2 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     6     ARMSSC2 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC2 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    80     ARMSSC2 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0    68     ARMSSC2 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0   142     ARMSSC2 
 (SC: CHI3) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    47     ARMSSC3 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    33     ARMSSC3 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0    22     ARMSSC3 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    33     ARMSSC3 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    32     ARMSSC3 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0    19     ARMSSC3 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0    17     ARMSSC3 
     LARGE SHIFTS/INSERTIONS     0.00            0.0     0     0.0     2     ARMSSC3 
     LIGAND CONTACTS . . . .     0.00            0.0     0     0.0     0     ARMSSC3 
     SURFACE . . . . . . . .     0.00            0.0     0     0.0    39     ARMSSC3 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     8     ARMSSC3 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    45     ARMSSC3 
 (SC: CHI4) DIHED RMS:         ARMSSC            PC     NP     PP     TN 
     ALL . . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
     WELL ORDERED  . . . . .     0.00            0.0     0     0.0    11     ARMSSC4 
     NO INTER CONTACTS . . .     0.00            0.0     0     0.0     7     ARMSSC4 
     RELIABLE SIDE CHAINS  .     0.00            0.0     0     0.0    18     ARMSSC4 
     CHANGED ANGLES  . . . .     0.00            0.0     0     0.0    13     ARMSSC4 
     SHIFTED CHAIN . . . . .     0.00            0.0     0     0.0     5     ARMSSC4 
     ALTERNATIVE PARENT  . .     0.00            0.0     0     0.0     0     ARMSSC4 
     SECONDARY STRUCTURE . .     0.00            0.0     0     0.0     6     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 . . . . . . . .     0.00            0.0     0     0.0    15     ARMSSC4 
     BURIED  . . . . . . . .     0.00            0.0     0     0.0     3     ARMSSC4 
     CORE  . . . . . . . . .     0.00            0.0     0     0.0    18     ARMSSC4 
 
COORDINATES RMS : model <-> target 
 
 
UNITARY 3.3 RIGHT HANDED ROTATION MATRIX: 
 r(1,1) =  -0.40033     r(1,2) =   0.65743     r(1,3) =  -0.63838 
 r(2,1) =   0.91430     r(2,2) =   0.23976     r(2,3) =  -0.32645 
 r(3,1) =  -0.06156     r(3,2) =  -0.71435     r(3,3) =  -0.69707 
THE OFFSET VECTOR: 
 v(1) =  10.33558     v(2) =  14.58613     v(3) =  -8.92580 
 
 Number of iteration 25                   (CUTOFF:  2.50) 
 TEST (CA iter) RMS =   0.91           (Number of atoms:  213) 
 
 (CA)  RMS:                   CRMSCA         NP     PP     TN 
     ALL . . . . . . . . . .    1.00        217    96.4   225     CRMSCA  
     CRN = ALL/NP  . . . . .    0.0046                            CRMSCA  
     WELL ORDERED  . . . . .    1.00        217    96.9   224     CRMSCA  
     NO INTER CONTACTS . . .    0.99        156    98.7   158     CRMSCA  
     SHIFTED CHAIN . . . . .    1.64         60    88.2    68     CRMSCA  
     ALTERNATIVE PARENT  . .    3.29          2   100.0     2     CRMSCA  
     SECONDARY STRUCTURE . .    0.72         79   100.0    79     CRMSCA  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSCA  
     LARGE SHIFTS/INSERTIONS    3.23          4    33.3    12     CRMSCA  
     SURFACE . . . . . . . .    1.15        107    93.0   115     CRMSCA  
     BURIED  . . . . . . . .    0.83        110   100.0   110     CRMSCA  
     CORE  . . . . . . . . .    0.91        213   100.0   213     CRMSCA  
 (MC)  RMS:                   CRMSMC         NP     PP     TN 
     ALL . . . . . . . . . .    1.03        868    78.4  1107     CRMSMC  
     WELL ORDERED  . . . . .    1.02        864    78.9  1095     CRMSMC  
     NO INTER CONTACTS . . .    1.02        624    80.2   778     CRMSMC  
     SHIFTED CHAIN . . . . .    1.64        240    71.9   334     CRMSMC  
     ALTERNATIVE PARENT  . .    3.10          8    80.0    10     CRMSMC  
     SECONDARY STRUCTURE . .    0.73        316    80.2   394     CRMSMC  
     SHIFTED SS UNITS  . . .    0.00          0     0.0     0     CRMSMC  
     LARGE SHIFTS/INSERTIONS    3.35         16    27.1    59     CRMSMC  
     SURFACE . . . . . . . .    1.18        428    75.6   566     CRMSMC  
     BURIED  . . . . . . . .    0.86        440    81.3   541     CRMSMC  
     CORE  . . . . . . . . .    0.93        852    81.3  1048     CRMSMC  
 (SC)  RMS:                   CRMSSC         NP     PP     TN 
     ALL . . . . . . . . . .    0.00          0     0.0   884     CRMSSC  
     WELL ORDERED  . . . . .    0.00          0     0.0   816     CRMSSC  
     NO INTER CONTACTS . . .    0.00          0     0.0   630     CRMSSC  
     RELIABLE SIDE CHAINS  .    0.00          0     0.0   704     CRMSSC  
     CHANGED ANGLES  . . . .    0.00          0     0.0   328     CRMSSC  
     SECONDARY STRUCTURE . .    0.00          0     0.0   341     CRMSSC  
     LARGE SHIFTS/INSERTIONS    0.00          0     0.0    36     CRMSSC  
     SURFACE . . . . . . . .    0.00          0     0.0   448     CRMSSC  
     BURIED  . . . . . . . .    0.00          0     0.0   436     CRMSSC  
     CORE  . . . . . . . . .    0.00          0     0.0   848     CRMSSC  
 (ALL) RMS:                   CRMSALL        NP     PP     TN 
     ALL . . . . . . . . . .    1.03        868    48.7  1784     CRMSALL 
     WELL ORDERED  . . . . .    1.02        864    50.6  1708     CRMSALL 
     NO INTER CONTACTS . . .    1.02        624    49.4  1262     CRMSALL 
     SHIFTED CHAIN . . . . .    1.64        240    45.3   530     CRMSALL 
     ALTERNATIVE PARENT  . .    3.10          8    61.5    13     CRMSALL 
     SECONDARY STRUCTURE . .    0.73        316    48.1   657     CRMSALL 
     LARGE SHIFTS/INSERTIONS    3.35         16    19.0    84     CRMSALL 
     SURFACE . . . . . . . .    1.18        428    47.1   908     CRMSALL 
     BURIED  . . . . . . . .    0.86        440    50.2   876     CRMSALL 
     CORE  . . . . . . . . .    0.93        852    50.1  1700     CRMSALL 
 
 
RMS Details of loops: 
 
 GLOBAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 CA  LOOP  1     3.60      2    25.0     8     222-PVLPAESE-229  
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 MC  LOOP  1     3.50      8    20.0    40     222-PVLPAESE-229  
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 ALL LOOP  1     3.50      8    13.8    58     222-PVLPAESE-229  
 
 LOCAL SUPERPOSITION 
 RMS:          CRMSCA     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 RMS:          CRMSMC     NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 RMS:          CRMSALL    NP     PP     TN        LOOPS 
 WARNING! LOOP  1 cannot be considered (not enough atoms). 
 
 
 
Accuracy of estimates of atomic coordinate errors: model <-> target 
 
 (CA)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.179      0.678       0.722    217    96.4   225     ERRCA  
     WELL ORDERED  . . . . .    3.179      0.678       0.722    217    96.9   224     ERRCA  
     NO INTER CONTACTS . . .    3.225      0.696       0.734    156    98.7   158     ERRCA  
     SHIFTED CHAIN . . . . .    2.487      0.463       0.550     60    88.2    68     ERRCA  
     ALTERNATIVE PARENT  . .    1.457      0.253       0.299      2   100.0     2     ERRCA  
     SECONDARY STRUCTURE . .    3.375      0.740       0.775     79   100.0    79     ERRCA  
     LARGE SHIFTS/INSERTIONS    1.060      0.155       0.125      4    33.3    12     ERRCA  
     SURFACE . . . . . . . .    2.981      0.610       0.670    107    93.0   115     ERRCA  
     BURIED  . . . . . . . .    3.372      0.744       0.773    110   100.0   110     ERRCA  
     CORE  . . . . . . . . .    3.219      0.688       0.733    213   100.0   213     ERRCA  
 (MC)  ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.175      0.677       0.721    868    78.4  1107     ERRMC  
     WELL ORDERED  . . . . .    3.179      0.679       0.722    864    78.9  1095     ERRMC  
     NO INTER CONTACTS . . .    3.217      0.694       0.731    624    80.2   778     ERRMC  
     SHIFTED CHAIN . . . . .    2.529      0.477       0.559    240    71.9   334     ERRMC  
     ALTERNATIVE PARENT  . .    1.693      0.320       0.346      8    80.0    10     ERRMC  
     SECONDARY STRUCTURE . .    3.371      0.738       0.773    316    80.2   394     ERRMC  
     LARGE SHIFTS/INSERTIONS    1.146      0.166       0.145     16    27.1    59     ERRMC  
     SURFACE . . . . . . . .    2.986      0.612       0.670    428    75.6   566     ERRMC  
     BURIED  . . . . . . . .    3.358      0.741       0.770    440    81.3   541     ERRMC  
     CORE  . . . . . . . . .    3.213      0.687       0.732    852    81.3  1048     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   884     ERRSC  
     WELL ORDERED  . . . . .    0.000      0.000       0.000      0     0.0   816     ERRSC  
     NO INTER CONTACTS . . .    0.000      0.000       0.000      0     0.0   630     ERRSC  
     RELIABLE SIDE CHAINS  .    0.000      0.000       0.000      0     0.0   704     ERRSC  
     CHANGED ANGLES  . . . .    0.000      0.000       0.000      0     0.0   328     ERRSC  
     SHIFTED CHAIN . . . . .    0.000      0.000       0.000      0     0.0   258     ERRSC  
     ALTERNATIVE PARENT  . .    0.000      0.000       0.000      0     0.0     5     ERRSC  
     SECONDARY STRUCTURE . .    0.000      0.000       0.000      0     0.0   341     ERRSC  
     LARGE SHIFTS/INSERTIONS    0.000      0.000       0.000      0     0.0    36     ERRSC  
     SURFACE . . . . . . . .    0.000      0.000       0.000      0     0.0   448     ERRSC  
     BURIED  . . . . . . . .    0.000      0.000       0.000      0     0.0   436     ERRSC  
     CORE  . . . . . . . . .    0.000      0.000       0.000      0     0.0   848     ERRSC  
 (ALL) ERRORS:                  |D-E|   |D-E|/|D+E|   SR(D,E)    NP     PP     TN 
     ALL . . . . . . . . . .    3.175      0.677       0.721    868    48.7  1784     ERRALL 
     WELL ORDERED  . . . . .    3.179      0.679       0.722    864    50.6  1708     ERRALL 
     NO INTER CONTACTS . . .    3.217      0.694       0.731    624    49.4  1262     ERRALL 
     SHIFTED CHAIN . . . . .    2.529      0.477       0.559    240    45.3   530     ERRALL 
     ALTERNATIVE PARENT  . .    1.693      0.320       0.346      8    61.5    13     ERRALL 
     SECONDARY STRUCTURE . .    3.371      0.738       0.773    316    48.1   657     ERRALL 
     LARGE SHIFTS/INSERTIONS    1.146      0.166       0.145     16    19.0    84     ERRALL 
     SURFACE . . . . . . . .    2.986      0.612       0.670    428    47.1   908     ERRALL 
     BURIED  . . . . . . . .    3.358      0.741       0.770    440    50.2   876     ERRALL 
     CORE  . . . . . . . . .    3.213      0.687       0.732    852    50.1  1700     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)       158       208       216       217       217     217     225   DISTCA 
CA  (P)     70.22     92.44     96.00     96.44     96.44             225   DISTCA 
CA  (RMS)    0.60      0.85      0.96      1.00      1.00                   DISTCA 
 
ALL (N)       628       825       858       867       868     868    1784   DISTALL 
ALL (P)     35.20     46.24     48.09     48.60     48.65            1784   DISTALL 
ALL (RMS)    0.59      0.84      0.94      1.01      1.03                   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)         213           213             4          RMSLSI 
CA  (P)       94.67         94.67          1.78          RMSLSI 
CA  (RMS)      0.91          0.91          3.23          RMSLSI 
 
 
 
END of the results output 
