------------------------------------------------------------------------------- phenix.real_space_refine: tool for extensive real-space refinement of atomic coordinates against provided map Usage: phenix.real_space_refine model.pdb ccp4_formatted_map.map or phenix.real_space_refine model.pdb map.mtz or phenix.real_space_refine model.pdb map.mtz label='2FOFCWT,PH2FOFCWT' Feedback: PAfonine@lbl.gov or phenixbb@phenix-online.org ------------------------------------------------------------------------------- ------------------------------------------------------------------------------- Initialize ********** ------------------------------------------------------------------------------- Gather and process all inputs: ****************************** ------------------------------------------------------------------------------- Processing inputs ***************** ------------------------------------------------------------------------------- Parameters: *********** map_coefficients_label = 2mFo-DFc,PHI2mFo-DFc rotamer_restraints = True c_beta_restraints = True resolution_factor = 0.25 ncs_constraints = True scattering_table = *n_gaussian wk1995 it1992 electron neutron refinement { run = *minimization_global rigid_body *local_grid_search *morphing \ *simulated_annealing adp max_iterations = 100 macro_cycles = 10 high_resolution = None target_bonds_rmsd = 0.01 target_angles_rmsd = 1.0 } output { file_name_prefix = reg_390 write_initial_geo_file = True write_final_geo_file = False } pdb_interpretation { cdl = False cdl_weight = 1. correct_hydrogens = True automatic_linking { link_all = False link_metals = False metal_coordination_cutoff = 3.5 amino_acid_bond_cutoff = 1.9 link_residues = False inter_residue_bond_cutoff = 2.5 buffer_for_second_row_elements = 0.5 link_carbohydrates = False carbohydrate_bond_cutoff = 1.99 } use_neutron_distances = False resolution_dependent_restraints { load = False resolution = Auto resolution_range = high *med low high_resolution_range_limit = 1.5 low_resolution_range_limit = 3.0 } apply_cif_modification { data_mod = None residue_selection = None } apply_cif_link { data_link = None residue_selection_1 = None residue_selection_2 = None } disulfide_bond_exclusions_selection_string = None exclusion_distance_cutoff = 3 link_distance_cutoff = 3 disulfide_distance_cutoff = 3 add_angle_and_dihedral_restraints_for_disulfides = True peptide_nucleotide_distance_cutoff = 3 dihedral_function_type = *determined_by_sign_of_periodicity \ all_sinusoidal all_harmonic chir_volume_esd = 0.2 peptide_link { ramachandran_restraints = True cis_threshold = 45 discard_omega = False discard_psi_phi = True omega_esd_override_value = None rama_weight = 1.0 scale_allowed = 1.0 rama_potential = oldfield *emsley oldfield { esd = 10.0 weight_scale = 1.0 dist_weight_max = 10.0 weight = None } rama_selection = None rama_exclude_sec_str = False } nucleic_acid_restraints { enabled = False bonds { enabled = True bond_distance_cutoff = 3.4 target_value = 2.89 sigma = 0.08 slack = 0.00 angle_between_bond_and_nucleobase_cutoff = 35.0 } basepair_planarity { enabled = True sigma = 0.176 } stacking { enabled = True sigma = 0.027 skip_additional_distance_checking = False } } max_reasonable_bond_distance = 50.0 nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 nonbonded_weight = None nonbonded_clashscore = False const_shrink_donor_acceptor = 0.6 vdw_1_4_factor = 0.8 min_distance_sym_equiv = 0.5 custom_nonbonded_symmetry_exclusions = None translate_cns_dna_rna_residue_names = None proceed_with_excessive_length_bonds = False rna_sugar_pucker_analysis { bond_min_distance = 1.2 bond_max_distance = 1.8 epsilon_range_min = 155.0 epsilon_range_max = 310.0 delta_range_2p_min = 129.0 delta_range_2p_max = 162.0 delta_range_3p_min = 65.0 delta_range_3p_max = 104.0 p_distance_c1p_outbound_line_2p_max = 2.9 o3p_distance_c1p_outbound_line_2p_max = 2.4 bond_detection_distance_tolerance = 0.5 } show_histogram_slots { bond_lengths = 5 nonbonded_interaction_distances = 5 bond_angle_deviations_from_ideal = 5 dihedral_angle_deviations_from_ideal = 5 chiral_volume_deviations_from_ideal = 5 } show_max_items { not_linked = 5 bond_restraints_sorted_by_residual = 5 nonbonded_interactions_sorted_by_model_distance = 5 bond_angle_restraints_sorted_by_residual = 5 dihedral_angle_restraints_sorted_by_residual = 3 chirality_restraints_sorted_by_residual = 3 planarity_restraints_sorted_by_residual = 3 residues_with_excluded_nonbonded_symmetry_interactions = 12 fatal_problem_max_lines = 10 } clash_guard { nonbonded_distance_threshold = 0.5 max_number_of_distances_below_threshold = 100 max_fraction_of_distances_below_threshold = 0.1 } } geometry_restraints { edits { excessive_bond_distance_limit = 10 bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None slack = None } angle { action = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None angle_ideal = None sigma = None } planarity { action = *add delete change atom_selection = None sigma = None } parallelity { action = *add delete change atom_selection_1 = None atom_selection_2 = None sigma = 0.027 target_angle_deg = 0 } scale_restraints { atom_selection = None scale = 1.0 apply_to = *bond *angle *dihedral *chirality } } remove { angles = None dihedrals = None chiralities = None planarities = None parallelities = None } } secondary_structure_restraints = True secondary_structure { idealization { enabled = False restrain_torsion_angles = False sigma_on_reference_non_ss = 1 sigma_on_reference_helix = 1 sigma_on_reference_sheet = 0.5 sigma_on_torsion_ss = 5 sigma_on_torsion_nonss = 5 sigma_on_ramachandran = 1 sigma_on_cbeta = 2.5 n_macro = 3 n_iter = 300 } input { file_name = None use_hydrogens = True include_helices = True include_sheets = True find_automatically = None helices_from_phi_psi = False force_nucleic_acids = False use_ksdssp = True } h_bond_restraints { verbose = False substitute_n_for_h = None restrain_helices = True alpha_only = False restrain_sheets = True restrain_base_pairs = True remove_outliers = True distance_ideal_n_o = 2.9 distance_cut_n_o = 3.5 distance_ideal_h_o = 1.975 distance_cut_h_o = 2.5 sigma = 0.05 slack = 0.0 top_out = False } helix { selection = None helix_type = *alpha pi 3_10 unknown restraint_sigma = None restraint_slack = None backbone_only = False } sheet { first_strand = None strand { selection = None sense = parallel antiparallel *unknown bond_start_current = None bond_start_previous = None } restraint_sigma = None restraint_slack = None backbone_only = False } nucleic_acids { sigma = None slack = None use_db_values = True base_pair { base1 = None base2 = None saenger_class = None leontis_westhof_class = *Auto wwt } } } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 50 time_step = 0.0005 initial_velocities_zero_fraction = 0 interleave_minimization = False verbose = -1 n_print = 100 update_grads_shift = 0.3 } Available suitable arrays: FEM,PHIFEM 2mFo-DFc,PHI2mFo-DFc Selected: 2mFo-DFc,PHI2mFo-DFc ------------------------------------------------------------------------------- Process PDB file: ***************** Monomer Library directory: "/net/chevy/raid1/afonine/sources/chem_data/mon_lib" Total number of atoms: 465 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 54} Time building chain proxies: 0.89, per 1000 atoms: 1.91 Number of scatterers: 465 At special positions: 0 Unit cell: (42.231, 42.231, 93.655, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 1 16.00 O 90 8.00 N 75 7.00 C 299 6.00 sf(0) = scattering factor at diffraction angle 0. ------------------------------------------------------------------------------- Extract target map: ******************* ------------------------------------------------------------------------------- Construct geometry restraints manager: ************************************** Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta No hydrogen bonds defined. Number of disulfides: simple=0, symmetry=0 55 Ramachandran restraints generated. Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 82 1.29 - 1.42: 114 1.42 - 1.56: 230 1.56 - 1.69: 44 1.69 - 1.82: 3 Bond restraints: 473 Sorted by residual: bond pdb=" CG LEU A 10 " pdb=" CD1 LEU A 10 " ideal model delta sigma weight residual 1.521 1.734 -0.213 3.30e-02 9.18e+02 4.18e+01 bond pdb=" CG TYR A 15 " pdb=" CD1 TYR A 15 " ideal model delta sigma weight residual 1.389 1.494 -0.105 2.10e-02 2.27e+03 2.51e+01 bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.374 0.084 1.90e-02 2.77e+03 1.95e+01 bond pdb=" CZ3 TRP A 41 " pdb=" CH2 TRP A 41 " ideal model delta sigma weight residual 1.400 1.509 -0.109 2.50e-02 1.60e+03 1.90e+01 bond pdb=" CB LYS A 59 " pdb=" CG LYS A 59 " ideal model delta sigma weight residual 1.520 1.645 -0.125 3.00e-02 1.11e+03 1.72e+01 ... (remaining 468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 462 3.10 - 6.20: 142 6.20 - 9.30: 30 9.30 - 12.40: 3 12.40 - 15.50: 1 Bond angle restraints: 638 Sorted by residual: angle pdb=" CA LEU A 8 " pdb=" CB LEU A 8 " pdb=" CG LEU A 8 " ideal model delta sigma weight residual 116.30 100.80 15.50 3.50e+00 8.16e-02 1.96e+01 angle pdb=" C ARG A 49 " pdb=" CA ARG A 49 " pdb=" CB ARG A 49 " ideal model delta sigma weight residual 110.10 117.98 -7.88 1.90e+00 2.77e-01 1.72e+01 angle pdb=" OD1 ASP A 14 " pdb=" CG ASP A 14 " pdb=" OD2 ASP A 14 " ideal model delta sigma weight residual 122.90 132.66 -9.76 2.40e+00 1.74e-01 1.65e+01 angle pdb=" CB LEU A 33 " pdb=" CG LEU A 33 " pdb=" CD2 LEU A 33 " ideal model delta sigma weight residual 110.70 98.54 12.16 3.00e+00 1.11e-01 1.64e+01 angle pdb=" CG LYS A 43 " pdb=" CD LYS A 43 " pdb=" CE LYS A 43 " ideal model delta sigma weight residual 111.30 120.53 -9.23 2.30e+00 1.89e-01 1.61e+01 ... (remaining 633 not shown) Histogram of dihedral angle deviations from ideal: 0.15 - 15.21: 98 15.21 - 30.27: 40 30.27 - 45.32: 21 45.32 - 60.38: 17 60.38 - 75.44: 1 Dihedral angle restraints: 177 sinusoidal: 118 harmonic: 59 Sorted by residual: dihedral pdb=" CA GLY A 28 " pdb=" C GLY A 28 " pdb=" N ASP A 29 " pdb=" CA ASP A 29 " ideal model delta harmonic sigma weight residual 180.00 -156.97 -23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA SER A 21 " pdb=" C SER A 21 " pdb=" N GLU A 22 " pdb=" CA GLU A 22 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA LYS A 6 " pdb=" C LYS A 6 " pdb=" N GLU A 7 " pdb=" CA GLU A 7 " ideal model delta harmonic sigma weight residual 0.00 18.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 174 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 33 0.115 - 0.230: 21 0.230 - 0.346: 14 0.346 - 0.461: 2 0.461 - 0.576: 1 Chirality restraints: 71 Sorted by residual: chirality pdb=" CG LEU A 33 " pdb=" CB LEU A 33 " pdb=" CD1 LEU A 33 " pdb=" CD2 LEU A 33 " both_signs ideal model delta sigma weight residual True 2.59 -3.17 -0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual True 2.59 -2.22 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR A 32 " pdb=" CA THR A 32 " pdb=" OG1 THR A 32 " pdb=" CG2 THR A 32 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 68 not shown) Planarity restraints: 79 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 29 " 0.027 2.00e-02 2.50e+03 5.65e-02 3.19e+01 pdb=" C ASP A 29 " -0.098 2.00e-02 2.50e+03 pdb=" O ASP A 29 " 0.038 2.00e-02 2.50e+03 pdb=" N ILE A 30 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 36 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 36 " -0.068 2.00e-02 2.50e+03 pdb=" O SER A 36 " 0.026 2.00e-02 2.50e+03 pdb=" N THR A 37 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 8 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C LEU A 8 " -0.066 2.00e-02 2.50e+03 pdb=" O LEU A 8 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL A 9 " 0.023 2.00e-02 2.50e+03 ... (remaining 76 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 158 2.88 - 3.38: 343 3.38 - 3.89: 628 3.89 - 4.39: 633 4.39 - 4.90: 1070 Nonbonded interactions: 2832 Sorted by model distance: nonbonded pdb=" O SER A 36 " pdb=" OG SER A 36 " model vdw 2.370 2.440 nonbonded pdb=" OD2 ASP A 14 " pdb=" NZ LYS A 27 " model vdw 2.377 2.520 nonbonded pdb=" N LYS A 39 " pdb=" N ASP A 40 " model vdw 2.450 2.560 nonbonded pdb=" OD1 ASN A 35 " pdb=" OG1 THR A 37 " model vdw 2.453 2.440 nonbonded pdb=" N THR A 37 " pdb=" OG1 THR A 37 " model vdw 2.463 2.496 ... (remaining 2827 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Adding C-beta torsion restraints... num c-beta restraints: 108 NCS constrained groups: 0 ------------------------------------------------------------------------------- Macro-cycles ************ ------------------------------------------------------------------------------- Set structure monitor ********************* ------------------------------------------------------------------------------- Start info (per residue) ************************ Residue CC CC CC Rotamer Clashes id all backbone sidechain id with ALYS6 -0.063 -0.172 0.233 OUTLIER none AGLU7 -0.127 -0.220 0.230 mt-10 none ALEU8 -0.115 -0.028 -0.122 tp none AVAL9 -0.266 -0.264 -0.173 m none ALEU10 -0.044 -0.009 0.010 OUTLIER none AALA11 -0.063 -0.063 None EXCEPTION none ALEU12 0.036 -0.025 0.382 OUTLIER none ATYR13 0.042 0.076 -0.007 m-85 none AASP14 0.373 0.411 0.330 OUTLIER none ATYR15 0.118 0.184 -0.051 OUTLIER none AGLN16 -0.010 -0.020 -0.235 mm-40 none AGLU17 0.128 0.154 0.157 pt-20 none ALYS18 0.027 0.037 0.055 tmtm? none AGLY19 0.043 0.043 None None none AASP20 0.019 0.149 -0.175 t0 none ASER21 -0.304 -0.315 -0.358 m none AGLU22 -0.228 -0.326 0.012 tt0 none AVAL23 -0.008 0.028 0.013 p none ATHR24 0.065 0.142 -0.070 m none AMET25 0.063 -0.105 0.169 ptp none ALYS26 0.024 0.098 -0.130 OUTLIER none ALYS27 -0.014 0.077 0.078 OUTLIER none AGLY28 -0.066 -0.066 None None none AASP29 0.127 0.187 0.114 p30 none AILE30 0.434 0.448 0.373 mt none ALEU31 0.232 0.295 -0.067 mt none ATHR32 0.035 0.032 -0.118 m none ALEU33 -0.025 -0.049 0.112 OUTLIER none ALEU34 -0.054 -0.070 -0.102 tp none AASN35 -0.095 -0.153 0.096 t-20 none ASER36 0.037 0.033 -0.122 t none ATHR37 -0.043 -0.024 -0.166 p none AASN38 -0.058 -0.040 0.032 OUTLIER none ALYS39 0.159 0.176 -0.060 OUTLIER none AASP40 0.141 0.122 0.212 m-20 none ATRP41 -0.041 -0.104 0.048 m0 none ATRP42 -0.045 -0.050 -0.029 m0 none ALYS43 0.137 0.100 0.306 tttm none AVAL44 0.208 0.187 0.206 OUTLIER none AGLU45 -0.065 -0.018 -0.206 tt0 none AVAL46 -0.097 -0.214 0.080 OUTLIER none AASN47 -0.062 -0.059 -0.253 m-80 none AASP48 -0.195 -0.252 -0.128 OUTLIER none AARG49 -0.021 -0.033 0.151 OUTLIER none AGLN50 0.034 -0.003 0.003 OUTLIER none AGLY51 0.105 0.105 None None none APHE52 0.030 0.084 -0.058 m-85 none AVAL53 0.110 0.081 0.086 m none APRO54 -0.118 -0.141 -0.197 Cg_endo none AALA55 0.068 0.068 None EXCEPTION none AALA56 0.001 0.001 None EXCEPTION none ATYR57 0.206 0.120 0.245 OUTLIER none AVAL58 0.262 0.200 0.347 m none ALYS59 0.024 0.043 -0.105 mtmt none ALYS60 0.239 0.230 0.343 OUTLIER none ALEU61 0.069 0.136 -0.313 tp none AASP62 -0.087 -0.056 -0.457 p-10 none ------------------------------------------------------------------------------- Start info (overall) ******************** Map CC (whole unit cell): 0.013 Map CC (around atoms): 0.032 rmsd (bonds): 0.0386 rmsd (angles): 3.08 Dist. moved from start: 0.000 Dist. moved from previous: 0.000 All-atom clashscore 26.82 Ramachandran plot: outliers: 3.64 % allowed: 29.09 % favored: 67.27 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Set refinery object ******************* ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.038 Map CC (around atoms): 0.060 rmsd (bonds): 0.0605 rmsd (angles): 4.64 Dist. moved from start: 0.925 Dist. moved from previous: 0.925 All-atom clashscore 83.51 Ramachandran plot: outliers: 10.91 % allowed: 20.00 % favored: 69.09 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.092 Map CC (around atoms): 0.141 rmsd (bonds): 0.0875 rmsd (angles): 6.63 Dist. moved from start: 1.472 Dist. moved from previous: 0.742 All-atom clashscore 149.73 Ramachandran plot: outliers: 9.09 % allowed: 30.91 % favored: 60.00 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.115 Map CC (around atoms): 0.171 rmsd (bonds): 0.1032 rmsd (angles): 7.93 Dist. moved from start: 1.889 Dist. moved from previous: 0.614 All-atom clashscore 209.43 Ramachandran plot: outliers: 10.91 % allowed: 30.91 % favored: 58.18 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.115 Map CC (around atoms): 0.168 rmsd (bonds): 0.1224 rmsd (angles): 9.00 Dist. moved from start: 2.118 Dist. moved from previous: 0.319 All-atom clashscore 240.88 Ramachandran plot: outliers: 14.55 % allowed: 32.73 % favored: 52.73 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.115 Map CC (around atoms): 0.166 rmsd (bonds): 0.1405 rmsd (angles): 9.85 Dist. moved from start: 2.197 Dist. moved from previous: 0.250 All-atom clashscore 237.78 Ramachandran plot: outliers: 18.18 % allowed: 29.09 % favored: 52.73 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Local refinement **************** Map CC (whole unit cell): 0.171 Map CC (around atoms): 0.244 rmsd (bonds): 0.1405 rmsd (angles): 11.37 Dist. moved from start: 2.626 Dist. moved from previous: 0.000 All-atom clashscore 266.67 Ramachandran plot: outliers: 16.36 % allowed: 34.55 % favored: 49.09 % Rotamer outliers: 13.73 % C-beta deviations: 0 ------------------------------------------------------------------------------- Global refinement ***************** Traceback (most recent call last): File "/net/chevy/raid1/afonine/build/../sources/phenix/phenix/command_line/real_space_refine.py", line 481, in o = run(sys.argv[1:]) File "/net/chevy/raid1/afonine/build/../sources/phenix/phenix/command_line/real_space_refine.py", line 376, in __init__ self.caller(func = self.run_macro_cycles, prefix="Macro-cycles") File "/net/chevy/raid1/afonine/build/../sources/phenix/phenix/command_line/real_space_refine.py", line 401, in caller status = func(prefix=prefix, **kwargs) File "/net/chevy/raid1/afonine/build/../sources/phenix/phenix/command_line/real_space_refine.py", line 394, in run_macro_cycles log = self.log) File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/macro_cycle_real_space.py", line 50, in __init__ self.caller(self.minimization, "Global refinement") File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/macro_cycle_real_space.py", line 57, in caller status = func(prefix=prefix) File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/macro_cycle_real_space.py", line 168, in minimization self.minimization_no_ncs() File "/net/chevy/raid1/afonine/sources/phenix/phenix/refinement/macro_cycle_real_space.py", line 104, in minimization_no_ncs log = self.log) File "/net/chevy/raid1/afonine/sources/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 56, in __init__ self.rmsd_bonds_final, self.rmsd_angles_final = refine_object.rmsds() File "/net/chevy/raid1/afonine/sources/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 146, in rmsds sites_cart = self.sites_cart()) File "/net/chevy/raid1/afonine/sources/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 140, in sites_cart tolerance = 1) File "/net/chevy/raid1/afonine/sources/cctbx_project/cctbx/crystal/__init__.py", line 614, in correct_special_position raise AssertionError(error_message) AssertionError: Excessive special position correction: unit_cell: (42.231, 42.231, 93.655, 90, 90, 90) space_group_info: P 41 21 2 special_op: 1/2*x+1/2*y,1/2*x+1/2*y,0 site_frac: (0.019441445275697907, -0.02102814811976574, -0.014422803640405577) site_special_frac: (-0.0007933514220339159, -0.0007933514220339159, 0.0) distance_moved: 1.81247