servalcat 0.4.131__cp314-cp314t-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

servalcat/spa/run_refmac.py

@@ -0,0 +1,979 @@
+"""
+Author: "Keitaro Yamashita, Garib N. Murshudov"
+MRC Laboratory of Molecular Biology
+    
+This software is released under the
+Mozilla Public License, version 2.0; see LICENSE.
+"""
+from __future__ import absolute_import, division, print_function, generators
+import gemmi
+import numpy
+import json
+import os
+import shutil
+import argparse
+from servalcat.utils import logger
+from servalcat import utils
+from servalcat import spa # this is not a right style
+from servalcat.spa import shift_maps
+from servalcat.refmac.refmac_wrapper import prepare_crd
+
+def add_arguments(parser):
+    parser.description = 'Run REFMAC5 for SPA'
+
+    parser.add_argument('--exe', default="refmac5",
+                        help='refmac5 binary (default: %(default)s)')
+    parser.add_argument("--monlib",
+                        help="Monomer library path. Default: $CLIBD_MON")
+    # sfcalc options
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument("--halfmaps", nargs=2, help="Input half map files")
+    group.add_argument("--map", help="Use this only if you really do not have half maps.")
+    parser.add_argument('--mask',
+                        help='Mask file')
+    parser.add_argument('--model', required=True,
+                        help='Input atomic model file')
+    parser.add_argument('--mask_radius',
+                        type=float, default=3,
+                        help='')
+    parser.add_argument('--mask_soft_edge',
+                        type=float, default=0,
+                        help='Add soft edge to model mask. Should use with --no_sharpen_before_mask?')
+    parser.add_argument('--padding',
+                        type=float, 
+                        help='Default: 2*mask_radius')
+    parser.add_argument('--no_mask', action='store_true')
+    parser.add_argument('--invert_mask', action='store_true', help='not for refinement.')
+    parser.add_argument('--pixel_size', type=float,
+                        help='Override pixel size (A)')
+    parser.add_argument('--resolution',
+                        type=float,
+                        help='')
+    parser.add_argument('--no_trim',
+                        action='store_true',
+                        help='Keep original box (not recommended)')
+    parser.add_argument('--blur',
+                        type=float, default=0,
+                        help='Sharpening or blurring B')
+    utils.symmetry.add_symmetry_args(parser) # add --pg etc
+    parser.add_argument('--contacting_only', action="store_true", help="Filter out non-contacting NCS")
+    parser.add_argument('--ignore_symmetry', action='store_true',
+                        help='Ignore symmetry information (MTRIX/_struct_ncs_oper) in the model file')
+    parser.add_argument('--find_links', action='store_true', 
+                        help='Automatically add links')
+    parser.add_argument("--b_before_mask", type=float,
+                        help="sharpening B value for sharpen-mask-unsharpen procedure. By default it is determined automatically.")
+    parser.add_argument('--no_sharpen_before_mask', action='store_true',
+                        help='By default half maps are sharpened before masking by std of signal and unsharpened after masking. This option disables it.')
+    parser.add_argument('--no_fix_microheterogeneity', action='store_true', 
+                        help='By default it will fix microheterogeneity for Refmac')
+    parser.add_argument('--no_fix_resi9999', action='store_true', 
+                        help='By default it will split chain if max residue number > 9999 which is not supported by Refmac')
+    parser.add_argument('--no_check_ncs_overlaps', action='store_true', 
+                        help='Disable model overlap (e.g. expanded model is used with --pg) test')
+    parser.add_argument('--no_check_ncs_map', action='store_true', 
+                        help='Disable map NCS consistency test')
+    parser.add_argument('--no_check_mask_with_model', action='store_true', 
+                        help='Disable mask test using model')
+    parser.add_argument("--prepare_only", action='store_true',
+                        help="Stop before refinement")
+    parser.add_argument("--no_refmacat", action='store_true',
+                        help="By default uses gemmi for crd/rst file preparation (do not use makecif)")
+    # run_refmac options
+    # TODO use group! like refmac options
+    parser.add_argument('--ligand', nargs="*", action="append",
+                        help="restraint dictionary cif file(s)")
+    parser.add_argument('--bfactor', type=float,
+                        help="reset all atomic B values to specified value")
+    parser.add_argument('--ncsr', default="local", choices=["local", "global"],
+                        help="local or global NCS restrained (default: %(default)s)")
+    parser.add_argument('--ncycle', type=int, default=10,
+                        help="number of cycles in Refmac (default: %(default)d)")
+    parser.add_argument('--tlscycle', type=int, default=0,
+                        help="number of TLS cycles in Refmac (default: %(default)d)")
+    parser.add_argument('--tlsin',
+                        help="TLS parameter input for Refmac")
+    parser.add_argument('--hydrogen', default="all", choices=["all", "yes", "no"],
+                        help="all: add riding hydrogen atoms, yes: use hydrogen atoms if present, no: remove hydrogen atoms in input. "
+                        "Default: %(default)s")
+    parser.add_argument('--jellybody', action='store_true',
+                        help="Use jelly body restraints")
+    parser.add_argument('--jellybody_params', nargs=2, type=float,
+                        metavar=("sigma", "dmax"), default=[0.01, 4.2],
+                        help="Jelly body sigma and dmax (default: %(default)s)")
+    parser.add_argument('--hout', action='store_true', help="write hydrogen atoms in the output model")
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument('--weight_auto_scale', type=float,
+                       help="'weight auto' scale value. automatically determined from resolution and mask/box volume ratio if unspecified")
+    parser.add_argument('--keywords', nargs='+', action="append",
+                        help="refmac keyword(s)")
+    parser.add_argument('--keyword_file', nargs='+', action="append",
+                        help="refmac keyword file(s)")
+    parser.add_argument('--external_restraints_json')
+    parser.add_argument('--show_refmac_log', action='store_true',
+                        help="show all Refmac log instead of summary")
+    parser.add_argument('--output_prefix', default="refined",
+                        help='output file name prefix (default: %(default)s)')
+    parser.add_argument('--cross_validation', action='store_true',
+                        help='Run cross validation')
+    parser.add_argument('--cross_validation_method', default="shake", choices=["throughout", "shake"],
+                        help="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: %(default)s")
+    parser.add_argument('--shake_radius', default=0.3,
+                        help='Shake rmsd in case of --cross_validation_method=shake (default: %(default).1f)')
+    group = parser.add_mutually_exclusive_group()
+    group.add_argument('--mask_for_fofc', help="Mask file for Fo-Fc map calculation")
+    group.add_argument('--mask_radius_for_fofc', type=float, help="Mask radius for Fo-Fc map calculation")
+    parser.add_argument('--trim_fofc_mtz', action="store_true", help="maps mtz will have smaller cell (if --mask_for_fofc is given)")
+    parser.add_argument("--fsc_resolution", type=float,
+                        help="High resolution limit for FSC calculation. Default: Nyquist")
+
+# add_arguments()
+                        
+def parse_args(arg_list):
+    parser = argparse.ArgumentParser()
+    add_arguments(parser)
+    return parser.parse_args(arg_list)
+# parse_args()
+
+def calc_fsc(st, output_prefix, maps, d_min, mask, mask_radius, soft_edge, b_before_mask, no_sharpen_before_mask, make_hydrogen, monlib,
+             blur=0, d_min_fsc=None, cross_validation=False, cross_validation_method=None, st_sr=None,
+             source="electron"):
+    # st_sr: shaken-and-refined st in case of cross_validation_method=="shake"
+    if cross_validation:
+        assert len(maps) == 2
+        assert cross_validation_method in ("shake", "throughout")
+    if cross_validation and cross_validation_method == "shake":
+        assert st_sr is not None
+    else:
+        assert st_sr is None
+    
+    logger.writeln("Calculating map-model FSC..")
+    ret = {"summary": {}}
+
+    if d_min_fsc is None:
+        d_min_fsc = utils.maps.nyquist_resolution(maps[0][0])
+        logger.writeln("  --fsc_resolution is not specified. Using Nyquist resolution: {:.2f}".format(d_min_fsc))
+    
+    st = st.clone()
+    if st_sr is not None: st_sr = st_sr.clone()
+
+    if make_hydrogen == "all":
+        utils.restraints.add_hydrogens(st, monlib)
+        if st_sr is not None: utils.restraints.add_hydrogens(st_sr, monlib)
+
+    if mask is not None or mask_radius is not None:
+        if mask is None:
+            assert maps[0][0].unit_cell == st.cell
+            mask = utils.maps.mask_from_model(st, mask_radius, soft_edge=soft_edge, grid=maps[0][0])
+        if no_sharpen_before_mask or len(maps) < 2:
+            for ma in maps: ma[0].array[:] *= mask
+        else:
+            # It seems we need different B for different resolution limit
+            if b_before_mask is None: b_before_mask = determine_b_before_mask(st, maps, maps[0][1], mask, d_min_fsc)
+            maps = utils.maps.sharpen_mask_unsharpen(maps, mask, d_min_fsc, b=b_before_mask)
+        
+    hkldata = utils.maps.mask_and_fft_maps(maps, d_min_fsc)
+    hkldata.df["FC"] = utils.model.calc_fc_fft(st, d_min_fsc - 1e-6, monlib=monlib, source=source,
+                                               miller_array=hkldata.miller_array())
+    # XXX didn't apply mask to FC!!
+    labs_fc = ["FC"]
+
+    if st_sr is not None:
+        hkldata.df["FC_sr"] = utils.model.calc_fc_fft(st_sr, d_min_fsc - 1e-6, monlib=monlib, source=source,
+                                                      miller_array=hkldata.miller_array())
+        labs_fc.append("FC_sr")
+
+    if blur != 0:
+        logger.writeln(" Unblurring Fc with B={} for FSC calculation".format(blur))
+        unblur = numpy.exp(blur/hkldata.d_spacings().to_numpy()**2/4.)
+        for lab in labs_fc:
+            hkldata.df[lab] *= unblur
+    
+    hkldata.setup_relion_binning("stat")
+    stats = spa.fsc.calc_fsc_all(hkldata, labs_fc=labs_fc, lab_f="FP",
+                                 labs_half=["F_map1", "F_map2"] if len(maps)==2 else None)
+
+    hkldata2 = hkldata.copy(d_min=d_min) # for FSCaverage at resolution for refinement # XXX more efficient way
+    hkldata2.setup_relion_binning("stat")
+    stats2 = spa.fsc.calc_fsc_all(hkldata2, labs_fc=labs_fc, lab_f="FP",
+                                  labs_half=["F_map1", "F_map2"] if len(maps)==2 else None)
+    
+    if "fsc_half" in stats:
+        with numpy.errstate(invalid="ignore"): # XXX negative fsc results in nan!
+            stats.loc[:,"fsc_full_sqrt"] = numpy.sqrt(2*stats.fsc_half/(1+stats.fsc_half))
+
+    logger.writeln(stats.to_string()+"\n")
+
+    # remove and rename columns
+    for s in (stats, stats2):
+        s.rename(columns=dict(fsc_FC_full="fsc_model", Rcmplx_FC_full="Rcmplx"), inplace=True)
+        if cross_validation:
+            if cross_validation_method == "shake":
+                s.drop(columns=["fsc_FC_half1", "fsc_FC_half2", "fsc_FC_sr_full", "Rcmplx_FC_sr_full"], inplace=True)
+                s.rename(columns=dict(fsc_FC_sr_half1="fsc_model_half1",
+                                          fsc_FC_sr_half2="fsc_model_half2"), inplace=True)
+            else:
+                s.rename(columns=dict(fsc_FC_half1="fsc_model_half1",
+                                          fsc_FC_half2="fsc_model_half2"), inplace=True)
+        else:
+            s.drop(columns=[x for x in s if x.startswith("fsc_FC") and x.endswith(("half1","half2"))], inplace=True)
+
+    # FSCaverages
+    ret["summary"]["d_min"] = d_min
+    ret["summary"]["FSCaverage"] = spa.fsc.fsc_average(stats2.ncoeffs, stats2.fsc_model)
+    if cross_validation:
+        ret["summary"]["FSCaverage_half1"] = spa.fsc.fsc_average(stats2.ncoeffs, stats2.fsc_model_half1)
+        ret["summary"]["FSCaverage_half2"] = spa.fsc.fsc_average(stats2.ncoeffs, stats2.fsc_model_half2)
+    fscavg_text  = "Map-model FSCaverages (at {:.2f} A):\n".format(d_min)
+    fscavg_text += " FSCaverage(full) = {: .4f}\n".format(ret["summary"]["FSCaverage"])
+    if cross_validation:
+        fscavg_text += "Cross-validated map-model FSCaverages:\n"
+        fscavg_text += " FSCaverage(half1)= {: .4f}\n".format(ret["summary"]["FSCaverage_half1"])
+        fscavg_text += " FSCaverage(half2)= {: .4f}\n".format(ret["summary"]["FSCaverage_half2"])
+    
+    # for loggraph
+    fsc_logfile = "{}_fsc.log".format(output_prefix)
+    with open(fsc_logfile, "w") as ofs:
+        columns = "1/resol^2 ncoef ln(Mn(|Fo|^2)) ln(Mn(|Fc|^2)) FSC(full,model) FSC_half FSC_full_sqrt FSC(half1,model) FSC(half2,model) Rcmplx(full,model)".split()
+        
+        ofs.write("$TABLE: Map-model FSC after refinement:\n")
+        if len(maps) == 2:
+            if cross_validation: fsc_cols = [5,6,7,8,9]
+            else:                fsc_cols = [5,6,7]
+        else: fsc_cols = [5]
+        fsc_cols.append(10)
+        if len(maps) == 2: ofs.write("$GRAPHS: FSC :A:1,5,6,7:\n")
+        else:              ofs.write("$GRAPHS: FSC :A:1,5:\n")
+        if cross_validation: ofs.write(": cross-validated FSC :A:1,8,9:\n".format(",".join(map(str,fsc_cols))))
+        ofs.write(": Rcmplx :A:1,{}:\n".format(4+len(fsc_cols)))
+        ofs.write(": ln(Mn(|F|^2)) :A:1,3,4:\n")
+        ofs.write(": number of Fourier coeffs :A:1,2:\n")
+        ofs.write("$$ {}$$\n".format(" ".join(columns[:4]+[columns[i-1] for i in fsc_cols])))
+        ofs.write("$$\n")
+
+        plot_columns = ["d_min", "ncoeffs", "power_FP", "power_FC", "fsc_model"]
+        if len(maps) == 2:
+            plot_columns.extend(["fsc_half", "fsc_full_sqrt"])
+            if cross_validation:
+                plot_columns.extend(["fsc_model_half1", "fsc_model_half2"])
+        plot_columns.append("Rcmplx")
+        with numpy.errstate(divide="ignore"):
+            log_format = lambda x: "{:.3f}".format(numpy.log(x))
+            ofs.write(stats.to_string(header=False, index=False, index_names=False, columns=plot_columns,
+                                      formatters=dict(d_min=lambda x: "{:.4f}".format(1/x**2),
+                                                      power_FP=log_format, power_FC=log_format)))
+        ofs.write("\n")
+        ofs.write("$$\n\n")
+        ofs.write(fscavg_text)
+    
+    logger.write(fscavg_text)
+    logger.writeln("Run loggraph {} to see plots.".format(fsc_logfile))
+    
+    # write json
+    with open("{}_fsc.json".format(output_prefix), "w") as f:
+        json.dump(stats.to_dict("records"), f, indent=True)
+    ret["binned"] = stats2.to_dict(orient="records")
+    return fscavg_text, ret
+# calc_fsc()
+
+def calc_fofc(st, st_expanded, maps, monlib, model_format, args, diffmap_prefix="diffmap", source="electron"):
+    logger.writeln("Starting Fo-Fc calculation..")
+    if not args.halfmaps: logger.writeln(" with limited functionality because half maps were not provided")
+    logger.writeln(" model: {}".format(args.output_prefix+model_format))
+    
+    # for Fo-Fc in case of helical reconstruction, expand model more
+    # XXX should we do it for FSC calculation also? Probably we should not do sharpen-unsharpen procedure for FSC calc either.
+    if args.twist is not None:
+        logger.writeln("Generating all helical copies in the box")
+        st_expanded = st.clone()
+        utils.symmetry.update_ncs_from_args(args, st_expanded, map_and_start=maps[0], filter_contacting=False)
+        utils.model.expand_ncs(st_expanded)
+        utils.fileio.write_model(st_expanded, args.output_prefix+"_expanded_all", pdb=True, cif=True)
+
+    if args.mask_for_fofc:
+        logger.writeln("  mask: {}".format(args.mask_for_fofc))
+        mask = utils.fileio.read_ccp4_map(args.mask_for_fofc)[0]
+    elif args.mask_radius_for_fofc:
+        logger.writeln("  mask: using refined model with radius of {} A".format(args.mask_radius_for_fofc))
+        mask = utils.maps.mask_from_model(st_expanded, args.mask_radius_for_fofc, grid=maps[0][0]) # use soft edge?
+    else:
+        logger.writeln("  mask: not used")
+        mask = None
+        
+    hkldata, map_labs, stats_str = spa.fofc.calc_fofc(st_expanded, args.resolution, maps, mask=mask, monlib=monlib,
+                                                      half1_only=(args.cross_validation and args.cross_validation_method == "throughout"),
+                                                      sharpening_b=None if args.halfmaps else 0., # assume already sharpened if fullmap is given
+                                                      source=source)
+    spa.fofc.write_files(hkldata, map_labs, maps[0][1], stats_str,
+                         mask=mask, output_prefix=diffmap_prefix,
+                         trim_map=mask is not None, trim_mtz=args.trim_fofc_mtz)
+    
+    # Create Coot script
+    spa.fofc.write_coot_script("{}_coot.py".format(args.output_prefix),
+                               model_file="{}.pdb".format(args.output_prefix), # as Coot is not good at mmcif file..
+                               mtz_file="{}_maps.mtz".format(diffmap_prefix),
+                               contour_fo=None if mask is None else 1.2,
+                               contour_fofc=None if mask is None else 3.0,
+                               ncs_ops=st.ncs)
+
+    # Create ChimeraX script
+    spa.fofc.write_chimerax_script(cxc_out="{}_chimerax.cxc".format(args.output_prefix),
+                                   model_file="{}.mmcif".format(args.output_prefix), # ChimeraX handles mmcif just fine
+                                   fo_mrc_file="{}_normalized_fo.mrc".format(diffmap_prefix),
+                                   fofc_mrc_file="{}_normalized_fofc.mrc".format(diffmap_prefix))
+# calc_fofc()
+
+def write_final_summary(st, refmac_summary, fscavg_text, output_prefix, is_mask_given):
+    if len(refmac_summary["cycles"]) > 1 and "actual_weight" in refmac_summary["cycles"][-2]:
+        final_weight = refmac_summary["cycles"][-2]["actual_weight"]
+    else:
+        final_weight = "???"
+
+    adpstats_txt = ""
+    adp_stats = utils.model.adp_stats_per_chain(st[0])
+    max_chain_len = max([len(x[0]) for x in adp_stats])
+    max_num_len = max([len(str(x[1])) for x in adp_stats])
+    for chain, natoms, qs in adp_stats:
+        adpstats_txt += " Chain {0:{1}s}".format(chain, max_chain_len) if chain!="*" else " {0:{1}s}".format("All", max_chain_len+6)
+        adpstats_txt += " ({0:{1}d} atoms) min={2:5.1f} median={3:5.1f} max={4:5.1f} A^2\n".format(natoms, max_num_len, qs[0],qs[2],qs[4])
+
+    if is_mask_given:
+        map_peaks_str = """\
+List Fo-Fc map peaks in the ASU:
+servalcat util map_peaks --map diffmap_normalized_fofc.mrc --model {prefix}.pdb --abs_level 4.0 \
+""".format(prefix=output_prefix)
+    else:
+        map_peaks_str = "WARNING: --mask_for_fofc was not given, so the Fo-Fc map was not normalized."
+
+    logger.writeln("""
+=============================================================================
+* Final Summary *
+
+Rmsd from ideal
+  bond lengths: {rmsbond} A
+  bond  angles: {rmsangle} deg
+
+{fscavgs}
+ Run loggraph {fsclog} to see plots
+
+ADP statistics
+{adpstats}
+
+Weight used: {final_weight}
+             If you want to change the weight, give larger (looser restraints)
+             or smaller (tighter) value to --weight_auto_scale=.
+             
+Open refined model and maps mtz with COOT:
+coot --script {prefix}_coot.py
+
+Open refined model, map and difference map with ChimeraX/ISOLDE:
+chimerax {prefix}_chimerax.cxc
+
+{map_peaks_msg}
+=============================================================================
+""".format(rmsbond=refmac_summary["cycles"][-1].get("rms_bond", "???"),
+           rmsangle=refmac_summary["cycles"][-1].get("rms_angle", "???"),
+           fscavgs=fscavg_text.rstrip(),
+           fsclog="{}_fsc.log".format(output_prefix),
+           adpstats=adpstats_txt.rstrip(),
+           final_weight=final_weight,
+           prefix=output_prefix,
+           map_peaks_msg=map_peaks_str))
+# write_final_summary()
+
+def lab_f_suffix(blur):
+    if blur is None or blur == 0.:
+        return ""
+    elif blur > 0:
+        return "Blur_{:.2f}".format(blur)
+    else:
+        return "Sharp_{:.2f}".format(-blur)
+# lab_f_suffix()
+
+def write_map_mtz(hkldata, mtz_out, map_labs, sig_lab=None, blur=0):
+    nblur = 2 if blur != 0 else 1
+    mean_f = hkldata.df[map_labs].abs().mean().min()
+    data_labs = map_labs + ([sig_lab] if sig_lab else [])
+
+    if mean_f < 1:
+        scale = 10. / mean_f
+        logger.writeln("Mean(|F|)= {:.2e} may be too small for Refmac. Applying scale= {:.1f}".format(mean_f, scale))
+        for lab in data_labs:
+            hkldata.df[lab] *= scale
+
+    mtz_labs = data_labs + []
+    mtz_types = {}
+    if sig_lab: mtz_types[sig_lab] = "Q"
+
+    if blur != 0:
+        temp = hkldata.debye_waller_factors(b_iso=blur)
+        for lab in data_labs:
+            data = hkldata.df[lab]
+            newlab = lab + lab_f_suffix(blur)
+            if numpy.iscomplexobj(data): data = numpy.abs(data)
+            hkldata.df[newlab] = data * temp
+            mtz_labs.append(newlab)
+            mtz_types[newlab] = "F" if lab != sig_lab else "Q"
+
+    hkldata.write_mtz(mtz_out, labs=mtz_labs, types=mtz_types,
+                      phase_label_decorator=lambda x: "P"+x[1:])
+# write_map_mtz()
+
+def determine_b_before_mask(st, maps, grid_start, mask, resolution):
+    logger.writeln("Determining b_before_mask..")
+    # work in masked map for the speed
+    new_cell, new_shape, starts, shifts = shift_maps.determine_shape_and_shift(mask=mask,
+                                                                               grid_start=grid_start,
+                                                                               padding=5,
+                                                                               mask_cutoff=0.5,
+                                                                               noncentered=True,
+                                                                               noncubic=True,
+                                                                               json_out=None)
+    st = st.clone()
+    st.cell = new_cell
+    st.spacegroup_hm = "P 1"
+    for cra in st[0].all():
+        cra.atom.pos += shifts
+        cra.atom.b_iso = 0
+        cra.atom.aniso = gemmi.SMat33f(0,0,0,0,0,0)
+
+    newmaps = []
+    for i in range(len(maps)): # Update maps
+        g = gemmi.FloatGrid(maps[i][0].array*mask,
+                            maps[i][0].unit_cell, maps[i][0].spacegroup)
+
+        suba = g.get_subarray(starts, new_shape)
+        new_grid = gemmi.FloatGrid(suba, new_cell, st.find_spacegroup())
+        newmaps.append([new_grid]+maps[i][1:])
+
+    hkldata = utils.maps.mask_and_fft_maps(newmaps, resolution)
+    hkldata.df["FC"] = utils.model.calc_fc_fft(st, resolution - 1e-6, source="electron",
+                                               miller_array=hkldata.miller_array())
+    k, b = hkldata.scale_k_and_b("FC", "FP")
+    return -b
+# determine_b_before_mask()
+
+def process_input(st, maps, resolution, monlib, mask_in, args,
+                  shifted_model_prefix="shifted",
+                  output_masked_prefix="masked_fs",
+                  output_mtz_prefix="starting_map",
+                  use_gemmi_prep=False, no_refmac_fix=False,
+                  use_refmac=True, find_links=False):
+    ret = {} # instructions for refinement
+    maps = utils.maps.copy_maps(maps) # not to modify maps
+    
+    grid_start = maps[0][1]
+    unit_cell = maps[0][0].unit_cell
+    spacegroup = gemmi.SpaceGroup(1)
+    start_xyz = numpy.array(maps[0][0].get_position(*grid_start).tolist())
+    A = unit_cell.orth.mat.array
+    center = numpy.sum(A, axis=1) / 2 #+ start_xyz
+
+    # Create mask
+    if mask_in:
+        logger.writeln("Input mask file: {}".format(mask_in))
+        mask = utils.fileio.read_ccp4_map(mask_in)[0]
+    else:
+        mask = None
+    
+    st.cell = unit_cell
+    st.spacegroup_hm = "P 1"
+    if use_refmac:
+        ret["model_format"] = ".mmcif" if st.input_format == gemmi.CoorFormat.Mmcif else ".pdb"
+        max_seq_num = max([max(res.seqid.num for res in chain) for model in st for chain in model])
+        if max_seq_num > 9999 and ret["model_format"] == ".pdb":
+            logger.writeln("Max residue number ({}) exceeds 9999. Will use mmcif format".format(max_seq_num))
+            ret["model_format"] = ".mmcif"
+
+    if len(st.ncs) > 0 and args.ignore_symmetry:
+        logger.writeln("Removing symmetry information from model.")
+        st.ncs.clear()
+    utils.symmetry.update_ncs_from_args(args, st, map_and_start=maps[0], filter_contacting=args.contacting_only)
+    st_expanded = st.clone()
+    if not all(op.given for op in st.ncs):
+        # symmetry is not exact in helical reconstructions
+        cc_cutoff = 0.9 if args.twist is None else 0.7
+        if not args.no_check_ncs_overlaps and utils.model.check_symmetry_related_model_duplication(st):
+            raise SystemExit("\nError: Too many symmetry-related contacts detected.\n"
+                             "Please provide an asymmetric unit model along with symmetry operators.")
+        if not args.no_check_ncs_map and utils.maps.check_symmetry_related_map_values(st, maps[0][0], cc_cutoff=cc_cutoff):
+            raise SystemExit("\nError: Map correlation is too small. Please ensure your map follows the model's symmetry")
+        args.keywords.extend(utils.symmetry.ncs_ops_for_refmac(st.ncs))
+        utils.model.expand_ncs(st_expanded)
+        logger.writeln(" Saving expanded model: input_model_expanded.*")
+        utils.fileio.write_model(st_expanded, "input_model_expanded", pdb=True, cif=True)
+
+    if mask is not None and not args.no_check_mask_with_model:
+        if not utils.maps.test_mask_with_model(mask, st_expanded):
+            raise SystemExit("\nError: Model is out of mask.\n"
+                             "Please check your --model and --mask. You can disable this test with --no_check_mask_with_model.")
+    if args.mask_for_fofc:
+        masktmp = utils.fileio.read_ccp4_map(args.mask_for_fofc)[0]
+        if masktmp.shape != maps[0][0].shape:
+            raise SystemExit("\nError: mask from --mask_for_fofc has a different shape from input map(s)")
+        if not args.no_check_mask_with_model and not utils.maps.test_mask_with_model(masktmp, st):
+            raise SystemExit("\nError: Model is out of mask.\n"
+                             "Please check your --model and --mask_for_fofc. You can disable this test with --no_check_mask_with_model.")
+        del masktmp
+
+    if mask is None and args.mask_radius:
+        logger.writeln("Creating mask..")
+        mask = utils.maps.mask_from_model(st_expanded, args.mask_radius, soft_edge=args.mask_soft_edge, grid=maps[0][0])
+        #utils.maps.write_ccp4_map("mask_from_model.ccp4", mask)
+
+    if use_refmac:
+        logger.writeln(" Saving input model with unit cell information")
+        utils.fileio.write_model(st, "starting_model", pdb=True, cif=True)
+        ret["model_file"] = "starting_model" + ret["model_format"]
+
+    if mask is not None:
+        if args.invert_mask:
+            logger.writeln("Inverting mask..")
+            mask_max, mask_min = numpy.max(mask), numpy.min(mask)
+            logger.writeln("  mask_max, mask_min= {}, {}".format(mask_max, mask_min))
+            mask = mask_max + mask_min - mask
+        
+        # Mask maps
+        if args.no_sharpen_before_mask or len(maps) < 2:
+            logger.writeln("Applying mask..")
+            for ma in maps: ma[0].array[:] *= mask
+        else:
+            logger.writeln("Sharpen-mask-unsharpen..")
+            b_before_mask = args.b_before_mask
+            if b_before_mask is None: b_before_mask = determine_b_before_mask(st, maps, grid_start, mask, resolution)                
+            maps = utils.maps.sharpen_mask_unsharpen(maps, mask, resolution, b=b_before_mask)
+
+        if not args.no_trim:
+            logger.writeln(" Shifting maps and/or model..")
+            if args.padding is None: args.padding = args.mask_radius * 2
+            new_cell, new_shape, starts, shifts = shift_maps.determine_shape_and_shift(mask=mask,
+                                                                                       grid_start=grid_start,
+                                                                                       padding=args.padding,
+                                                                                       mask_cutoff=0.5,
+                                                                                       noncentered=True,
+                                                                                       noncubic=True,
+                                                                                       json_out=None)
+            ret["shifts"] = shifts
+            vol_mask = numpy.count_nonzero(mask.array>0.5)
+            vol_map = new_shape[0] * new_shape[1] * new_shape[2]
+            ret["vol_ratio"] = vol_mask / vol_map
+            logger.writeln(" Vol_mask/Vol_map= {:.2e}".format(ret["vol_ratio"]))
+
+            # Model may be built out of the box (with 'unit cell' translation symmetry)
+            # It is only valid with original unit cell, but no longer valid with the new cell
+            # It still would not work if model is built over multiple 'cells'.
+            extra_shift = utils.model.translate_into_box(st,
+                                                         origin=gemmi.Position(*start_xyz),
+                                                         apply_shift=False)
+            if numpy.linalg.norm(extra_shift) > 0:
+                logger.writeln("Input model is out of the box. Required shift= {}".format(extra_shift))
+                ret["shifts"] += gemmi.Position(*extra_shift)
+                logger.writeln("Shift for model has been adjusted: {}".format(numpy.array(ret["shifts"].tolist())))
+            
+            st.cell = new_cell
+            st.spacegroup_hm = "P 1"
+            if use_refmac:
+                logger.writeln(" Saving model in trimmed map..")
+                utils.fileio.write_model(st, shifted_model_prefix, pdb=True, cif=True)
+                ret["model_file"] = shifted_model_prefix + ret["model_format"]
+
+            logger.writeln(" Trimming maps..")
+            for i in range(len(maps)): # Update maps
+                suba = maps[i][0].get_subarray(starts, new_shape)
+                new_grid = gemmi.FloatGrid(suba, new_cell, spacegroup)
+                maps[i][0] = new_grid
+
+    st.setup_cell_images()
+    utils.restraints.find_and_fix_links(st, monlib, add_found=find_links,
+                                        # link via ncsc is not supported as of Refmac5.8.0411
+                                        find_symmetry_related=not use_refmac)
+    # workaround for Refmac
+    # TODO need to check external restraints
+    if use_refmac:
+        if use_gemmi_prep:
+            h_change = {"all":gemmi.HydrogenChange.ReAddButWater,
+                        "yes":gemmi.HydrogenChange.NoChange,
+                        "no":gemmi.HydrogenChange.Remove}[args.hydrogen]
+            topo, metal_kws = utils.restraints.prepare_topology(st, monlib, h_change=h_change, raise_error=False)
+            args.keywords = metal_kws + args.keywords
+        elif not no_refmac_fix:
+            topo = gemmi.prepare_topology(st, monlib, warnings=logger.silent(), ignore_unknown_links=True)
+        else:
+            topo = None # not used
+        if not no_refmac_fix:
+            ret["refmac_fixes"] = utils.refmac.FixForRefmac()
+            ret["refmac_fixes"].fix_before_topology(st, topo, 
+                                                    fix_microheterogeneity=not args.no_fix_microheterogeneity and not use_gemmi_prep,
+                                                    fix_resimax=not args.no_fix_resi9999,
+                                                    fix_nonpolymer=False)
+        chain_id_len_max = max([len(x) for x in utils.model.all_chain_ids(st)])
+        if chain_id_len_max > 1 and ret["model_format"] == ".pdb":
+            logger.writeln("Long chain ID (length: {}) detected. Will use mmcif format".format(chain_id_len_max))
+            ret["model_format"] = ".mmcif"
+        if not no_refmac_fix and ret["model_format"] == ".mmcif" and not use_gemmi_prep:
+            ret["refmac_fixes"].fix_nonpolymer(st)
+
+    if use_refmac and use_gemmi_prep:
+        # TODO: make cispept, make link, remove unknown link id
+        # TODO: cross validation?
+        crdout = os.path.splitext(ret["model_file"])[0] + ".crd"
+        ret["model_file"] = crdout
+        ret["model_format"] = ".mmcif"
+        args.keywords.append("make cr prepared")
+        gemmi.setup_for_crd(st)
+        doc = gemmi.prepare_refmac_crd(st, topo, monlib, h_change)
+        doc.write_file(crdout, options=gemmi.cif.Style.NoBlankLines)
+        logger.writeln("crd file written: {}".format(crdout))
+
+    hkldata = utils.maps.mask_and_fft_maps(maps, resolution, None, with_000=False)
+    hkldata.setup_relion_binning("ml")
+    hkldata.copy_binning(src="ml", dst="stat") # todo test usual binning for ml
+    if len(maps) == 2:
+        map_labs = ["Fmap1", "Fmap2", "Fout"]
+        ret["lab_f_half1"] = "Fmap1" + lab_f_suffix(args.blur)
+        # TODO Add SIGF in case of half maps, when refmac is ready
+        ret["lab_phi_half1"] = "Pmap1"
+        ret["lab_f_half2"] = "Fmap2" + lab_f_suffix(args.blur)
+        ret["lab_phi_half2"] = "Pmap2"
+        utils.maps.calc_noise_var_from_halfmaps(hkldata)
+        d_eff_full = hkldata.d_eff("ml", "FSCfull")
+        logger.writeln("Effective resolution from FSCfull= {:.2f}".format(d_eff_full))
+        ret["d_eff"] = d_eff_full
+    else:
+        map_labs = ["Fout"]
+        sig_lab = None
+
+    if use_refmac:
+        if args.no_mask:
+            logger.writeln("Saving unmasked maps as mtz file..")
+            mtzout = output_mtz_prefix+".mtz"
+        else:
+            logger.writeln(" Saving masked maps as mtz file..")
+            mtzout = output_masked_prefix+"_obs.mtz"
+
+        hkldata.df.rename(columns=dict(F_map1="Fmap1", F_map2="Fmap2", FP="Fout"), inplace=True)
+        if "shifts" in ret:
+            for lab in map_labs: # apply phase shift
+                logger.writeln("  applying phase shift for {} with translation {}".format(lab, -ret["shifts"]))
+                hkldata.translate(lab, -ret["shifts"])
+
+        write_map_mtz(hkldata, mtzout, map_labs=map_labs, blur=args.blur)
+        ret["mtz_file"] = mtzout
+        ret["lab_f"] = "Fout" + lab_f_suffix(args.blur)
+        ret["lab_phi"] = "Pout"
+    else:
+        fac = hkldata.debye_waller_factors(b_iso=args.blur)
+        if "shifts" in ret: fac *= hkldata.translation_factor(-ret["shifts"])
+        for lab in ("F_map1", "F_map2", "FP"):
+            if lab in hkldata.df: hkldata.df[lab] *= fac
+    return hkldata, ret
+# process_input()
+
+def check_args(args):
+    if not os.path.exists(args.model):
+        raise SystemExit("Error: --model {} does not exist.".format(args.model))
+
+    if args.cross_validation and not args.halfmaps:
+        raise SystemExit("Error: half maps are needed when --cross_validation is given")
+    
+    if args.mask_for_fofc and not os.path.exists(args.mask_for_fofc):
+        raise SystemExit("Error: --mask_for_fofc {} does not exist".format(args.mask_for_fofc))
+
+    if args.mask_for_fofc and args.mask_radius_for_fofc:
+        raise SystemExit("Error: you cannot specify both --mask_for_fofc and --mask_radius_for_fofc")
+
+    if args.trim_fofc_mtz and not (args.mask_for_fofc or args.mask_radius_for_fofc):
+        raise SystemExit("Error: --trim_fofc_mtz is specified but --mask_for_fofc is not given")
+
+    if args.ligand: args.ligand = sum(args.ligand, [])
+
+    if args.keywords:
+        args.keywords = sum(args.keywords, [])
+    else:
+        args.keywords = []
+
+    if args.keyword_file:
+        args.keyword_file = sum(args.keyword_file, [])
+        for f in args.keyword_file:
+            if not os.path.exists(f):
+                raise SystemExit(f"Error: keyword file was not found: {f}")
+            logger.writeln("Keyword file: {}".format(f))
+    else:
+        args.keyword_file = []
+
+    if (args.twist, args.rise).count(None) == 1:
+        raise SystemExit("ERROR: give both helical parameters --twist and --rise")
+    if args.twist is not None:
+        logger.writeln("INFO: setting --contacting_only because helical symmetry is given")
+        args.contacting_only = True
+    if args.no_mask:
+        args.mask_radius = None
+        if not args.no_trim:
+            logger.writeln("WARNING: setting --no_trim because --no_mask is given")
+            args.no_trim = True
+        if args.mask:
+            logger.writeln("WARNING: Your --mask is ignored because --no_mask is given")
+            args.mask = None
+
+    #if args.mask_soft_edge > 0:
+    #    logger.writeln("INFO: --mask_soft_edge={} is given. Turning off sharpen_before_mask.".format(args.mask_soft_edge))
+    #    args.no_sharpen_before_mask = True
+
+    if args.resolution is None and args.model and utils.fileio.splitext(args.model)[1].endswith("cif"):
+        doc = gemmi.cif.read(args.model)
+        if len(doc) != 1:
+            raise SystemExit("cannot find resolution from cif. Give --resolution")
+        block = doc.sole_block()
+        reso_str = block.find_value("_em_3d_reconstruction.resolution")
+        try:
+            args.resolution = float(reso_str)
+        except:
+            raise SystemExit("ERROR: _em_3d_reconstruction.resolution is invalid. Give --resolution")
+        logger.writeln("WARNING: --resolution not given. Using _em_3d_reconstruction.resolution = {}".format(reso_str))
+
+    if args.resolution is None:
+        raise SystemExit("ERROR: --resolution is needed.")
+# check_args()
+
+def main(args):
+    check_args(args)
+    use_gemmi_prep = False
+    if not args.prepare_only:
+        refmac_ver = utils.refmac.check_version(args.exe)
+        if not refmac_ver:
+            raise SystemExit("Error: Check Refmac installation or use --exe to give the location.")
+        if not args.no_refmacat and refmac_ver >= (5, 8, 404):
+            logger.writeln(" will use gemmi to prepare restraints")
+            use_gemmi_prep = True
+        else:
+            logger.writeln(" will use makecif to prepare restraints")
+
+    logger.writeln("Input model: {}".format(args.model))
+    st = utils.fileio.read_structure(args.model)
+    if len(st) > 1:
+        logger.writeln(" Removing models 2-{}".format(len(st)))
+        for i in reversed(range(1, len(st))):
+            del st[i]
+
+    try:
+        monlib = utils.restraints.load_monomer_library(st, monomer_dir=args.monlib, cif_files=args.ligand, 
+                                                       stop_for_unknowns=True)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+
+    utils.model.setup_entities(st, clear=True, force_subchain_names=True, overwrite_entity_type=True)
+    try:
+        utils.restraints.prepare_topology(st.clone(), monlib, h_change=gemmi.HydrogenChange.NoChange,
+                                          check_hydrogen=(args.hydrogen=="yes"))
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+
+    if args.halfmaps:
+        maps = utils.fileio.read_halfmaps(args.halfmaps, pixel_size=args.pixel_size)
+    else:
+        maps = [utils.fileio.read_ccp4_map(args.map, pixel_size=args.pixel_size)]
+        
+    utils.model.remove_charge([st])
+    shifted_model_prefix = "shifted"
+    _, file_info = process_input(st, maps, resolution=args.resolution - 1e-6, monlib=monlib,
+                                 mask_in=args.mask, args=args,
+                                 shifted_model_prefix=shifted_model_prefix,
+                                 use_gemmi_prep=use_gemmi_prep,
+                                 find_links=args.find_links)
+    if args.prepare_only:
+        logger.writeln("\n--prepare_only is given. Stopping.")
+        return
+
+    args.mtz = file_info["mtz_file"]
+    if args.halfmaps: # FIXME if no_mask?
+        args.mtz_half = [file_info["mtz_file"], file_info["mtz_file"]]
+    args.lab_phi = file_info["lab_phi"]  #"Pout0"
+    args.lab_f = file_info["lab_f"]
+    args.lab_sigf = None
+    args.model = file_info["model_file"] # refmac xyzin
+    model_format = file_info["model_format"]
+
+    if args.cross_validation and args.cross_validation_method == "throughout":
+        args.lab_f = file_info["lab_f_half1"]
+        args.lab_phi = file_info["lab_phi_half1"]
+        # XXX args.lab_sigf?
+
+    chain_id_lens = [len(x) for x in utils.model.all_chain_ids(st)]
+    keep_chain_ids = (chain_id_lens and max(chain_id_lens) == 1) # always kept unless one-letter chain IDs
+
+    # FIXME if mtz is given and sfcalc() not ran?
+
+    if not args.no_trim:
+        refmac_prefix = "{}_{}".format(shifted_model_prefix, args.output_prefix)
+    else:
+        refmac_prefix = args.output_prefix # XXX this should be different name (nomask etc?)
+
+    # Weight auto scale
+    if args.weight_auto_scale is None:
+        reso = file_info["d_eff"] if "d_eff" in file_info else args.resolution
+        if "vol_ratio" in file_info:
+            if "d_eff" in file_info:
+                rlmc = (-9.503541, 3.129882, 15.439744)
+            else:
+                rlmc = (-8.329418, 3.032409, 14.381907)
+            logger.writeln("Estimating weight auto scale using resolution and volume ratio")
+            ws = rlmc[0] + reso*rlmc[1] +file_info["vol_ratio"]*rlmc[2]
+        else:
+            if "d_eff" in file_info:
+                rlmc = (-5.903807, 2.870723)
+            else:
+                rlmc = (-4.891140, 2.746791)
+            logger.writeln("Estimating weight auto scale using resolution")
+            ws =  rlmc[0] + args.resolution*rlmc[1]
+        args.weight_auto_scale = max(0.2, min(18.0, ws))
+        logger.writeln(" Will use weight auto {:.2f}".format(args.weight_auto_scale))
+        
+    # Run Refmac
+    refmac = utils.refmac.Refmac(prefix=refmac_prefix, args=args, global_mode="spa",
+                                 keep_chain_ids=keep_chain_ids)
+    refmac.set_libin(args.ligand)
+    try:
+        refmac_summary = refmac.run_refmac()
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+
+    # Modify output
+    st, cif_ref = utils.fileio.read_structure_from_pdb_and_mmcif(refmac_prefix+model_format)
+    utils.model.setup_entities(st, clear=True, overwrite_entity_type=True, force_subchain_names=True)
+
+    if not args.no_trim:
+        st.cell = maps[0][0].unit_cell
+        st.setup_cell_images()
+    if "refmac_fixes" in file_info:
+        file_info["refmac_fixes"].modify_back(st)
+    utils.model.adp_analysis(st)
+    utils.fileio.write_model(st, prefix=args.output_prefix,
+                             pdb=True, cif=True, cif_ref=cif_ref)
+
+    # Take care of TLS out
+    if not args.no_trim: # if no_trim, there is nothing to do.
+        tlsout = refmac.tlsout()
+        if os.path.exists(tlsout):
+            logger.writeln("Copying tlsout")
+            shutil.copyfile(refmac.tlsout(), args.output_prefix+".tls")
+
+    # Expand sym here
+    st_expanded = st.clone()
+    if not all(op.given for op in st.ncs):
+        utils.model.expand_ncs(st_expanded)
+        utils.fileio.write_model(st_expanded, args.output_prefix+"_expanded", pdb=True, cif=True,
+                                 cif_ref=cif_ref)
+
+    if args.cross_validation and args.cross_validation_method == "shake":
+        logger.writeln("Cross validation is requested.")
+        refmac_prefix_shaken = refmac_prefix+"_shaken_refined"
+        logger.writeln("Starting refinement using half map 1 (model is shaken first)")
+        logger.writeln("In this refinement, hydrogen is removed regardless of --hydrogen option")
+        if use_gemmi_prep:
+            xyzin = refmac_prefix + ".crd"
+            st_tmp = utils.fileio.read_structure(refmac_prefix+model_format)
+            utils.model.setup_entities(st_tmp, clear=True, overwrite_entity_type=True, force_subchain_names=True)
+            prepare_crd(st_tmp,
+                        crdout=xyzin, ligand=[refmac_prefix+model_format],
+                        make={"hydr":"n"},
+                        fix_long_resnames=False) # we do not need output file - do we?
+        else:
+            xyzin = refmac_prefix + model_format
+        refmac_hm1 = refmac.copy(hklin=args.mtz_half[0],
+                                 xyzin=xyzin,
+                                 prefix=refmac_prefix_shaken,
+                                 shake=args.shake_radius,
+                                 jellybody=False, # makes no sense to use jelly body after shaking
+                                 hydrogen="no") # should not use hydrogen after shaking
+        if args.jellybody: logger.writeln("  Turning off jelly body")
+        if "lab_f_half1" in file_info:
+            refmac_hm1.lab_f = file_info["lab_f_half1"]
+            refmac_hm1.lab_phi = file_info["lab_phi_half1"]
+            # SIGMA?
+            
+        try:
+            refmac_hm1.run_refmac()
+        except RuntimeError as e:
+            raise SystemExit("Error: {}".format(e))
+
+        if args.hydrogen != "no": # does not work properly when 'yes' - we would need to keep hydrogen in input
+            logger.writeln("Cross validation: 2nd run with hydrogen")
+            if use_gemmi_prep:
+                xyzin = refmac_prefix_shaken + ".crd"
+                st_tmp = utils.fileio.read_structure(refmac_prefix_shaken+model_format)
+                utils.model.setup_entities(st_tmp, clear=True, overwrite_entity_type=True, force_subchain_names=True)
+                prepare_crd(st_tmp,
+                            crdout=xyzin, ligand=[refmac_prefix+model_format],
+                            make={"hydr":"a"},
+                            fix_long_resnames=False) # we do not need output file - do we?
+            else:
+                xyzin = refmac_prefix_shaken + model_format
+            refmac_prefix_shaken = refmac_prefix+"_shaken_refined2"
+            refmac_hm1_2 = refmac_hm1.copy(xyzin=xyzin,
+                                           prefix=refmac_prefix_shaken,
+                                           shake=None,
+                                           hydrogen="all")
+            try:
+                refmac_hm1_2.run_refmac()
+            except RuntimeError as e:
+                raise SystemExit("Error: {}".format(e))
+        
+        # Modify output
+        st_sr, cif_ref_sr = utils.fileio.read_structure_from_pdb_and_mmcif(refmac_prefix_shaken+model_format)
+        utils.model.setup_entities(st_sr, clear=True, overwrite_entity_type=True, force_subchain_names=True)
+        if not args.no_trim:
+            st_sr.cell = maps[0][0].unit_cell
+            st_sr.setup_cell_images()
+        if "refmac_fixes" in file_info:
+            file_info["refmac_fixes"].modify_back(st_sr)
+
+        utils.fileio.write_model(st_sr, prefix=args.output_prefix+"_shaken_refined",
+                                 pdb=True, cif=True, cif_ref=cif_ref_sr)
+
+        # Expand sym here
+        st_sr_expanded = st_sr.clone()
+        if not all(op.given for op in st_sr.ncs):
+            utils.model.expand_ncs(st_sr_expanded)
+            utils.fileio.write_model(st_sr_expanded, args.output_prefix+"_shaken_refined_expanded",
+                                     pdb=True, cif=True, cif_ref=cif_ref_sr)
+            if args.twist is not None: # as requested by a user
+                st_sr_expanded_all = st_sr.clone()
+                utils.symmetry.update_ncs_from_args(args, st_sr_expanded_all, map_and_start=maps[0], filter_contacting=False)
+                utils.model.expand_ncs(st_sr_expanded_all)
+                utils.fileio.write_model(st_sr_expanded_all, args.output_prefix+"_shaken_refined_expanded_all", pdb=True, cif=True,
+                                         cif_ref=cif_ref)
+    else:
+        st_sr_expanded = None
+
+    if args.mask:
+        mask = utils.fileio.read_ccp4_map(args.mask)[0]
+    else:
+        mask = None
+        
+    # Calc FSC
+    fscavg_text = calc_fsc(st_expanded, args.output_prefix, maps,
+                           args.resolution, mask=mask, mask_radius=args.mask_radius if not args.no_mask else None,
+                           soft_edge=args.mask_soft_edge,
+                           b_before_mask=args.b_before_mask,
+                           no_sharpen_before_mask=args.no_sharpen_before_mask,
+                           make_hydrogen=args.hydrogen,
+                           monlib=monlib, cross_validation=args.cross_validation,
+                           blur=args.blur,
+                           d_min_fsc=args.fsc_resolution,
+                           cross_validation_method=args.cross_validation_method, st_sr=st_sr_expanded)[0]
+
+    # Calc Fo-Fc (and updated) maps
+    calc_fofc(st, st_expanded, maps, monlib, model_format, args)
+    
+    # Final summary
+    write_final_summary(st, refmac_summary, fscavg_text, args.output_prefix,
+                        args.mask_for_fofc or args.mask_radius_for_fofc)
+# main()
+        
+if __name__ == "__main__":
+    import sys
+    args = parse_args(sys.argv[1:])
+    main(args)
+