$ servalcat refine_spa_norefmac -h
usage: servalcat refine_spa_norefmac [-h] (--halfmaps HALFMAPS HALFMAPS | --map MAP | --hklin HKLIN)
                                     [--pixel_size PIXEL_SIZE] [--labin LABIN] --model MODEL -d
                                     RESOLUTION [-r MASK_RADIUS] [--padding PADDING] [--no_mask]
                                     [--no_trim] [--mask_soft_edge MASK_SOFT_EDGE]
                                     [--no_sharpen_before_mask] [--b_before_mask B_BEFORE_MASK]
                                     [--blur BLUR] [--monlib MONLIB] [--ligand [LIGAND ...]]
                                     [--newligand_continue] [--hydrogen {all,yes,no}] [--hout]
                                     [--jellybody] [--jellybody_params sigma dmax] [--jellyonly]
                                     [--pg PG] [--twist TWIST] [--rise RISE]
                                     [--center CENTER CENTER CENTER] [--axis1 AXIS1 AXIS1 AXIS1]
                                     [--axis2 AXIS2 AXIS2 AXIS2] [--contacting_only]
                                     [--ignore_symmetry IGNORE_SYMMETRY] [--find_links]
                                     [--no_check_ncs_overlaps] [--no_check_ncs_map]
                                     [--no_check_mask_with_model] [--keywords KEYWORDS [KEYWORDS ...]]
                                     [--keyword_file KEYWORD_FILE [KEYWORD_FILE ...]]
                                     [--randomize RANDOMIZE] [--ncycle NCYCLE] [--weight WEIGHT]
                                     [--no_weight_adjust]
                                     [--target_bond_rmsz_range TARGET_BOND_RMSZ_RANGE TARGET_BOND_RMSZ_RANGE]
                                     [--adpr_weight ADPR_WEIGHT] [--ncsr] [--bfactor BFACTOR]
                                     [--fix_xyz] [--adp {fix,iso,aniso}] [--refine_all_occ]
                                     [--max_dist_for_adp_restraint MAX_DIST_FOR_ADP_RESTRAINT]
                                     [--adp_restraint_power ADP_RESTRAINT_POWER]
                                     [--adp_restraint_exp_fac ADP_RESTRAINT_EXP_FAC]
                                     [--adp_restraint_no_long_range]
                                     [--adp_restraint_mode {diff,kldiv}] [--refine_h]
                                     [--source {electron,xray,neutron}] [-o OUTPUT_PREFIX]
                                     [--cross_validation]
                                     [--mask_for_fofc MASK_FOR_FOFC | --mask_radius_for_fofc MASK_RADIUS_FOR_FOFC]
                                     [--fsc_resolution FSC_RESOLUTION] [--keep_charges]
                                     [--keep_entities] [--write_trajectory]

EXPERIMENTAL program to refine cryo-EM SPA structures

options:
  -h, --help            show this help message and exit
  --halfmaps HALFMAPS HALFMAPS
                        Input half map files
  --map MAP             Use this only if you really do not have half maps.
  --hklin HKLIN         Use mtz file. With limited functionality.
  --pixel_size PIXEL_SIZE
                        Override pixel size (A)
  --labin LABIN         F,PHI for hklin
  --model MODEL         Input atomic model file
  -d RESOLUTION, --resolution RESOLUTION
  -r MASK_RADIUS, --mask_radius MASK_RADIUS
                        mask radius
  --padding PADDING     Default: 2*mask_radius
  --no_mask
  --no_trim             Keep original box (not recommended)
  --mask_soft_edge MASK_SOFT_EDGE
                        Add soft edge to model mask. Should use with --no_sharpen_before_mask?
  --no_sharpen_before_mask
                        By default half maps are sharpened before masking by std of signal and
                        unsharpened after masking. This option disables it.
  --b_before_mask B_BEFORE_MASK
                        sharpening B value for sharpen-mask-unsharpen procedure. By default it is
                        determined automatically.
  --blur BLUR           Sharpening or blurring B
  --monlib MONLIB       Monomer library path. Default: $CLIBD_MON
  --ligand [LIGAND ...]
                        restraint dictionary cif file(s)
  --newligand_continue  Make ad-hoc restraints for unknown ligands (not recommended)
  --hydrogen {all,yes,no}
                        all: (re)generate hydrogen atoms, yes: use hydrogen atoms if present, no:
                        remove hydrogen atoms in input. Default: all
  --hout                write hydrogen atoms in the output model
  --jellybody           Use jelly body restraints
  --jellybody_params sigma dmax
                        Jelly body sigma and dmax (default: [0.01, 4.2])
  --jellyonly           Jelly body only (experimental, may not be useful)
  --pg PG               Point group symbol
  --twist TWIST         Helical twist (degree)
  --rise RISE           Helical rise (Angstrom)
  --center CENTER CENTER CENTER
                        Origin of symmetry. Default: center of the box
  --axis1 AXIS1 AXIS1 AXIS1
                        Axis1 (if I: 5-fold, O: 4-fold, T: 3-fold)
  --axis2 AXIS2 AXIS2 AXIS2
                        Axis2 (if I: 5-fold, O: 4-fold, T: 3-fold, Dn: 2-fold)
  --contacting_only     Filter out non-contacting strict NCS copies
  --ignore_symmetry IGNORE_SYMMETRY
                        Ignore symmetry information (MTRIX/_struct_ncs_oper) in the model file
  --find_links          Automatically add links
  --no_check_ncs_overlaps
                        Disable model overlap test due to strict NCS
  --no_check_ncs_map    Disable map symmetry test due to strict NCS
  --no_check_mask_with_model
                        Disable mask test using model
  --keywords KEYWORDS [KEYWORDS ...]
                        refmac keyword(s)
  --keyword_file KEYWORD_FILE [KEYWORD_FILE ...]
                        refmac keyword file(s)
  --randomize RANDOMIZE
                        Shake coordinates with the specified rmsd value
  --ncycle NCYCLE       number of CG cycles (default: 10)
  --weight WEIGHT       refinement weight. default: automatic
  --no_weight_adjust    Do not adjust weight during refinement
  --target_bond_rmsz_range TARGET_BOND_RMSZ_RANGE TARGET_BOND_RMSZ_RANGE
                        Bond rmsz range for weight adjustment (default: [0.5, 1.0])
  --adpr_weight ADPR_WEIGHT
                        ADP restraint weight (default: 1.000000)
  --ncsr                Use local NCS restraints
  --bfactor BFACTOR     reset all atomic B values to the specified value
  --fix_xyz             Fix atomic coordinates
  --adp {fix,iso,aniso}
                        ADP parameterization
  --refine_all_occ
  --max_dist_for_adp_restraint MAX_DIST_FOR_ADP_RESTRAINT
  --adp_restraint_power ADP_RESTRAINT_POWER
  --adp_restraint_exp_fac ADP_RESTRAINT_EXP_FAC
  --adp_restraint_no_long_range
  --adp_restraint_mode {diff,kldiv}
  --refine_h            Refine hydrogen against data (default: only restraints apply)
  --source {electron,xray,neutron}
  -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX
  --cross_validation    Run cross validation. Only "throughout" mode is available (no "shake" mode)
  --mask_for_fofc MASK_FOR_FOFC
                        Mask file for Fo-Fc map calculation
  --mask_radius_for_fofc MASK_RADIUS_FOR_FOFC
                        Mask radius for Fo-Fc map calculation
  --fsc_resolution FSC_RESOLUTION
                        High resolution limit for FSC calculation. Default: Nyquist
  --keep_charges        Use scattering factor for charged atoms. Use it with care.
  --keep_entities       Do not override entities
  --write_trajectory    Write all output from cycles
