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Question on 1fdx example



Fellow Modellers,

        I ran the first example in the Modeller tutorial, 1fdx,
and I got several restraint violations in the final structure. I ran the
diagnostics, and I dod not receive any error messages.
Is this as it should be?
Is there anywhere in which one can obtain a standard 1fdx run that can be
used as a "known"?

I  know that, based upon faq #23, interpreting restraint violations is
something of an art. I am asking to make sure that I ran the program
correctly, and that the program is  running as it should be.

My violated restraints are:

Summary of the restraint violations:

   NUM     ... number of restraints.
   NUMVI   ... number of restraints with RVIOL > VIOL_REPORT_CUT[i].
   RVIOL   ... relative difference from the best value.
   NUMVP   ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i].
   RMS_1   ... RMS(feature, minimally_violated_basis_restraint, NUMB).
   RMS_2   ... RMS(feature, best_value, NUMB).
   MOL.PDF ... scaled contribution to -Ln(Molecular pdf).

 #                     RESTRAINT_GROUP      NUM   NUMVI  NUMVP   RMS_1   RMS_2         MOL.PDF     S_i
------------------------------------------------------------------------------------------------------
 1 Bond length potential              :     379       0      0   0.005   0.005      2.8642       1.000
 2 Bond angle potential               :     520       0      0   2.444   2.444      59.089       1.000
 3 Stereochemical cosine torsion poten:     244       0     10  55.593  55.593      103.81       1.000
 4 Stereochemical improper torsion pot:     146       0      0   1.474   1.474      6.3455       1.000
 5 Soft-sphere overlap restraints     :     663       0      0   0.002   0.002     0.47318       1.000
 6 Lennard-Jones 6-12 potential       :       0       0      0   0.000   0.000      0.0000       1.000
 7 Coulomb point-point electrostatic p:       0       0      0   0.000   0.000      0.0000       1.000
 8 H-bonding potential                :       0       0      0   0.000   0.000      0.0000       1.000
 9 Distance restraints 1 (CA-CA)      :     804       0      0   0.344   0.344      30.114       1.000
10 Distance restraints 2 (N-O)        :     832       0      1   0.467   0.467      37.873       1.000
11 Mainchain Phi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
12 Mainchain Psi dihedral restraints  :       0       0      0   0.000   0.000      0.0000       1.000
13 Mainchain Omega dihedral restraints:      53       0      0   4.634   4.634      13.423       1.000
14 Sidechain Chi_1 dihedral restraints:      43       0      1  72.693  72.693      11.147       1.000
15 Sidechain Chi_2 dihedral restraints:      26       0      1  68.739  68.739      16.513       1.000
16 Sidechain Chi_3 dihedral restraints:       9       0      0  37.987  37.987      3.4346       1.000
17 Sidechain Chi_4 dihedral restraints:       1       0      0 124.535 124.535      1.0173       1.000
18 Disulfide distance restraints      :       0       0      0   0.000   0.000      0.0000       1.000
19 Disulfide angle restraints         :       0       0      0   0.000   0.000      0.0000       1.000
20 Disulfide dihedral angle restraints:       0       0      0   0.000   0.000      0.0000       1.000
21 Lower bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
22 Upper bound distance restraints    :       0       0      0   0.000   0.000      0.0000       1.000
23 Distance restraints 3 (SDCH-MNCH)  :     553       0      0   0.540   0.540      18.286       1.000
24 Sidechain Chi_5 dihedral restraints:       0       0      0   0.000   0.000      0.0000       1.000
25 Phi/Psi pair of dihedral restraints:      52       9      5  29.961  67.309      9.4985       1.000
26 Distance restraints 4 (SDCH-SDCH)  :     100       0      2   1.196   1.196      15.584       1.000
27 Distance restraints 5 (X-Y)        :       0       0      0   0.000   0.000      0.0000       1.000
28 NMR distance restraints 6 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
29 NMR distance restraints 7 (X-Y)    :       0       0      0   0.000   0.000      0.0000       1.000
30 Minimal distance restraints        :       0       0      0   0.000   0.000      0.0000       1.000
31 Non-bonded restraints              :       0       0      0   0.000   0.000      0.0000       1.000
32 Atomic accessibility restraints    :       0       0      0   0.000   0.000      0.0000       1.000
33 Atomic density restraints          :       0       0      0   0.000   0.000      0.0000       1.000



openf5__224_> Open       17  UNKNOWN  SEQUENTIAL  1fdx.V99990001
# Heavy relative violation of each residue is written to: 1fdx.V99990001
# The profile is NOT normalized by the number of restraints.
# The profiles are smoothed over a window of residues:    1



List of the violated restraints:
   A restraint is violated when the relative difference
   from the best value (RVIOL) is larger than CUTOFF.

   ICSR   ... index of a restraint in the current set.
   RESNO  ... residue numbers of the first two atoms.
   ATM    ... IUPAC atom names of the first two atoms.
   FEAT   ... the value of the feature in the model.
   restr  ... the mean of the basis restraint with the smallest
              difference from the model (local minimum).
   viol   ... difference from the local minimum.
   rviol  ... relative difference from the local minimum.
   RESTR  ... the best value (global minimum).
   VIOL   ... difference from the best value.
   RVIOL  ... relative difference from the best value.


-------------------------------------------------------------------------------------------------

Feature 25                           : Phi/Psi pair of dihedral restraints
List of the RVIOL violations larger than   :       6.5000

    #   ICSR  RESNO1/2 ATM1/2   INDATM1/2    FEAT   restr    viol   rviol   RESTR    VIOL   RVIOL
    1   1296   7S   8C C   N      53   55  -75.51 -117.90   43.16    1.34  -63.00  174.54   20.46
    1          8C   8C N   CA     55   56  133.00  141.10                  -41.10
    2   1297   8C   9I C   N      59   61 -109.33  -97.30   83.47    8.55  -63.40   99.45   15.16
    2          9I   9I N   CA     61   62   44.60  127.20                  -43.60
    3   1298   9I  10A C   N      67   69   43.10   55.40   23.15    0.89  -62.50  144.55   28.99
    3         10A  10A N   CA     69   70   57.81   38.20                  -40.90
    4   1299  10A  11C C   N      72   74  -61.78  -63.00    1.43    0.25 -117.90 -172.86    8.06
    4         11C  11C N   CA     74   75  -40.37  -41.10                  141.10
    5   1310  21N  22I C   N     146  148 -109.14 -120.60   69.78    3.55  -63.40  114.60   17.55
    5         22I  22I N   CA    148  149   61.47  130.30                  -43.60
    6   1313  24Q  25G C   N     171  173   98.62   78.70   39.64    0.60   82.20  152.01    8.20
    6         25G  25G N   CA    173  174  159.62 -166.10                    8.50
    7   1314  25G  26S C   N     175  177  -65.61  -64.10   21.61    1.66 -136.60  167.99    9.49
    7         26S  26S N   CA    177  178  -56.55  -35.00                  151.20
    8   1315  26S  27I C   N     181  183  -64.03  -63.40    6.55    1.10 -120.60 -171.73   12.88
    8         27I  27I N   CA    183  184  -50.13  -43.60                  130.30
    9   1316  27I  28Y C   N     189  191  104.14 -124.30  131.89   10.18 -124.30  131.89   10.18
    9         28Y  28Y N   CA    191  192  126.16  135.40                  135.40

Thanks and best wishes,
Rich
--------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Medical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University
630 W. 168th St.
New York, NY 10032
(212)305-6901 (5-6901) (voice)

http://cancercenter.ccc.columbia.edu/~friedman/

In Memoriam, Robert Kanigher