$ servalcat refine_spa -h
usage: servalcat refine_spa [-h] [--exe EXE] [--monlib MONLIB]
                            [--halfmaps HALFMAPS HALFMAPS | --map MAP]
                            [--mapref MAPREF] [--mask MASK] [--model MODEL]
                            [--mask_radius MASK_RADIUS] [--padding PADDING]
                            [--no_mask] [--invert_mask]
                            [--pixel_size PIXEL_SIZE]
                            [--resolution RESOLUTION] [--no_trim] [--no_shift]
                            [--blur BLUR [BLUR ...]] [--pg PG] [--twist TWIST]
                            [--rise RISE] [--center CENTER CENTER CENTER]
                            [--axis1 AXIS1 AXIS1 AXIS1]
                            [--axis2 AXIS2 AXIS2 AXIS2]
                            [--ignore_symmetry IGNORE_SYMMETRY]
                            [--keep_multiple_models] [--no_link_check]
                            [--b_before_mask B_BEFORE_MASK]
                            [--no_sharpen_before_mask]
                            [--no_fix_microheterogeneity] [--no_fix_resi9999]
                            [--no_check_ncs_overlaps]
                            [--ligand [LIGAND [LIGAND ...]]]
                            [--bfactor BFACTOR] [--ncsr {local,global}]
                            [--ncycle NCYCLE] [--tlscycle TLSCYCLE]
                            [--tlsin TLSIN] [--hydrogen {all,yes,no}]
                            [--jellybody] [--jellybody_params sigma dmax]
                            [--hout]
                            [--weight_auto_scale WEIGHT_AUTO_SCALE | --weight_matrix WEIGHT_MATRIX]
                            [--keywords KEYWORDS [KEYWORDS ...]]
                            [--keyword_file KEYWORD_FILE [KEYWORD_FILE ...]]
                            [--external_restraints_json EXTERNAL_RESTRAINTS_JSON]
                            [--show_refmac_log]
                            [--output_prefix OUTPUT_PREFIX]
                            [--cross_validation]
                            [--cross_validation_method {throughout,shake}]
                            [--shake_radius SHAKE_RADIUS]
                            [--mask_for_fofc MASK_FOR_FOFC | --mask_radius_for_fofc MASK_RADIUS_FOR_FOFC]
                            [--trim_fofc_mtz]
                            [--fsc_resolution FSC_RESOLUTION]

Run REFMAC5 for SPA

optional arguments:
  -h, --help            show this help message and exit
  --exe EXE             refmac5 binary (default: refmac5)
  --monlib MONLIB       Monomer library path. Default: $CLIBD_MON
  --ligand [LIGAND [LIGAND ...]]
                        restraint dictionary cif file(s)
  --bfactor BFACTOR     reset all atomic B values to specified value
  --ncsr {local,global}
                        local or global NCS restrained (default: local)
  --ncycle NCYCLE       number of cycles in Refmac (default: 10)
  --tlscycle TLSCYCLE   number of TLS cycles in Refmac (default: 0)
  --tlsin TLSIN         TLS parameter input for Refmac
  --hydrogen {all,yes,no}
                        all: add riding hydrogen atoms, yes: use hydrogen
                        atoms if present, no: remove hydrogen atoms in input.
                        Default: all
  --jellybody           Use jelly body restraints
  --jellybody_params sigma dmax
                        Jelly body sigma and dmax (default: [0.01, 4.2])
  --hout                write hydrogen atoms in the output model
  --weight_auto_scale WEIGHT_AUTO_SCALE
                        'weight auto' scale value. automatically determined
                        from resolution and mask/box volume ratio if
                        unspecified
  --weight_matrix WEIGHT_MATRIX
                        weight matrix value
  --keywords KEYWORDS [KEYWORDS ...]
                        refmac keyword(s)
  --keyword_file KEYWORD_FILE [KEYWORD_FILE ...]
                        refmac keyword file(s)
  --external_restraints_json EXTERNAL_RESTRAINTS_JSON
  --show_refmac_log     show all Refmac log instead of summary
  --output_prefix OUTPUT_PREFIX
                        output file name prefix (default: refined)
  --cross_validation    Run cross validation
  --cross_validation_method {throughout,shake}
                        shake: randomize a model refined against a full map
                        and then refine it against a half map, throughout: use
                        only a half map for refinement (another half map is
                        used for error estimation) Default: shake
  --shake_radius SHAKE_RADIUS
                        Shake rmsd in case of --cross_validation_method=shake
                        (default: 0.3)
  --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
  --trim_fofc_mtz       diffmap.mtz will have smaller cell (if --mask_for_fofc
                        is given)
  --fsc_resolution FSC_RESOLUTION
                        High resolution limit for FSC calculation. Default:
                        Nyquist

sfcalc:
  --halfmaps HALFMAPS HALFMAPS
                        Input half map files
  --map MAP             Use this only if you really do not have half maps.
  --mapref MAPREF       Reference map file
  --mask MASK           Mask file
  --model MODEL         Input atomic model file
  --mask_radius MASK_RADIUS
  --padding PADDING     Default: 2*mask_radius
  --no_mask
  --invert_mask         not for refinement.
  --pixel_size PIXEL_SIZE
                        Override pixel size (A)
  --resolution RESOLUTION
  --no_trim             Keep original box (not recommended)
  --no_shift            Keep map origin so that output maps overlap with the
                        input maps.
  --blur BLUR [BLUR ...]
                        Sharpening or blurring B
  --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)
  --ignore_symmetry IGNORE_SYMMETRY
                        Ignore symmetry information (MTRIX/_struct_ncs_oper)
                        in the model file
  --keep_multiple_models
                        Multi-models will be kept; by default only 1st model
                        is kept because REFMAC5 does not support it
  --no_link_check       Do not find and fix link records in input model.
  --b_before_mask B_BEFORE_MASK
                        sharpening B value for sharpen-mask-unsharpen
                        procedure. By default it is determined automatically.
  --no_sharpen_before_mask
                        By default half maps are sharpened before masking by
                        std of signal and unsharpened after masking. This
                        option disables it.
  --no_fix_microheterogeneity
                        By default it will fix microheterogeneity for Refmac
  --no_fix_resi9999     By default it will split chain if max residue number >
                        9999 which is not supported by Refmac
  --no_check_ncs_overlaps
                        Disable model overlap (e.g. expanded model is used
                        with --pg) test

