servalcat 0.4.131__cp314-cp314t-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

servalcat/refine/refine_geom.py

@@ -0,0 +1,245 @@
+"""
+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 argparse
+import os
+import gemmi
+import numpy
+import json
+import servalcat # for version
+from servalcat.utils import logger
+from servalcat import utils
+from servalcat.refine.refine import RefineParams, Geom, Refine, convert_stats_to_dicts, update_meta, print_h_options, load_config
+from servalcat.refmac import refmac_keywords
+
+def add_arguments(parser):
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument('--model',
+                        help='Input atomic model file')
+    group.add_argument('--update_dictionary', 
+                       help="Dictionary file to be updated")
+    parser.add_argument("--monlib",
+                        help="Monomer library path. Default: $CLIBD_MON")
+    parser.add_argument('--ligand', nargs="*", action="append",
+                        help="restraint dictionary cif file(s)")
+    parser.add_argument('--ncycle', type=int, default=10,
+                        help="(when --model is used) number of CG cycles (default: %(default)d)")
+    parser.add_argument('--ncycle_update', type=int, nargs=2, default=[10,30], metavar=("NCYCLE_1", "NCYCLE_2"),
+                        help="(when --update_dictionary is used) number of cycles for the first and second steps (default: %(default)s)")
+    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('--find_links', action='store_true', 
+                        help='Automatically add links')
+    parser.add_argument('--randomize', type=float, default=0,
+                        help='Shake coordinates with specified rmsd')
+    parser.add_argument('--ncsr', action='store_true', 
+                        help='Use local NCS restraints')
+    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('-o','--output_prefix',
+                        help="Output prefix")
+    parser.add_argument("--write_trajectory", action='store_true',
+                        help="Write all output from cycles")
+    parser.add_argument("--config",
+                        help="Config file (.yaml)")
+    parser.add_argument('--adp',  choices=["fix"], default="fix", help=argparse.SUPPRESS) # dummy for omegaconf
+# add_arguments()
+
+def parse_args(arg_list):
+    parser = argparse.ArgumentParser()
+    add_arguments(parser)
+    return parser.parse_args(arg_list)
+# parse_args()
+
+def add_program_info_to_dictionary(block, comp_id, program_name="servalcat", descriptor="optimization tool"):
+    # old acedrg used _pdbx_chem_comp_description_generator. and descriptor
+    # new acedrg (>280?) uses _acedrg_chem_comp_descriptor. and type
+    for tag, name in (("_acedrg_chem_comp_descriptor.", "type"),
+                      ("_pdbx_chem_comp_description_generator.", "descriptor")):
+        tab = block.find(tag, ["program_name", "program_version", name])
+        if tab:
+            loop = tab.loop
+            # just overwrite version if it's there
+            for row in tab:
+                if row.str(0) == program_name and row.str(2) == descriptor:
+                    row[1] = gemmi.cif.quote(servalcat.__version__)
+                    return
+            break
+    else:
+        # it may be strange to say _acedrg in this case..
+        name = "type"
+        loop = block.init_loop("_acedrg_chem_comp_descriptor.", ["comp_id",
+                                                                 "program_name",
+                                                                 "program_version",
+                                                                 name])
+    tags = [x[x.index(".")+1:] for x in loop.tags]
+    row = ["" for _ in range(len(tags))]
+    for tag, val in (("comp_id", comp_id),
+                     ("program_name", program_name),
+                     ("program_version", servalcat.__version__),
+                     (name, descriptor)):
+        if tag in tags: row[tags.index(tag)] = val
+    loop.add_row(gemmi.cif.quote_list(row))
+# add_program_info_to_dictionary()
+
+def refine_and_update_dictionary(cif_in, monomer_dir, output_prefix, refine_cfg, randomize=0, ncycle1=10, ncycle2=30):
+    doc = gemmi.cif.read(cif_in)
+    for block in doc: # this block will be reused below
+        st = gemmi.make_structure_from_chemcomp_block(block)
+        if len(st) > 0: break
+    else:
+        raise SystemExit("No model in the cif file")
+    for i in range(len(st)-1):
+        del st[1]
+    try:
+        monlib = utils.restraints.load_monomer_library(st, monomer_dir=monomer_dir, # monlib is needed for ener_lib
+                                                       cif_files=[cif_in],
+                                                       stop_for_unknowns=True)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+    all_stats = []
+    for i_macro in 0, 1:
+        try:
+            topo, _ = utils.restraints.prepare_topology(st, monlib, h_change=[gemmi.HydrogenChange.Remove, gemmi.HydrogenChange.ReAdd][i_macro],
+                                                        check_hydrogen=(i_macro == 1))
+        except RuntimeError as e:
+            raise SystemExit("Error: {}".format(e))
+
+        refine_params = RefineParams(st, refine_xyz=True)
+        geom = Geom(st, topo, monlib, refine_params, shake_rms=randomize)
+        refiner = Refine(st, geom, refine_cfg, refine_params)
+        logger.writeln("Running {} cycles with wchir=4 wvdw=2 {} hydrogen".format(ncycle1, ["without","with"][i_macro]))
+        geom.calc_kwds["wchir"] = 4
+        geom.calc_kwds["wvdw"] = 2
+        all_stats.append(refiner.run_cycles(ncycle1))
+
+        logger.writeln("Running {} cycles with wchir=1 wvdw=2 {} hydrogen".format(ncycle2, ["without","with"][i_macro]))
+        geom.calc_kwds["wchir"] = 1
+        geom.calc_kwds["wvdw"] = 2
+        all_stats.append(refiner.run_cycles(ncycle2))
+
+    # replace xyz
+    pos = {cra.atom.name: cra.atom.pos.tolist() for cra in refiner.st[0].all()}
+    for row in block.find("_chem_comp_atom.", ["atom_id", "?x", "?y", "?z",
+                                               "?pdbx_model_Cartn_x_ideal",
+                                               "?pdbx_model_Cartn_y_ideal",
+                                               "?pdbx_model_Cartn_z_ideal",
+                                               "?model_Cartn_x", "?model_Cartn_y", "?model_Cartn_z"]):
+        p = pos[row.str(0)]
+        for i in range(3):
+            if row.has(i+1):
+                row[i+1] = "{:.3f}".format(p[i])
+            if row.has(i+4):
+                row[i+4] = "{:.3f}".format(p[i])
+            if row.has(i+7):
+                row[i+7] = "{:.3f}".format(p[i])
+    # add description
+    add_program_info_to_dictionary(block, st[0][0][0].name)
+    doc.write_file(output_prefix + "_updated.cif", options=gemmi.cif.Style.Aligned)
+    logger.writeln("Updated dictionary saved: {}".format(output_prefix + "_updated.cif"))
+    with open(output_prefix + "_stats.json", "w") as ofs:
+        json.dump([convert_stats_to_dicts(x) for x in all_stats],
+                  ofs, indent=2)
+        logger.writeln("Refinement statistics saved: {}".format(ofs.name))
+# refine_and_update_dictionary()
+
+def refine_geom(model_in, monomer_dir, cif_files, h_change, ncycle, output_prefix, randomize, params,
+                refine_cfg, find_links=False, use_ncsr=False):
+    st = utils.fileio.read_structure(model_in)
+    utils.model.setup_entities(st, clear=True, force_subchain_names=True, overwrite_entity_type=True,
+                               fix_sequences=True)
+    if not all(op.given for op in st.ncs):
+        st2 = st.clone()
+        logger.writeln("Take NCS constraints into account.")
+        st2.expand_ncs(gemmi.HowToNameCopiedChain.Dup, merge_dist=0)
+        utils.fileio.write_model(st2, file_name="input_expanded.pdb")
+    try:
+        monlib = utils.restraints.load_monomer_library(st, monomer_dir=monomer_dir,
+                                                       cif_files=cif_files,
+                                                       stop_for_unknowns=True,
+                                                       params=params)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+    utils.restraints.find_and_fix_links(st, monlib, find_metal_links=find_links,
+                                        add_found=find_links) # should remove unknown id here?
+    try:
+        topo, _ = utils.restraints.prepare_topology(st, monlib, h_change=h_change,
+                                                    check_hydrogen=(h_change==gemmi.HydrogenChange.NoChange),
+                                                    params=params)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+
+    print_h_options(h_change, st[0].has_hydrogen(), refine_h=True, hout=True, geom_only=True)
+        
+    if use_ncsr:
+        ncslist = utils.restraints.prepare_ncs_restraints(st)
+    else:
+        ncslist = False
+    refine_params = RefineParams(st, refine_xyz=True, cfg=refine_cfg)
+    geom = Geom(st, topo, monlib, refine_params, shake_rms=randomize, params=params, ncslist=ncslist)
+    refiner = Refine(st, geom, refine_cfg, refine_params)
+    stats = refiner.run_cycles(ncycle,
+                               stats_json_out=output_prefix + "_stats.json")
+    update_meta(st, stats[-1])
+    refiner.st.name = output_prefix
+    utils.fileio.write_model(refiner.st, output_prefix, pdb=True, cif=True)
+    if refine_cfg.write_trajectory:
+        utils.fileio.write_model(refiner.st_traj, output_prefix + "_traj", cif=True)
+# refine_geom()
+
+def main(args):
+    keywords = []
+    if args.keywords: keywords = sum(args.keywords, [])
+    if args.keyword_file: keywords.extend(l for f in sum(args.keyword_file, []) for l in open(f))
+    params = refmac_keywords.parse_keywords(keywords)
+    refine_cfg = load_config(args.config, args, params)
+    decide_prefix = lambda f: utils.fileio.splitext(os.path.basename(f))[0] + "_refined"
+    if args.model:
+        if not args.output_prefix:
+            args.output_prefix = decide_prefix(args.model)
+        if args.ligand:
+            args.ligand = sum(args.ligand, [])
+        h_change = {"all":gemmi.HydrogenChange.ReAddButWater,
+                    "full":gemmi.HydrogenChange.ReAdd,
+                    "yes":gemmi.HydrogenChange.NoChange,
+                    "no":gemmi.HydrogenChange.Remove}[args.hydrogen]
+        refine_geom(model_in=args.model,
+                    monomer_dir=args.monlib,
+                    cif_files=args.ligand,
+                    h_change=h_change,
+                    ncycle=args.ncycle,
+                    output_prefix=args.output_prefix,
+                    randomize=args.randomize,
+                    params=params,
+                    refine_cfg=refine_cfg,
+                    find_links=args.find_links,
+                    use_ncsr=args.ncsr)
+    else:
+        if not args.output_prefix:
+            args.output_prefix = decide_prefix(args.update_dictionary)
+        if args.ligand:
+            logger.writeln("WARNING: monlib and ligand are ignored in the dictionary updating mode")
+        if keywords:
+            logger.writeln("WARNING: refmac keywords are ignored in the dictionary updating mode")
+        refine_and_update_dictionary(cif_in=args.update_dictionary,
+                                     monomer_dir=args.monlib,
+                                     output_prefix=args.output_prefix,
+                                     refine_cfg=refine_cfg,
+                                     randomize=args.randomize,
+                                     ncycle1=args.ncycle_update[0],
+                                     ncycle2=args.ncycle_update[1])
+
+# main()
+
+if __name__ == "__main__":
+    import sys
+    args = parse_args(sys.argv[1:])
+    main(args)

servalcat/refine/refine_spa.py

@@ -0,0 +1,400 @@
+"""
+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 argparse
+import numpy
+from servalcat.utils import logger
+from servalcat import utils
+from servalcat.spa.run_refmac import check_args, process_input, calc_fsc, calc_fofc
+from servalcat.spa import fofc
+from servalcat.refine import spa
+from servalcat.refine.refine import Geom, Refine, RefineParams, update_meta, print_h_options, load_config
+from servalcat.refmac import refmac_keywords
+b_to_u = utils.model.b_to_u
+
+def add_arguments(parser):
+    parser.description = "program to refine cryo-EM SPA structures"
+    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.")
+    group.add_argument("--hklin", help="Use mtz file. With limited functionality.")
+    parser.add_argument('--pixel_size', type=float,
+                        help='Override pixel size (A)')
+    parser.add_argument('--labin', 
+                        help='F,PHI for hklin')
+    parser.add_argument('--model', required=True,
+                        help='Input atomic model file')
+    parser.add_argument("-d", '--resolution', type=float, required=True)
+    parser.add_argument('-r', '--mask_radius', type=float, default=3, help="mask radius")
+    parser.add_argument('--padding',
+                        type=float, 
+                        help='Default: 2*mask_radius')
+    parser.add_argument('--no_mask', action='store_true')
+    parser.add_argument('--no_trim',
+                        action='store_true',
+                        help='Keep original box (not recommended)')
+    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('--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("--b_before_mask", type=float,
+                        help="sharpening B value for sharpen-mask-unsharpen procedure. By default it is determined automatically.")
+    parser.add_argument('--blur',
+                        type=float, default=0,
+                        help='Sharpening or blurring B')
+    parser.add_argument("--monlib",
+                        help="Monomer library path. Default: $CLIBD_MON")
+    parser.add_argument('--ligand', nargs="*", action="append",
+                        help="restraint dictionary cif file(s)")
+    parser.add_argument('--newligand_continue', action='store_true',
+                        help="Make ad-hoc restraints for unknown ligands (not recommended)")
+    parser.add_argument('--hydrogen', default="all", choices=["all", "yes", "no"],
+                        help="all: (re)generate hydrogen atoms, yes: use hydrogen atoms if present, no: remove hydrogen atoms in input. "
+                        "Default: %(default)s")
+    parser.add_argument('--hout', action='store_true', help="write hydrogen atoms in the output model")
+    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('--jellyonly', action='store_true',
+                        help="Jelly body only (experimental, may not be useful)")
+    utils.symmetry.add_symmetry_args(parser) # add --pg etc
+    parser.add_argument('--contacting_only', action="store_true", help="Filter out non-contacting strict NCS copies")
+    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('--no_check_ncs_overlaps', action='store_true', 
+                        help='Disable model overlap test due to strict NCS')
+    parser.add_argument('--no_check_ncs_map', action='store_true', 
+                        help='Disable map symmetry test due to strict NCS')
+    parser.add_argument('--no_check_mask_with_model', action='store_true', 
+                        help='Disable mask test using model')
+    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('--randomize', type=float, default=0,
+                        help='Shake coordinates with the specified rmsd value')
+    parser.add_argument('--ncycle', type=int, default=10,
+                        help="number of CG cycles (default: %(default)d)")
+    parser.add_argument('--weight', type=float,
+                        help="refinement weight. default: automatic")
+    parser.add_argument('--no_weight_adjust', action='store_true', 
+                        help='Do not adjust weight during refinement')
+    parser.add_argument('--target_bond_rmsz_range', nargs=2, type=float, default=[0.5, 1.],
+                        help='Bond rmsz range for weight adjustment (default: %(default)s)')
+    parser.add_argument('--adpr_weight', type=float, default=1.,
+                        help="ADP restraint weight (default: %(default)f)")
+    parser.add_argument('--occr_weight', type=float, default=0.,
+                        help="Occupancy restraint weight (default: %(default)f)")
+    parser.add_argument('--ncsr', action='store_true', 
+                        help='Use local NCS restraints')
+    parser.add_argument('--bfactor', type=float,
+                        help="reset all atomic B values to the specified value")
+    parser.add_argument('--fix_xyz', action="store_true",
+                        help="Fix atomic coordinates")
+    parser.add_argument('--adp',  choices=["fix", "iso", "aniso"], default="iso",
+                        help="ADP parameterization")
+    parser.add_argument('--refine_all_occ', action="store_true")
+    parser.add_argument('--max_dist_for_adp_restraint', type=float, default=4.)
+    parser.add_argument('--adp_restraint_power', type=float)
+    parser.add_argument('--adp_restraint_exp_fac', type=float)
+    parser.add_argument('--adp_restraint_no_long_range', action='store_true')
+    parser.add_argument('--adp_restraint_mode', choices=["diff", "kldiv"], default="diff")
+    parser.add_argument('--unrestrained',  action='store_true', help="No positional restraints")
+    parser.add_argument('--refine_h', action="store_true", help="Refine hydrogen against data (default: only restraints apply)")
+    parser.add_argument("-s", "--source", choices=["electron", "xray", "neutron", "custom"], default="electron")
+    parser.add_argument('-o','--output_prefix', default="refined")
+    parser.add_argument('--cross_validation', action='store_true',
+                        help='Run cross validation. Only "throughout" mode is available (no "shake" mode)')
+    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("--fsc_resolution", type=float,
+                        help="High resolution limit for FSC calculation. Default: Nyquist")
+    parser.add_argument('--keep_charges',  action='store_true',
+                        help="Use scattering factor for charged atoms. Use it with care.")
+    parser.add_argument("--keep_entities", action='store_true',
+                        help="Do not override entities")
+    parser.add_argument("--write_trajectory", action='store_true',
+                        help="Write all output from cycles")
+    parser.add_argument("--config",
+                        help="Config file (.yaml)")
+    parser.add_argument("--halfmapcc_for_dynamic_weighting", help=argparse.SUPPRESS) # testing
+# add_arguments()
+
+def parse_args(arg_list):
+    parser = argparse.ArgumentParser()
+    add_arguments(parser)
+    return parser.parse_args(arg_list)
+# parse_args()
+
+def main(args):
+    args.mask = None
+    args.invert_mask = False
+    args.trim_fofc_mtz = args.mask_for_fofc is not None
+    args.cross_validation_method = "throughout"
+    check_args(args)
+    params = refmac_keywords.parse_keywords(args.keywords + [l for f in args.keyword_file for l in open(f)])
+    refine_cfg = load_config(args.config, args, params)
+
+    st = utils.fileio.read_structure(args.model)
+    ccu = utils.model.CustomCoefUtil()
+    if args.source == "custom":
+        ccu.read_from_cif(st, args.model)
+    if args.unrestrained:
+        monlib = gemmi.MonLib()
+        topo = None
+        if args.hydrogen == "all":
+            logger.writeln("\nWARNING: in unrestrained refinement hydrogen atoms are not generated.\n")
+        if args.hydrogen != "yes":
+            args.hydrogen = "no"
+            st.remove_hydrogens()
+        for i, cra in enumerate(st[0].all()):
+            cra.atom.serial = i + 1
+    else:
+        try:
+            monlib = utils.restraints.load_monomer_library(st, monomer_dir=args.monlib, cif_files=args.ligand,
+                                                           stop_for_unknowns=not args.newligand_continue,
+                                                           params=params)
+        except RuntimeError as e:
+            raise SystemExit("Error: {}".format(e))
+    if not args.keep_entities:
+        utils.model.setup_entities(st, clear=True, force_subchain_names=True, overwrite_entity_type=True,
+                                   fix_sequences=True)
+    if not args.keep_charges:
+        utils.model.remove_charge([st])
+    if args.source == "custom":
+        ccu.show_info()
+    else:
+        utils.model.check_atomsf([st], args.source)
+    if args.hklin:
+        assert not args.cross_validation
+        mtz = utils.fileio.read_mmhkl(args.hklin)
+        hkldata = utils.hkl.hkldata_from_mtz(mtz, args.labin.split(","),
+                                             newlabels=["FP", ""],
+                                             require_types=["F", "P"])
+        hkldata.df = hkldata.df.dropna() # workaround for missing data
+        #hkldata.setup_relion_binning()
+        hkldata.setup_binning(n_bins=10, name="ml") # need to sort out
+        hkldata.copy_binning(src="ml", dst="stat")
+        st.cell = hkldata.cell
+        st.spacegroup_hm = hkldata.sg.xhm()
+        st.setup_cell_images()
+        info = {}
+        utils.restraints.find_and_fix_links(st, monlib, find_metal_links=args.find_links,
+                                            add_found=args.find_links)
+    else:
+        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)]
+        hkldata, info = process_input(st, maps, resolution=args.resolution - 1e-6, monlib=monlib,
+                                      mask_in=args.mask, args=args, use_refmac=False,
+                                      find_links=args.find_links)
+    h_change = {"all":gemmi.HydrogenChange.ReAddKnown,
+                "yes":gemmi.HydrogenChange.NoChange,
+                "no":gemmi.HydrogenChange.Remove}[args.hydrogen]
+    try:
+        topo, _ = utils.restraints.prepare_topology(st, monlib, h_change=h_change,
+                                                    check_hydrogen=(args.hydrogen=="yes"),
+                                                    params=params)
+    except RuntimeError as e:
+        raise SystemExit("Error: {}".format(e))
+
+    print_h_options(h_change, st[0].has_hydrogen(), args.refine_h, args.hout, geom_only=False)
+
+    # initialize values
+    utils.model.reset_adp(st[0], args.bfactor, args.adp)
+    utils.model.initialize_values(st[0], refine_cfg.initialisation)
+
+    # auto weight
+    if args.weight is None:
+        # from 230303_weight_test using 472 test cases
+        reso = info["d_eff"] if "d_eff" in info else args.resolution
+        if "vol_ratio" in info:
+            if "d_eff" in info:
+                rlmc = (-2.3976, 0.5933, 3.5160)
+            else:
+                rlmc = (-2.5151, 0.6681, 3.6467)
+            logger.writeln("Estimating weight auto scale using resolution and volume ratio")
+            ws = numpy.exp(rlmc[0] + reso*rlmc[1] +info["vol_ratio"]*rlmc[2])
+        else:
+            if "d_eff" in info:
+                rlmc = (-1.6908, 0.5668)
+            else:
+                rlmc = (-1.7588, 0.6311)
+            logger.writeln("Estimating weight auto scale using resolution")
+            ws =  numpy.exp(rlmc[0] + args.resolution*rlmc[1])
+        args.weight = max(0.2, min(18.0, ws))
+        logger.writeln(" Will use weight= {:.2f}".format(args.weight))
+
+    if args.ncsr:
+        ncslist = utils.restraints.prepare_ncs_restraints(st)
+    else:
+        ncslist = False
+    refine_params = RefineParams(st, refine_xyz=not args.fix_xyz,
+                                 adp_mode=dict(fix=0, iso=1, aniso=2)[args.adp],
+                                 refine_occ=args.refine_all_occ,
+                                 refine_dfrac=False, cfg=refine_cfg,
+                                 exclude_h_ll=not args.refine_h)
+    if args.halfmapcc_for_dynamic_weighting:
+        localcc, _, _ = utils.fileio.read_ccp4_map(args.halfmapcc_for_dynamic_weighting, pixel_size=args.pixel_size)
+        max_w = 2
+        pos_all = numpy.array([a.pos.tolist() for a in refine_params.atoms])
+        cc = numpy.maximum(0, localcc.interpolate_position_array(pos_all))
+        cc_true = numpy.sqrt(2 * cc / (1 + cc))
+        w = max_w - 0.5 * (numpy.tanh(6 * cc_true - 3) + 1) * (max_w - 1)
+        refine_params.geom_weights[:] = w
+        # debug output
+        st_debug = st.clone()
+        for cra in st_debug[0].all():
+            i = cra.atom.serial - 1
+            cra.atom.b_iso = w[i]
+            cra.atom.occ = cc[i]
+            logger.writeln(f"{cra} {cc[i]} {w[i]}")
+        utils.fileio.write_model(st_debug, file_name="debug_weights.mmcif")
+        
+    geom = Geom(st, topo, monlib, refine_params,
+                shake_rms=args.randomize, adpr_w=args.adpr_weight, occr_w=args.occr_weight,
+                params=params, unrestrained=args.unrestrained or args.jellyonly,
+                ncslist=ncslist)
+    if args.source == "custom":
+        ccu.set_coeffs(st)
+    ll = spa.LL_SPA(hkldata, st, monlib,
+                    lab_obs="F_map1" if args.cross_validation else "FP",
+                    source=args.source)
+    refiner = Refine(st, geom, refine_cfg, refine_params, ll,
+                     unrestrained=args.unrestrained)
+
+    geom.geom.adpr_max_dist = args.max_dist_for_adp_restraint
+    if args.adp_restraint_power is not None: geom.geom.adpr_d_power = args.adp_restraint_power
+    if args.adp_restraint_exp_fac is not None: geom.geom.adpr_exp_fac = args.adp_restraint_exp_fac
+    if args.adp_restraint_no_long_range: geom.geom.adpr_long_range = False
+    geom.geom.adpr_mode = args.adp_restraint_mode
+    if args.jellybody or args.jellyonly: geom.geom.ridge_sigma, geom.geom.ridge_dmax = args.jellybody_params
+    if args.jellyonly: geom.geom.ridge_exclude_short_dist = False
+
+    #logger.writeln("TEST: shift x+0.3 A")
+    #for cra in st[0].all():
+    #    cra.atom.pos += gemmi.Position(0.3,0,0)
+
+    stats = refiner.run_cycles(args.ncycle, weight=args.weight,
+                               weight_adjust=not args.no_weight_adjust,
+                               weight_adjust_bond_rmsz_range=args.target_bond_rmsz_range,
+                               stats_json_out=args.output_prefix + "_stats.json")
+    if not args.hklin and not args.no_trim:
+        refiner.st.cell = maps[0][0].unit_cell
+        refiner.st.setup_cell_images()
+
+    if refine_cfg.write_trajectory:
+        utils.fileio.write_model(refiner.st_traj, args.output_prefix + "_traj", cif=True)
+        
+    # Expand sym here
+    st_expanded = refiner.st.clone()
+    if not all(op.given for op in st.ncs):
+        utils.model.expand_ncs(st_expanded)
+
+    # Calc FSC
+    if args.hklin: # cannot update a mask
+        stats_for_meta = stats[-1]
+    else:
+        mask = utils.fileio.read_ccp4_map(args.mask)[0] if args.mask else None
+        fscavg_text, stats2 = 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="yes", # no change needed in the model
+                                       monlib=monlib,
+                                       blur=args.blur,
+                                       d_min_fsc=args.fsc_resolution,
+                                       cross_validation=args.cross_validation,
+                                       cross_validation_method=args.cross_validation_method,
+                                       source=args.source
+                                       )
+        stats_for_meta = {"geom": stats[-1]["geom"], "data": stats2}
+    update_meta(refiner.st, stats_for_meta, ll)
+    refiner.st.name = args.output_prefix
+    utils.fileio.write_model(refiner.st, args.output_prefix, pdb=True, cif=True, hout=args.hout)
+    if not all(op.given for op in st.ncs): # to apply updated metadata
+        st_expanded = refiner.st.clone()
+        utils.model.expand_ncs(st_expanded)
+        utils.fileio.write_model(st_expanded, args.output_prefix+"_expanded", pdb=True, cif=True, hout=args.hout)
+    if args.hklin:
+        return
+    # Calc Fo-Fc (and updated) maps
+    calc_fofc(refiner.st, st_expanded, maps, monlib, ".mmcif", args, diffmap_prefix=args.output_prefix, source=args.source)
+    
+    # Final summary
+    adpstats_txt = ""
+    adp_stats = utils.model.adp_stats_per_chain(refiner.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 "geom" in stats[-1] and "Bond distances, non H" in stats[-1]["geom"]["summary"].index:
+        rmsbond = stats[-1]["geom"]["summary"]["r.m.s.d."]["Bond distances, non H"]
+        rmsangle = stats[-1]["geom"]["summary"]["r.m.s.d."]["Bond angles, non H"]
+    else:
+        rmsbond, rmsangle = numpy.nan, numpy.nan
+    if args.mask_for_fofc:
+        map_peaks_str = """\
+List Fo-Fc map peaks in the ASU:
+servalcat util map_peaks --map {prefix}_normalized_fofc.mrc --model {prefix}.pdb --abs_level 4.0 \
+""".format(prefix=args.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:.4f} A
+  bond  angles: {rmsangle:.3f} deg
+
+{fscavgs}
+ Run loggraph {fsclog} to see plots
+
+ADP statistics
+{adpstats}
+
+Weight used: {final_weight:.3e}
+             If you want to change the weight, give larger (looser restraints)
+             or smaller (tighter) value to --weight=.
+             
+Open refined model and {prefix}_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=rmsbond,
+           rmsangle=rmsangle,
+           fscavgs=fscavg_text.rstrip(),
+           fsclog="{}_fsc.log".format(args.output_prefix),
+           adpstats=adpstats_txt.rstrip(),
+           final_weight=args.weight,
+           prefix=args.output_prefix,
+           map_peaks_msg=map_peaks_str))
+
+# main()
+
+if __name__ == "__main__":
+    import sys
+    args = parse_args(sys.argv[1:])
+    main(args)