yes, it is OK.
but if you are interested in subsequently "evaluate" the model you obtained, you have many different programs that can do that, using various criteria. Here is a link to collection of links and you can read more about this in our reviews.
http://salilab.org/modeller/methenz/ http://salilab.org/~andras/watanabe/main2.ps http://salilab.org/modeller/downloads/andras.pdf Andras Richard Friedman wrote: > > 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) > friedman@cancercenter.ccc.columbia.edu > http://cancercenter.ccc.columbia.edu/~friedman/ > > In Memoriam, Robert Kanigher