Within this routine only, the scaling factors for the physical restraint types are obtained from the SCHEDULE_STEP step of the current schedule, multipled by SCHEDULE_SCALE (the original values are returned upon exit from the routine). This allows easy reporting of only a selected subset of all restraints.
Most of the output goes to the log file. The output of the ENERGY command has to be examined carefully, at least at the end of the optimization, when the final model is produced. Additional output files, for the ASGL plotting program are created if ASGL_OUTPUT = on (undocumented).
OUTPUT selects various kinds of output information:
VIOL_REPORT_CUT is a vector with one real number for each physical restraint type. A restraint is reported when its `heavy relative violation' is larger than the corresponding cutoff. The heavy relative violation is calculated by finding the global minimum of a feature according to the restraint, taking the difference between the actual feature in the model and this global minimum, and then normalizing the difference by the standard deviation of the global minimum. The `minimal violation' of a restraint is defined as the difference from the local minimum closest to the value of the feature in the model (with the exception of the spline restraints; see next paragraph).
VIOL_REPORT_CUT2 is similar to VIOL_REPORT_CUT, except that it contains cutoffs for restraint `energies', not heavy relative violations.
The meaning of various other reported properties of the violated restraints
is briefly described in the log file. Note that for multi-modal
restraints that are described by
cubic splines (by default, all multimodal homology-derived restraints),
only one optimal value is defined, not the local and global minimum
as for the multi-modal Gaussian restraints. As a result, the
minimal violations and heaviest violations are the same.
For interpreting the seriousness of violations, use the following
rule of thumb: There should be at most a few small violations
(e.g., 4 standard deviations) for all monomodal restraints. In comparative
modeling, the monomodal restraints include the stereochemical restraints
and distance restraints when only one homologous structure is used.
For the multimodal restraints, there are usually many violations reported
because the heaviest violations are used in deciding whether or not to
report a violation. In comparative modeling, the multimodal restraints
include the 
restraints, (
, 
) binormal restraints
and distance restraints when more than one template is used. See also
Section 1.8, Question 22.
For profiles:
This command calculates residue energies or heavy relative violations, depending on OUTPUT, for all physical restraint types (there are NPHYCNS of them). Relative heavy violations (Table 2.2) are used because only relative violations of different features are comparable. In both cases, the residue sum is the sum over all restraints that have at least one atom in a given residue. The contribution of each restraint is counted exactly once for each residue, without any weighting. Restraints spanning more than one residue contribute equally to all of them. Thus, the sum of residue energies is generally larger than molecular pdf. The command also calculates the sum of the NPHYCNS contributions for each residue and writes all NPHYCNS+1 columns to a file suitable for plotting by ASGL.
If NORMALIZE_PROFILE is on the profile for each residue is normalized by the number of terms applying to each residue.
All the curves are smoothed by the running window
averaging method if SMOOTHING_WINDOW is larger than 0: The window
is centered on residue 
and extends for (SMOOTHING_WINDOW/2) - 1
residues on each side. Thus, SMOOTHING_WINDOW has to be an even
number (or it is made such by the program automatically).
The only exceptions are the
two terminii, where a smaller number of residues are available for
smoothing. The relative weight of residue 
when calculating the
smoothed value at residue is
.
The energy or the violations profile is written to the fourth column of the MODEL atomic records (atomic isotropic temperature factors for X-ray structures). Note that all the atoms in one residue get the same number. This output is useful for exploring the violations on a graphics terminal.
# Example for: ENERGY
# This will calculate the stereochemical energy (bonds,
# angles, dihedrals, impropers) for a given model.
READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib'
READ_PARAMETERS FILE = '$(LIB)/par.lib'
READ_MODEL FILE = '1fas'
SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas'
SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ;
ALIGN_CODES = ALIGN_CODES '1fas-ini'
GENERATE_TOPOLOGY SEQUENCE = '1fas-ini'
# Must patch disulfides here to calculate the non-bonded
# energy properly. Also, when you use hydrogens, disulfides
# must always be patched so that sulfhydril hydrogens are
# removed from the model.
PATCH RESIDUE_TYPE = DISU, RESIDUE_IDS = '17' '39'
PATCH RESIDUE_TYPE = DISU, RESIDUE_IDS = '3' '22'
PATCH RESIDUE_TYPE = DISU, RESIDUE_IDS = '53' '59'
PATCH RESIDUE_TYPE = DISU, RESIDUE_IDS = '41' '52'
TRANSFER_XYZ
BUILD_MODEL INITIALIZE_XYZ = off
MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo'
ENERGY DYNAMIC_SPHERE = on