The following formula is used to calculate the degrees of freedom, df. Because the result of the calculation is usually not an integer, the value of df is rounded to the nearest integer to obtain a critical value from the t table. The Excel worksheet function T.TEST uses the calculated df value without rounding, because it is possible to compute a value for T.TEST with a noninteger df. Because of these different approaches to determining the degrees of freedom, the results of T.TEST and this t-Test tool will differ in the Unequal Variances case.
To make it easier and quicker to define the actions that are associated with each location directive line, use one of the predefined strategies. For example, you can use the Empty location with no incoming work strategy to search for free locations in a warehouse, or you can use FEFO batch reservation strategy for outbound sales picking.
Windows.Bins.Beta Setup Free
3.18.18 (2022-02-17)digilent.waveforms_beta_v3.18.18_64bit.exedigilent.waveforms_beta_v3.18.18.dmgdigilent.waveforms_beta_3.18.18_amd64.debdigilent.waveforms_beta_3.18.18.x86_64.rpmAdding:- Logic: Rate option for Import binary file- Patterns: Import binary for custom signal- Protocol/SDK I2C: freeing up DIOs with I2C clock stretching for AD1,2,DD,ADP3X50- Protocol: I2C Slave and Custom/Script functions also for spying- SDK: FDwfDigitalOutPlayUpdateSet DigitalDiscovery_PlayUpdate.py
where C(f) is the coherence at the frequency f and d.f. the degrees of freedom. A non-parametric test (Maris et al. 2007) was then used to test the linear relation between CMC and MEP. The average of the z-values from the EEG channels of interest was estimated, yielding 1 z-value for each group of bins. The average of the peak-to-peak MEP amplitude of each group of bins was now used as the MEP amplitude for correlation with the corresponding bin. This procedure resulted in16 pairs of bias-corrected CMC and MEP amplitudes.
McAfee Safe Connect VPN includes five devices, and is compatible with Windows, Chrome OS, iOS and Android devices. However, the free version of the McAfee Safe Connect only supports one device and is limited to 250MB of data per month.
Kibana is a free and open user interface that lets you visualize your Elasticsearch data and navigate the Elastic Stack. Do anything from tracking query load to understanding the way requests flow through your apps.
Kibana gives you the freedom to select the way you give shape to your data. With its interactive visualizations, start with one question and see where it leads you. See the full list of Kibana features.
The aSPECT setup at the cold neutron beam line of PF1b at the ILL in 2013. Clearly visible are (1) the detector electronics on top, (2) the vertically aligned aSPECT cryostat system, (3) the massive magnetic field return yoke for the magnetic shielding, and (4) the beam dump in front.
Ideogram of a values for each configuration fitted separately without any systematic correction. The blue data points are derived from configuration runs with standard parameter settings. Forced enhancement of the edge effect by a reduced beam profile leads to more negative a values (green data points), whereas config 2b (EM off) shows the trend from systematic shifts to positive a values. The total error from the fit is shown together with the uncorrelated error which reflects the count rate statistics and which essentially constitutes the total error. The error bars of the extracted a values are scaled with χ2/ν whenever the p value is less than the conventionally accepted significance level of α=0.05 (cf. Table 3) which is indicated by an asterisk (*). The degrees of freedom are ν=15 for each configuration.
phenix.refine uses automatic procedure to determine the weights between X-raytarget and stereochemistry or ADP restraints. To optimize these weights (that isto find those resulting in lowest Rfree factors):
Although the automatic calculation of weight between X-ray and stereochemistryor ADP restraint targets is good for most of cases, it may happen that rmsddeviations from ideal bonds length or angles are looking too tight or loose (depending on resolution). Or the difference between R-work and R-free is toobig (significantly bigger than approx. 5%). In such cases one definitelyneed to try loose or tighten the restraints. Hers is how for coordinatesrefinement:
It is important to understand that reflections selected for test set must benever used in any refinement of any parameters. If the newly selected testreflections were used in refinement before then the corresponding R-freestatistics will be wrong. In such case "refinement memory" removal proceduremust be applied to recover proper statistics.
refinementScope of parameters for structure refinement with phenix.refinedry_run = False Read and process inputs and quit (no refinement)custom_scattering_factors = None Use custom scattering factors and replaces default values entirelycrystal_symmetryScope of space group and unit cell parametersunit_cell = None space_group = None inputScope of input file names, labels, processing directionssymmetry_safety_check = *error warning Check for consistency of crystal symmetry from model and data filespdbfile_name = None Model file(s) name (PDB)neutron_dataScope of neutron data and neutron free-R flagsignore_xn_free_r_mismatch = False file_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True Remove basic wilson outliers , extreme wilson outliers , and beamstop shadow outliersfrench_wilson_scale = True sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None convert_to_non_anomalous_if_ratio_pairs_lone_less_than_threshold = 0.5 french_wilsonmax_bins = 60 Maximum number of resolution binsmin_bin_size = 40 Minimum number of reflections per binr_free_flagsfile_name = None This is normally the same as the file containing Fobs and is usually selected automatically.label = None test_flag_value = None This value is usually selected automatically - do not change unless you really know what you're doing!ignore_r_free_flags = False Use all reflections in refinement (work and test)disable_suitability_test = False ignore_pdb_hexdigest = False If True, disables safety check based on MD5 hexdigests stored in PDB files produced by previous runs.generate = False Generate R-free flags (if not available in input files)fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True use_dataman_shells = False Used to avoid biasing of the test set by certain types of non-crystallographic symmetry.n_shells = 20 xray_dataScope of X-ray data and free-R flagsfile_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True Remove basic wilson outliers , extreme wilson outliers , and beamstop shadow outliersfrench_wilson_scale = True sigma_fobs_rejection_criterion = None sigma_iobs_rejection_criterion = None ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None convert_to_non_anomalous_if_ratio_pairs_lone_less_than_threshold = 0.5 french_wilsonmax_bins = 60 Maximum number of resolution binsmin_bin_size = 40 Minimum number of reflections per binr_free_flagsfile_name = None This is normally the same as the file containing Fobs and is usually selected automatically.label = None test_flag_value = None This value is usually selected automatically - do not change unless you really know what you're doing!ignore_r_free_flags = False Use all reflections in refinement (work and test)disable_suitability_test = False ignore_pdb_hexdigest = False If True, disables safety check based on MD5 hexdigests stored in PDB files produced by previous runs.generate = False Generate R-free flags (if not available in input files)fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True use_dataman_shells = False Used to avoid biasing of the test set by certain types of non-crystallographic symmetry.n_shells = 20 experimental_phasesScope of experimental phase information (HL coefficients)file_name = None labels = None monomersScope of monomers information (CIF files)file_name = None Monomer file(s) name (CIF)sequencefile_name = None Sequence data in a text file (supported formats include FASTA, PIR, and raw text). Currently this is only used by the PHENIX GUI for validation.outputScope for output filesprefix = None Prefix for all output filesserial = None Serial number for consequtive refinement runsserial_format = "%03d" Format serial number in output file namejob_title = None Job title in PHENIX GUI, not used on command linewrite_eff_file = True write_geo_file = True write_final_geo_file = False write_def_file = True write_model_cif_file = True write_reflection_cif_file = False export_final_f_model = False Write Fobs, Fmodel, various scales and more to MTZ filewrite_maps = False write_map_coefficients = True write_map_coefficients_only = False pickle_fmodel = False Dump final fmodel object into a pickle file.n_resolution_bins = None Sets the number of bins used for resolution-dependent statistics in output files and the Phenix GUI. If None, the binning will be determined automatically.electron_density_mapsElectron density maps calculation parametersapply_default_maps = None map_coefficientsmap_type = None format = *mtz phs mtz_label_amplitudes = None mtz_label_phases = None fill_missing_f_obs = False acentrics_scale = 2.0 Scale terms corresponding to acentric reflections (residual maps only: k==n)centrics_pre_scale = 1.0 Centric reflections, k!=n and k*n != 0: max(k-centrics_pre_scale,0)*Fo-max(n-centrics_pre_scale,0)*Fcsharpening = False Apply B-factor sharpeningsharpening_b_factor = None Optional sharpening B-factor valueexclude_free_r_reflections = False Exclude free-R selected reflections from output map coefficientsisotropize = True devcomplete_set_up_to_d_min = False aply_same_incompleteness_to_complete_set_at = randomly low high mapmap_type = None format = xplor *ccp4 file_name = None fill_missing_f_obs = False grid_resolution_factor = 1/4. scale = *sigma volume region = *selection cell atom_selection = None atom_selection_buffer = 3 acentrics_scale = 2.0 Scale terms corresponding to acentric reflections (residual maps only: k==n)centrics_pre_scale = 1.0 Centric reflections, k!=n and k*n != 0: max(k-centrics_pre_scale,0)*Fo-max(n-centrics_pre_scale,0)*Fcsharpening = False Apply B-factor sharpeningsharpening_b_factor = None Optional sharpening B-factor valueexclude_free_r_reflections = False Exclude free-R selected reflections from map calculationisotropize = True refineScope of refinement flags (=flags defining what to refine) and atom selections (=atoms to be refined)strategy = *individual_sites *individual_sites_real_space rigid_body *individual_adp group_adp tls *occupancies group_anomalous Atomic parameters to be refinedsitesScope of atom selections for coordinates refinementindividual = None Atom selections for individual atomstorsion_angles = None Atom selections for Torsion Angle Refinement and Dynamicsrigid_body = None Atom selections for rigid groupsadpScope of atom selections for ADP (Atomic Displacement Parameters) refinementgroup_adp_refinement_mode = *one_adp_group_per_residue two_adp_groups_per_residue group_selection Select one of three available modes for group B-factors refinement. For two groups per residue, the groups will be main-chain and side-chain atoms. Provide selections for groups if group_selection is chosen.group = None One isotropic ADP for group of selected here atoms will be refinedtls = None Selection(s) for TLS group(s)individualScope of atom selections for refinement of individual ADPisotropic = None Selections for atoms to be refinement with isotropic ADPanisotropic = None Selections for atoms to be refinement with anisotropic ADPoccupanciesScope of atom selections for occupancy refinementindividual = None Selection(s) for individual atoms. None is default which is to refine the individual occupancies for atoms in alternative conformations or for atoms with partial occupancies only.remove_selection = None Occupancies of selected atoms will not be refined (even though they might satisfy the default criteria for occupancy refinement).constrained_groupSelections to define constrained occupancies. If only one selection is provided then one occupancy factor per selected atoms will be refined and it will be constrained between predefined max and min values.selection = None Atom selection string.anomalous_scatterersgroupselection = None f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime mainScope for most common and frequently used parametersshow_process_info = False Track memory consumption. Works on Linux onlystop_for_unknowns = True Stop if undefined entity is ecountered (such as novel ligand)bulk_solvent_and_scale = True Do bulk solvent correction and anisotropic scalingapply_overall_isotropic_scale_to_adp = True flip_peptides = False nqh_flips = True simulated_annealing = False Do simulated annealingsimulated_annealing_torsion = False Do simulated annealing in torsion angle spaceordered_solvent = False Add (or/and remove) and refine ordered solvent molecules (water)real_space_refinement = *local global rotamer_restraints = False place_ions = None If enabled, Phenix will attempt to replace specific solvent atoms with elemental ions. A value of Auto will search for Mg, Ca, Zn, and Cl using relatively restrictive rules, but an explicit list of elements is recommended. See associated ion_placement parameters for more options.ias = False Build and use IAS (interatomic scatterers) model (at resolutions higher than approx. 0.9 A)number_of_macro_cycles = 3 Number of macro-cycles to be performedmax_number_of_iterations = 25 use_form_factor_weights = False tan_u_iso = False Use tan() reparameterization in ADP refinement (currently disabeled)use_geometry_restraints = True use_convergence_test = False Determine if refinement converged and stop thentarget = *auto ml mlhl ml_sad ls mli Choices for refinement targetmin_number_of_test_set_reflections_for_max_likelihood_target = 50 minimum number of test reflections required for use of ML targetmax_number_of_resolution_bins = 30 use_experimental_phases = None Use experimental phases if available. If true, the target function must be set to mlhl , and a file containing Hendrickson-Lattman coefficients must be supplied.random_seed = 2679941 Ransom seedscattering_table = wk1995 it1992 *n_gaussian electron neutron Choices of scattering table for structure factors calculationswavelength = None X-ray wavelength, currently used only when ion placement is enabled (and anomalous data are supplied).use_normalized_geometry_target = True target_weights_only = False Calculate target weights only and exit refinementuse_f_model_scaled = False Use Fmodel structure factors multiplied by overall scale factor scale_k1max_d_min = 0.25 Highest allowable resolution limit for refinementfake_f_obs = False Substitute real experimental Fobs with those calculated from input model (scales and solvent can be added)optimize_mask = False Refine mask parameters (solvent_radius and shrink_truncation_radius)occupancy_max = 1.0 Maximum allowable occupancy of an atomoccupancy_min = 0.0 Minimum allowable occupancy of an atomstir = None Stepwise increase of resolution: start refinement at lower resolution and gradually proceed with higher resolutionshow_residual_map_peaks_and_holes = False Show highest peaks and deepest holes in residual_map.fft_vs_direct = False Check accuracy of approximations used in Fcalc calculationsswitch_to_isotropic_high_res_limit = 1.5 If the resolution is lower than this limit, all atoms selected for individual ADP refinement and not participating in TLS groups will be automatically converted to isotropic, whether or not ANISOU records are present in the input PDB file.find_and_add_hydrogens = False Find H or D atoms using difference map and add them to the model. This option should be used if ultra-high resolution data is available or when refining againts neutron data.correct_special_position_tolerance = 1.0 nproc = 1 Determines number of processor cores to use in parallel routines. Currently, this only applies to automatic TLS group identification.update_f_part1 = True tncs_correction = False Account for translational NCS (tNCS) in ML refinementstatistical_model_for_missing_atomssolvent_content = 0.5 map_type = *2mFo-DFc resolution_factor = 0.25 probability_mask = True diff_map_cutoff = 1.5 output_all_masks = False use_dm_map = False modify_start_modelScope of parameters to modify initial model before refinementmodifyremove = None Selection for the atoms to be removedkeep = None Select atoms to keepput_into_box_with_buffer = None Move molecule into center of boxselection = None Selection for atoms to be modifiedflip_symmetric_amino_acids = False Flip symmetric amino acid side chainschange_of_basis = None Apply change-of-basis operator (e.g. reindexing operator) to the coordinates and symmetry. Example: a,c,b .renumber_residues = False Re-number residuesincrement_resseq = None Increment residue numbertruncate_to_polyala = False Truncate a model to poly-Ala.truncate_to_polygly = False Truncate a model to poly-Gly.remove_alt_confs = False Deletes atoms whose altloc identifier is not blank or A , and resets the occupancies of the remaining atoms to 1.0.always_keep_one_conformer = False Modifies behavior of remove_alt_confs so that residues with no conformer labeled blank or A are not deleted. Silent if remove_alt_confs is False.set_chemical_element_simple_if_necessary = None Make a simple guess about what the chemical element is (based on atom name and the way how it is formatted) and write it into output file.set_seg_id_to_chain_id = False Sets the segID field to the chain ID (padded with spaces).clear_seg_id = False Erases the segID field.convert_semet_to_met = False convert_met_to_semet = False neutralize_scatterers = False remove_fraction = None random_seed = None Random seedmove_waters_last = False Transfer waters to the end of the model. Addresses some limitations of water picking in phenix.refine.adpScope of options to modify ADP of selected atomsatom_selection = None Selection for atoms to be modified. Overrides parent-level selection.randomize = False Randomize ADP within a certain rangeset_b_iso = None Set ADP of atoms to set_b_isoconvert_to_isotropic = False Convert atoms to isotropicconvert_to_anisotropic = False Convert atoms to anisotropicshift_b_iso = None Add shift_b_iso value to ADPscale_adp = None Multiply ADP by scale_adpsitesScope of options to modify coordinates of selected atomsatom_selection = None Selection for atoms to be modified. Overrides parent-level selection.shake = None Randomize coordinates with mean error value equal to shakeswitch_rotamers = max_distant min_distant exact_match fix_outliers translate = 0 0 0 Translational shift (x,y,z)rotate = 0 0 0 Rotational shift (x,y,z)euler_angle_convention = *xyz zyz Euler angles convention to be used for rotationoccupanciesScope of options to modify occupancies of selected atomsatom_selection = None Selection for atoms to be modified. Overrides parent-level selection.randomize = False Randomize occupancies within a certain rangeset = None Set all or selected occupancies to given valuerotate_about_axisaxis = None angle = None atom_selection = None rename_chain_idRename chainsold_id = None new_id = None set_chargecharge_selection = None charge = None outputWrite out file with modified model (file name is defined in write_modified)file_name = None Default is the original file name with the file extension replaced by _modified.pdb .format = *pdb mmcif Choose the output format of coordinate file (PDB or mmCIF)fake_f_obsScope of parameters to simulate Fobsr_free_flags_fraction = None scattering_table = wk1995 it1992 *n_gaussian neutron Choices of scattering table for structure factors calculationsfmodelk_sol = 0.0 Bulk solvent k_sol valuesb_sol = 0.0 Bulk solvent b_sol valuesb_cart = 0 0 0 0 0 0 Anisotropic scale matrixscale = 1.0 Overall scale factorstructure_factors_accuracyalgorithm = *fft direct cos_sin_table = False grid_resolution_factor = 1/3. quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None maskuse_asu_masks = True solvent_radius = 1.1 shrink_truncation_radius = 0.9 use_resolution_based_gridding = False If enabled, mask grid step = d_min / grid_step_factorstep = 0.6 Grid step (in A) for solvent mask calculationn_real = None Gridding for mask calculationgrid_step_factor = 4.0 Grid step is resolution divided by grid_step_factorverbose = 1 mean_shift_for_mask_update = 0.1 Value of overall model shift in refinement to updates the mask.ignore_zero_occupancy_atoms = True Include atoms with zero occupancy into mask calculationignore_hydrogens = True Ignore H or D atoms in mask calculationn_radial_shells = 1 Number of shells in a radial shell bulk solvent modelradial_shell_width = 1.3 Radial shell widthFmask_res_high = 3.0 Assume Fmask=0 for reflections outside the range inf>d>=Fmask_res_highhydrogensScope of parameters for H atoms refinementrefine = individual riding *Auto Choice for refinement: riding model or full (H is refined as other atoms, useful at very high resolutions only)force_riding_adp = None optimize_scattering_contribution = True contribute_to_f_calc = True Add H contribution to Xray (Fcalc) calculationshigh_resolution_limit_to_include_scattering_from_h = 1.6 real_space_optimize_x_h_orientation = True xh_bond_distance_deviation_limit = 0.0 Idealize XH bond distances if deviation from ideal is greater than xh_bond_distance_deviation_limitlocal_real_space_fit_angular_step = 0.5 buildmap_type = mFobs-DFmodel Map type to be used to find hydrogensmap_cutoff = 2.0 Map cutoffsecondary_map_type = 2mFobs-DFmodel Map type to be used to validate peaks in primary mapsecondary_map_cutoff = 1.4 Secondary map cutoffangular_step = 3.0 Step in degrees for 6D rigid body search for best fitdod_and_od = False Build DOD/OD/O types of waters for neutron modelsfilter_dod = False Filter DOD/OD/O by correlationmin_od_dist = 0.60 Minimum O-D distance when building water from peaksmax_od_dist = 1.35 Maximum O-D distance when building water from peaksmin_dod_angle = 85.0 Minimum D-O-D angle when building water from peaksmax_dod_angle = 170.0 Maximum D-O-D angle when building water from peaksh_bond_min_mac = 1.8 h_bond_max = 3.9 use_sigma_scaled_maps = True Default is sigma scaled map, map in absolute scale is used otherwise.resolution_factor = 1./4. max_number_of_peaks = None map_next_to_modelmin_model_peak_dist = 0.7 max_model_peak_dist = 1.05 min_peak_peak_dist = 0.7 use_hydrogens = False peak_searchpeak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = True min_cross_distance = 1.0 min_cubicle_edge = 5 group_b_isonumber_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False use_restraints = True restraints_weight = None adpisomax_number_of_iterations = 25 scalingscale_max = 3.0 scale_min = 10.0 tlsfind_automatically = None one_residue_one_group = None refine_T = True refine_L = True refine_S = True number_of_macro_cycles = 2 max_number_of_iterations = 25 start_tls_value = None run_finite_differences_test = False Test with finite differences instead of gradients. FOR DEVELOPMENT PURPOSES ONLY.eps = 1.e-6 Finite difference setting.min_tls_group_size = 5 min number of atoms allowed per TLS groupverbose = True adp_restraintsisouse_u_local_only = False sphere_radius = 5.0 distance_power = 1.69 average_power = 1.03 wilson_b_weight_auto = False wilson_b_weight = None plain_pairs_radius = 5.0 refine_ap_and_dp = False group_occupancynumber_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False constrain_correlated_3d_groups = False DEVELOPER OPTION: constrain occupancies for correlated alternate conformations.group_anomalousnumber_of_minimizer_cycles = 3 lbfgs_max_iterations = 20 number_of_finite_difference_tests = 0 find_automatically = False rigid_bodyScope of parameters for rigid body refinementmode = *first_macro_cycle_only every_macro_cycle Defines how many times the rigid body refinement is performed during refinement run. first_macro_cycle_only to run only once at first macrocycle, every_macro_cycle to do rigid body refinement main.number_of_macro_cycles timestarget = ls_wunit_k1 ml *auto Rigid body refinement target function: least-squares or maximum-likelihoodtarget_auto_switch_resolution = 6.0 Used if target=auto, use optimal target for given working resolution.disable_final_r_factor_check = False If True, the R-factor check after refinement will not revert to the previous model, even if the R-factors have increased.refine_rotation = True Only rotation is refined (translation is fixed).refine_translation = True Only translation is refined (rotation is fixed).max_iterations = 25 Number of LBFGS minimization iterationsbulk_solvent_and_scale = True Bulk-solvent and scaling within rigid body refinement (needed since large rigid body shifts invalidate the mask).euler_angle_convention = *xyz zyz Euler angles conventionlbfgs_line_search_max_function_evaluations = 10 min_number_of_reflections = 200 Number of reflections that defines the first lowest resolution zone for the multiple_zones protocol. If very large displacements are expected, decreasing this parameter to 100 may lead to a larger convergence radius.multi_body_factor = 1 zone_exponent = 3.0 high_resolution = 3.0 High resolution cutoff (used for rigid body refinement only)max_low_high_res_limit = None Maximum value for high resolution cutoff for the first lowest resolution zonenumber_of_zones = 5 Number of resolution zones for MZ protocolncstype = *torsion cartesian constraints coordinate_sigma = 0.05 restrain_b_factors = False If enabled, b-factors will be restrained for NCS-related atoms. Otherwise, atomic b-factors will be refined independently, and b_factor_weight will be set to 0.0b_factor_weight = 10 excessive_distance_limit = 1.5 special_position_warnings_only = False constraintsrefine_operators = True apply_to_coordinates = True apply_to_adp = True torsionsigma = 2.5 limit = 15.0 fix_outliers = False check_rotamer_consistency = Auto Check for rotamer differences between NCS matched sidechains and search for best fit amongst candidate rotamerstarget_damping = False damping_limit = 10.0 filter_phi_psi_outliers = True restrain_to_master_chain = False silence_warnings = False modify_f_obsremove = random strong weak strong_and_weak low other remove_fraction = 0.1 fill_mode = fobs_mean_mixed_with_dfmodel random fobs_mean *dfmodel pdb_interpretationsort_atoms = True flip_symmetric_amino_acids = True superpose_ideal_ligand = *None all SF4 F3S DVT disable_uc_volume_vs_n_atoms_check = False allow_polymer_cross_special_position = False correct_hydrogens = True c_beta_restraints = True use_neutron_distances = False Use neutron X-H distances (which are longer than X-ray ones)disulfide_bond_exclusions_selection_string = None exclusion_distance_cutoff = 3 If SG of CYS forming SS bond is closer than this distance to an atom that it may coordinate then this SG is excluded from SS bond.link_distance_cutoff = 3 Length of link between the linked residuesdisulfide_distance_cutoff = 3 add_angle_and_dihedral_restraints_for_disulfides = True dihedral_function_type = *determined_by_sign_of_periodicity all_sinusoidal all_harmonic chir_volume_esd = 0.2 max_reasonable_bond_distance = 50.0 nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 **EXPERIMENTAL, developers only**nonbonded_weight = None Weighting of nonbonded restraints term. By default, this will be set to 16 if explicit hydrogens are used (this was the default in earlier versions of Phenix), or 100 if hydrogens are missing.const_shrink_donor_acceptor = 0.6 **EXPERIMENTAL, developers only**vdw_1_4_factor = 0.8 min_distance_sym_equiv = 0.5 custom_nonbonded_symmetry_exclusions = None translate_cns_dna_rna_residue_names = None proceed_with_excessive_length_bonds = False restraints_librarycdl = True Use Conformation Dependent Library (CDL) for geometry restraintsmcl = True Use Metal Coordination Library (MCL) for tetrahedral Zn++ and iron-sulfur clusters SF4, FES, F3S, ...cis_pro_eh99 = True omega_cdl = False Use Omega Conformation Dependent Library (omega-CDL) for geometry restraintscdl_nucleotides = False Use RestraintsLib for DNA and RNA for geometry restraintscdl_nucleotides_esd = *phenix csd cdl_svl = False rdl = False rdl_selection = *all TRP hpdl = False secondary_structuress_by_chain = True Find secondary structure only within individual chains. Alternative is to allow H-bonds between chains. Can be much slower with ss_by_chain=False. If your model is complete use ss_by_chain=True. If your model is many fragments, use ss_by_chain=False.from_ca_conservative = False various parameters changed to make from_ca method more conservative, hopefully to closer resemble ksdssp.max_rmsd = 1 Maximum rmsd to consider two chains with identical sequences as the same for ss identificationuse_representative_chains = True Use a representative of all chains with the same sequence. Alternative is to examine each chain individually. Can be much slower with use_representative_of_chain=False if there are many symmetry copies. Ignored unless ss_by_chain is True.max_representative_chains = 100 Maximum number of representative chainsenabled = False Turn on secondary structure restraints (main switch)proteinenabled = True Turn on secondary structure restraints for proteinsearch_method = *ksdssp mmtbx_dssp from_ca cablam Particular method to search protein secondary structure.distance_ideal_n_o = 2.9 Target length for N-O hydrogen bonddistance_cut_n_o = 3.5 Hydrogen bond with length exceeding this value will not be establishedremove_outliers = True If true, h-bonds exceeding distance_cut_n_o length will not be establishedrestrain_hbond_angles = True helixserial_number = None helix_identifier = None enabled = True Restrain this particular helixselection = None helix_type = *alpha pi 3_10 unknown Type of helix, defaults to alpha. Only alpha, pi, and 3_10 helices are used for hydrogen-bond restraints.sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 Multiply sigmas for h-bond angles by this value. Original sigmas range from 5 to 10.angle_sigma_set = None Use this parameter to set sigmas for h-bond angles to a particular valuehbonddonor = None acceptor = None sheetenabled = True Restrain this particular sheetfirst_strand = None sheet_id = None sigma = 0.05 slack = 0 top_out = False angle_sigma_scale = 1 Multiply sigmas for h-bond angles by this value. Original sigmas range from 5 to 10.angle_sigma_set = None Use this parameter to set sigmas for h-bond angles to a particular valuestrandselection = None sense = parallel antiparallel *unknown bond_start_current = None bond_start_previous = None hbonddonor = None acceptor = None nucleic_acidenabled = True Turn on secondary structure restraints for nucleic acidshbond_distance_cutoff = 3.4 Hydrogen bonds with length exceeding this limit will not be establishedangle_between_bond_and_nucleobase_cutoff = 35.0 If angle between supposed hydrogen bond and basepair plane (defined by C4, C5, C6 atoms) is less than this value (in degrees), the bond will not be established.scale_bonds_sigma = 1. All sigmas for h-bond length will be multiplied by this number. The smaller number is tighter restraints.base_pairenabled = True Restraint this particular base-pairbase1 = None Selection string selecting at least one atom in the desired residuebase2 = None Selection string selecting at least one atom in the desired residuesaenger_class = 0 Type of base-pairingrestrain_planarity = False Apply planarity restraint to this base-pairplanarity_sigma = 0.176 restrain_hbonds = True Restrain hydrogen bonds length for this base-pairrestrain_hb_angles = True Restrain angles around hydrogen bonds for this base-pairrestrain_parallelity = True Apply parallelity restraint to this base-pairparallelity_target = 0 parallelity_sigma = 0.0335 stacking_pairenabled = True Restraint this particular base-pairbase1 = None Selection string selecting at least one atom in the desired residuebase2 = None Selection string selecting at least one atom in the desired residueangle = 0 sigma = 0.027 reference_coordinate_restraintsRestrains coordinates in Cartesian space to stay near their starting positions. This is intended for use in generating simulated annealing omit maps, to prevent refined atoms from collapsing in on the region missing atoms. For conserving geometry quality at low resolution, the more flexible reference model restraints should be used instead.enabled = False exclude_outliers = True selection = all sigma = 0.2 limit = 1.0 top_out = False automatic_linkinglink_all = False If True, bond restraints will be generated for any appropriate ligand-protein or ligand-nucleic acid covalent bonds. This includes sugars, amino acid modifications, and other prosthetic groups.link_none = False link_metals = Auto link_residues = False link_amino_acid_rna_dna = False link_carbohydrates = True link_ligands = True link_small_molecules = False metal_coordination_cutoff = 3.5 amino_acid_bond_cutoff = 1.9 inter_residue_bond_cutoff = 2.2 buffer_for_second_row_elements = 0.5 carbohydrate_bond_cutoff = 1.99 ligand_bond_cutoff = 1.99 small_molecule_bond_cutoff = 1.98 include_in_automatic_linkingselection_1 = None selection_2 = None bond_cutoff = 4.5 exclude_from_automatic_linkingselection_1 = None selection_2 = None apply_cis_trans_specificationcis_trans_mod = cis *trans residue_selection = None Residues containing C-alpha atom of omega dihedralapply_cif_restraintsrestraints_file_name = None residue_selection = None apply_cif_modificationdata_mod = None residue_selection = None apply_cif_linkdata_link = None residue_selection_1 = None residue_selection_2 = None peptide_linkramachandran_restraints = False !!! OBSOLETED. Kept for backward compatibility only !!! Restrains peptide backbone to fall within allowed regions of Ramachandran plot. Although it does not eliminate outliers, it can significantly improve the percent favored and percent outliers at low resolution. Probably not useful (and maybe even harmful) at resolutions much higher than 3.5A.cis_threshold = 45 apply_all_trans = False discard_omega = False discard_psi_phi = True apply_peptide_plane = False omega_esd_override_value = None rama_weight = 1.0 scale_allowed = 1.0 rama_potential = *oldfield emsley rama_selection = None Selection of part of the model for which Ramachandran restraints will be set up.restrain_rama_outliers = True Apply restraints to Ramachandran outliersrestrain_rama_allowed = True Apply restraints to residues in allowed region on Ramachandran plotrestrain_allowed_outliers_with_emsley = False In case of restrain_rama_outliers=True and/or restrain_rama_allowed=True still restrain these residues with emsley. Make sense only in case of using oldfield potential.oldfieldesd = 10.0 weight_scale = 1.0 dist_weight_max = 10.0 weight = None plot_cutoff = 0.027 ramachandran_plot_restraintsenabled = False favored = *oldfield emsley emsley8k phi_psi_2 allowed = *oldfield emsley emsley8k phi_psi_2 outlier = *oldfield emsley emsley8k phi_psi_2 selection = None Selection of part of the model for which Ramachandran restraints will be set up.inject_emsley8k_into_oldfield_favored = True Backdoor to disable temporary dirty hack to use botholdfieldweight = 0. Direct weight value. If 0 the weight will be calculated as following: (w, op.esd, op.dist_weight_max, 2.0, op.weight_scale) 1 / esd^2 * max(2.0, min(current_distance_to_allowed, dist_weight_max)) * weight_scale max(2.0, current_distance_to_allowed) 1 / esd^2 * weight_scale * max(distance_to_allowed_cutoff, current_distance_to_allowed) weight_scale(=0.01) * max(distance_weight_min(=2.), min(distance_weight_max(=10.), current_distance_to_allowed))weight_scale = 0.01 distance_weight_min = 2.0 minimum coefficient when scaling depending on how far the residue is from allowed region.distance_weight_max = 10.0 maximum coefficient when scaling depending on how far the residue is from allowed region.plot_cutoff = 0.027 emsleyweight = 1.0 scale_allowed = 1.0 emsley8kweight_favored = 5.0 weight_allowed = 10.0 weight_outlier = 10.0 phi_psi_2favored_strategy = *closest highest_probability random weighted_random allowed_strategy = *closest highest_probability random weighted_random outlier_strategy = *closest highest_probability random weighted_random rna_sugar_pucker_analysisbond_min_distance = 1.2 bond_max_distance = 1.8 epsilon_range_min = 155.0 epsilon_range_max = 310.0 delta_range_2p_min = 129.0 delta_range_2p_max = 162.0 delta_range_3p_min = 65.0 delta_range_3p_max = 104.0 p_distance_c1p_outbound_line_2p_max = 2.9 o3p_distance_c1p_outbound_line_2p_max = 2.4 bond_detection_distance_tolerance = 0.5 show_histogram_slotsbond_lengths = 5 nonbonded_interaction_distances = 5 bond_angle_deviations_from_ideal = 5 dihedral_angle_deviations_from_ideal = 5 chiral_volume_deviations_from_ideal = 5 show_max_itemsnot_linked = 5 bond_restraints_sorted_by_residual = 5 nonbonded_interactions_sorted_by_model_distance = 5 bond_angle_restraints_sorted_by_residual = 5 dihedral_angle_restraints_sorted_by_residual = 3 chirality_restraints_sorted_by_residual = 3 planarity_restraints_sorted_by_residual = 3 residues_with_excluded_nonbonded_symmetry_interactions = 12 fatal_problem_max_lines = 10 ncs_groupThe definition of one NCS group. Note, that almost always in refinement programs they will be checked and filtered if needed.reference = None Residue selection string for the complete master NCS copyselection = None Residue selection string for each NCS copy location in ASUncs_searchSet of parameters for NCS search procedure. Some of them also used for filtering user-supplied ncs_group.enabled = False Enable NCS restraints or constraints in refinement (in some cases may be switched on inside refinement program).exclude_selection = "element H or element D or water" Atoms selected by this selection will be excluded from the model before any NCS search and/or filtering procedures. There is no way atoms defined by this selection will be in NCS.chain_similarity_threshold = 0.85 Threshold for sequence similarity between matching chains. A smaller value may cause more chains to be grouped together and can lower the number of common residueschain_max_rmsd = 2. limit of rms difference between chains to be considered as copiesresidue_match_radius = 4.0 Maximum allowed distance difference between pairs of matching atoms of two residuestry_shortcuts = False Try very quick check to speed up the search when chains are identical. If failed, regular search will be performed automatically.minimum_number_of_atoms_in_copy = 3 Do not create ncs groups where master and copies would contain less than specified amount of atomsvalidate_user_supplied_groups = True Enable validation of user-supplied ncs_group. Need to exercise a lot of caution turning this off. This option is for developers only.clash_guardnonbonded_distance_threshold = 0.5 max_number_of_distances_below_threshold = 100 max_fraction_of_distances_below_threshold = 0.1 geometry_restraintseditsexcessive_bond_distance_limit = 10 bondaction = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None The bond is between atom_1 and symmetry_operation * atom_2, with atom_1 and atom_2 given in fractional coordinates. Example: symmetry_operation = -x-1,-y,zdistance_ideal = None sigma = None slack = None limit = -1.0 top_out = False angleaction = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None angle_ideal = None sigma = None dihedralaction = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None angle_ideal = None alt_angle_ideals = None sigma = None periodicity = 1 planarityaction = *add delete change atom_selection = None sigma = None parallelityaction = *add delete change atom_selection_1 = None atom_selection_2 = None sigma = 0.027 target_angle_deg = 0 geometry_restraintsremoveangles = None dihedrals = None chiralities = None planarities = None parallelities = None ordered_solventlow_resolution = 2.8 Low resolution limit for water picking (at lower resolution water will not be picked even if requessted)mode = *second_half filter_only every_macro_cycle every_macro_cycle_after_first Choices for water picking strategy: auto - start water picking after ferst few macro-cycles, filter_only - remove water only, every_macro_cycle - do water update every macro-cyclen_cycles = 1 output_residue_name = HOH output_chain_id = S output_atom_name = O scattering_type = O Defines scattering factors for newly added watersprimary_map_type = mFobs-DFmodel Map used to identify candidate water sites - by default this is the standard difference map.primary_map_cutoff = 3.0 h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 refine_adp = True Refine ADP for newly placed solvent.refine_occupancies = False Refine solvent occupancies.new_solvent = *isotropic anisotropic Based on the choice, added solvent will have isotropic or anisotropic b-factorsb_iso_min = 1.0 Minimum B-factor value, waters with smaller value will be rejectedb_iso_max = 80.0 Maximum B-factor value, waters with bigger value will be rejectedanisotropy_min = 0.1 For solvent refined as anisotropic: remove is less than this valueb_iso = None Initial B-factor value for newly added wateroccupancy_min = 0.1 Minimum occupancy value, waters with smaller value will be rejectedoccupancy_max = 1.0 Maximum occupancy value, waters with bigger value will be rejectedoccupancy = 1.0 Initial occupancy value for newly added waterfilter_at_start = True ignore_final_filtering_step = False correct_drifted_waters = True secondary_map_and_map_cc_filtercc_map_1_type = "Fc" cc_map_2_type = 2mFo-DFmodel poor_cc_threshold = 0.7 poor_map_value_threshold = 1.0 peak_searchuse_sigma_scaled_maps = True Default is sigma scaled map, map in absolute scale is used otherwise.resolution_factor = 1./4. max_number_of_peaks = None map_next_to_modelmin_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 use_hydrogens = False peak_searchpeak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 min_cubicle_edge = 5 bulk_solvent_and_scalemode = slow *fast apply_back_trace = True bulk_solvent = True anisotropic_scaling = True k_sol_b_sol_grid_search = True minimization_k_sol_b_sol = True minimization_b_cart = True target = ls_wunit_k1 *ml symmetry_constraints_on_b_cart = True k_sol_max = 0.6 k_sol_min = 0.0 b_sol_max = 300.0 b_sol_min = 0.0 k_sol_grid_search_max = 0.6 k_sol_grid_search_min = 0.0 b_sol_grid_search_max = 80.0 b_sol_grid_search_min = 20.0 k_sol_step = 0.2 b_sol_step = 20.0 number_of_macro_cycles = 1 max_iterations = 25 min_iterations = 25 fix_k_sol = None fix_b_sol = None fix_b_cartb11 = None b22 = None b33 = None b12 = None b13 = None b23 = None alpha_betafree_reflections_per_bin = 140 number_of_macromolecule_atoms_absent = 225 n_atoms_included = 0 bf_atoms_absent = 15.0 final_error = 0.0 absent_atom_type = "O" method = *est calc estimation_algorithm = *analytical iterative verbose = -1 interpolation = True number_of_waters_absent = 613 sigmaa_estimatorkernel_width_free_reflections = 100 kernel_on_chebyshev_nodes = True number_of_sampling_points = 20 number_of_chebyshev_terms = 10 use_sampling_sum_weights = True maskuse_asu_masks = True solvent_radius = 1.1 shrink_truncation_radius = 0.9 use_resolution_based_gridding = False If enabled, mask grid step = d_min / grid_step_factorstep = 0.6 Grid step (in A) for solvent mask calculationn_real = None Gridding for mask calculationgrid_step_factor = 4.0 Grid step is resolution divided by grid_step_factorverbose = 1 mean_shift_for_mask_update = 0.1 Value of overall model shift in refinement to updates the mask.ignore_zero_occupancy_atoms = True Include atoms with zero occupancy into mask calculationignore_hydrogens = True Ignore H or D atoms in mask calculationn_radial_shells = 1 Number of shells in a radial shell bulk solvent modelradial_shell_width = 1.3 Radial shell widthFmask_res_high = 3.0 Assume Fmask=0 for reflections outside the range inf>d>=Fmask_res_hightardyUnder developmentmode = every_macro_cycle *second_and_before_last once first first_half xray_weight_factor = 10 start_temperature_kelvin = 2500 final_temperature_kelvin = 300 velocity_scaling = True temperature_cap_factor = 1.5 excessive_temperature_factor = 5 number_of_cooling_steps = 500 number_of_time_steps = 1 time_step_pico_seconds = 0.001 temperature_degrees_of_freedom = *cartesian constrained minimization_max_iterations = 0 omit_bonds_with_slack_greater_than = 0 constrain_dihedrals_with_sigma_less_than = 10 near_singular_hinges_angular_tolerance_deg = 5 emulate_cartesian = False trajectory_directory = None prolsq_repulsion_function_changesenergy(delta) = c_rep*(max(0,(k_rep*vdw_distance)**irexp-delta**irexp))**rexpc_rep = None Usual value: 16k_rep = 0.75 Usual value: 1. Smaller values reduce the distance threshold at which the repulsive force becomes active.irexp = None Usual value: 1rexp = None Usual value: 4cartesian_dynamicstemperature = 300 number_of_steps = 200 time_step = 0.0005 initial_velocities_zero_fraction = 0 n_print = 100 verbose = -1 random_seed = None n_collect = 10 stop_cm_motion = True simulated_annealingstart_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 50 time_step = 0.0005 initial_velocities_zero_fraction = 0 interleave_minimization = False verbose = -1 n_print = 100 update_grads_shift = 0.3 random_seed = None refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first first_half target_weightsoptimize_xyz_weight = False optimize_adp_weight = False wxc_scale = 0.5 wxu_scale = 1.0 wc = 1.0 wu = 1.0 fix_wxc = None fix_wxu = None shake_sites = True shake_adp = 10.0 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1.0 rmsd_cutoff_for_gradient_filtering = 3.0 force_optimize_weights = False weight_selection_criteriabonds_rmsd = None angles_rmsd = None r_free_minus_r_work = None r_free_range_width = None mean_diff_b_iso_bonded_fraction = None min_diff_b_iso_bonded = None iasb_iso_max = 100.0 occupancy_min = -1.0 occupancy_max = 1.5 ias_b_iso_max = 100.0 ias_b_iso_min = 0.0 ias_occupancy_min = 0.01 ias_occupancy_max = 3.0 initial_ias_occupancy = 1.0 build_ias_types = L R B BH ring_atoms = None use_map = True build_only = False file_prefix = None lone_pairatom_x = CA atom_xo = C atom_o = O peak_search_mapmap_type = *Fobs-Fmodel mFobs-DFmodel grid_step = 0.25 scaling = *volume sigma ls_target_namestarget_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed lsm_k1ask3_fixed twinningtwin_law = None twin_target = *twin_lsq_f detwinmode = algebraic proportional *auto map_typestwofofc = *two_m_dtfo_d_fc two_dtfo_fc fofc = *m_dtfo_d_fc gradient m_gradient aniso_correct = False structure_factors_and_gradients_accuracyalgorithm = *fft direct cos_sin_table = False grid_resolution_factor = 1/3. quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None r_free_flagsfraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5.0 Tolerance used in the determination of the highest lattice symmetry. Can be thought of as angle between lattice vectors that should line up perfectly if the symmetry is ideal. A typical value is 3 degrees.use_lattice_symmetry = True When generating Rfree flags, do so in the asymmetric unit of the highest lattice symmetry. The result is an Rfree set suitable for twin refinement.reference_modelenabled = False Restrains the dihedral angles to a high-resolution reference structure to reduce overfitting at low resolution. You will need to specify a reference PDB file (in the input list in the main window) to use this option.file = None use_starting_model_as_reference = False sigma = 1.0 limit = 15.0 hydrogens = False Include dihedrals with hydrogen atomsmain_chain = True Include dihedrals formed by main chain atomsside_chain = True Include dihedrals formed by side chain atomsfix_outliers = True Try to fix rotamer outliers in refined modelstrict_rotamer_matching = False Make sure that rotamers in refinement model matches those in reference model even when they are not outliersauto_shutoff_for_ncs = False Do not apply to parts of structure covered by NCS restraintssecondary_structure_only = False Only apply reference model restraints to secondary structure elements (helices and sheets)reference_groupreference = None selection = None file_name = None this is to used internally to disambiguate cases where multiple reference models contain the same chain ID. This normally does not need to be set by the usersearch_optionsSet of parameters for NCS search procedure. Some of them also used for filtering user-supplied ncs_group.exclude_selection = "element H or element D or water" Atoms selected by this selection will be excluded from the model before any NCS search and/or filtering procedures. There is no way atoms defined by this selection will be in NCS.chain_similarity_threshold = 0.85 Threshold for sequence similarity between matching chains. A smaller value may cause more chains to be grouped together and can lower the number of common residueschain_max_rmsd = 100. limit of rms difference between chains to be considered as copiesresidue_match_radius = 1000 Maximum allowed distance difference between pairs of matching atoms of two residuestry_shortcuts = False Try very quick check to speed up the search when chains are identical. If failed, regular search will be performed automatically.minimum_number_of_atoms_in_copy = 3 Do not create ncs groups where master and copies would contain less than specified amount of atomsvalidate_user_supplied_groups = True Enable validation of user-supplied ncs_group. Need to exercise a lot of caution turning this off. This option is for developers only.ion_placementdebug = False ion_chain_id = X initial_occupancy = 1.0 Occupancy for newly placed ions - if less than 1.0, the occupancy may be refined automatically in future runs of phenix.refine.initial_b_iso = Auto refine_ion_occupancies = True Toggles refinement of occupancies for newly placed ions. This will only happen if the occupancy refinement strategy is selected.refine_ion_adp = *Auto isotropic anisotropic none B-factor refinement type for newly placed ions. At medium-to-high resolution, anisotropic refinement may be preferrable for the heavier elements.refine_anomalous = True If True and the wavelength is specified, any newly placed ions will have anomalous scattering factors refined. This is unlikely to affect R-factors but should flatten the anomalous LLG map.max_distance_between_like_charges = 3.5 use_svm = True require_valence = False Toggles the use of valence calculationsambiguous_valence_cutoff = 0.5 Cutoff to uniquely select one of many metals by comparing its observed and expected valenced_min_strict_valence = 1.5 anom_map_type = *residual simple llg Type of anomalous difference map to use. Default is a residual map, showing only unmodeled scattering.find_anomalous_substructure = Auto use_phaser = True Toggles the use of Phaser for calculation of f-prime values.aggressive = False Toggles more permissive settings for flagging waters as heavier elements. Not recommended for automated use.map_sampling_radius = 2.0 svmsvm_name = *Auto heavy merged_high_res Name of SVM classifier to usefiltered_outputs = True Apply an filter to the outputs of the SVM, ensuring they are chemically sanemin_score = 0.2 min_score_above = 0.1 min_fraction_of_next = 2.0 watermin_2fofc_level = 1.8 Minimum water 2mFo-DFc map value. Waters below this cutoff will not be analyzed further.max_fofc_level = 3.0 Maximum water mFo-DFc map valuemax_anom_level = 3.0 Maximum water anomalous map valuemax_occ = 1.0 Maximum water occupancymin_b_iso = 1.0 Minimum water isotropic B-factorfp_max = 1.0 fpp_max = 0 max_stddev_b_iso = 5 min_frac_b_iso = 0.2 min_frac_calpha_b_iso = 0.75 max_frac_calpha_2fofc = 1.2 min_2fofc_coordinating = 0.9 Minimum 2mFo-DFc for waters involved in coordination shells.phaserllgc_ncycles = None distance_cutoff = 1.5 distance_cutoff_same_site = 0.7 fpp_ratio_min = 0.2 Minimum ratio of refined/theoretical f-double-prime.fpp_ratio_max = 1.1 Maximum ratio of refined/theoretical f-double-prime.chloridemax_distance_to_amide_n = 3.5 Max distance to amide N atommax_distance_to_cation = 3.5 min_distance_to_anion = 3.5 min_distance_to_other_sites = 2.1 max_distance_to_hydroxyl = 3.5 delta_amide_h_angle = 20 Allowed deviation (in degrees) from ideal N-H-X angledelta_planar_angle = 10 max_deviation_from_plane = 0.8 guiMiscellaneous parameters for phenix.refine GUIbase_output_dir = None tmp_dir = None send_notification = False notify_email = None add_hydrogens = False Runs phenix.ready_set to add hydrogens prior to refinement.skip_rsr = False skip_kinemage = False phil_file = None ready_set_hydrogensneutron_option = *all_h all_d hd_and_h hd_and_d all_hd add_h_to_water = False add_d_to_water = False neutron_exchange_hydrogens = False Add deuteriums in exchangeable sitesperdeuterate = False Add deuteriums in all possible sitesamberParameters for using Amber in refinement.use_amber = False Use Amber for all the gradients in refinementtopology_file_name = None A topology file needed by Amber. Can be generated using phenix.AmberPrep.coordinate_file_name = None A coordinate file needed by Amber. Can be generated using phenix.AmberPrep.order_file_name = None A file that maps amber atom numbers to phenix atom numbers.wxc_factor = 1. restraint_wt = 0. restraintmask = '' reference_file_name = '' bellymask = '' If given, turn on belly in sanderqmmask = '' If given, turn on QM/MM with the given maskqmcharge = 0 Charge of the QM/MM regionnetcdf_trajectory_file_name = '' If given, turn on writing netcdf trajectoryprint_amber_energies = False Print details of Amber energies during refinement 2ff7e9595c
Comentarios