------------------------------------------------------------------------------- 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_566 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: 1.02, per 1000 atoms: 2.19 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: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 79 1.29 - 1.43: 129 1.43 - 1.57: 239 1.57 - 1.72: 24 1.72 - 1.86: 2 Bond restraints: 473 Sorted by residual: bond pdb=" CB LYS A 60 " pdb=" CG LYS A 60 " ideal model delta sigma weight residual 1.520 1.691 -0.171 3.00e-02 1.11e+03 3.23e+01 bond pdb=" CA ILE A 30 " pdb=" C ILE A 30 " ideal model delta sigma weight residual 1.525 1.639 -0.114 2.10e-02 2.27e+03 2.94e+01 bond pdb=" N GLY A 19 " pdb=" CA GLY A 19 " ideal model delta sigma weight residual 1.451 1.526 -0.075 1.60e-02 3.91e+03 2.17e+01 bond pdb=" CD GLU A 7 " pdb=" OE2 GLU A 7 " ideal model delta sigma weight residual 1.249 1.332 -0.083 1.90e-02 2.77e+03 1.89e+01 bond pdb=" CE LYS A 27 " pdb=" NZ LYS A 27 " ideal model delta sigma weight residual 1.489 1.617 -0.128 3.00e-02 1.11e+03 1.81e+01 ... (remaining 468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.14: 482 3.14 - 6.28: 128 6.28 - 9.41: 24 9.41 - 12.55: 3 12.55 - 15.69: 1 Bond angle restraints: 638 Sorted by residual: angle pdb=" C ASP A 29 " pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 121.70 133.07 -11.37 1.80e+00 3.09e-01 3.99e+01 angle pdb=" N GLY A 51 " pdb=" CA GLY A 51 " pdb=" C GLY A 51 " ideal model delta sigma weight residual 112.50 96.81 15.69 2.90e+00 1.19e-01 2.93e+01 angle pdb=" CB GLN A 50 " pdb=" CG GLN A 50 " pdb=" CD GLN A 50 " ideal model delta sigma weight residual 112.60 121.34 -8.74 1.70e+00 3.46e-01 2.65e+01 angle pdb=" C ALA A 55 " pdb=" N ALA A 56 " pdb=" CA ALA A 56 " ideal model delta sigma weight residual 121.70 113.65 8.05 1.80e+00 3.09e-01 2.00e+01 angle pdb=" CA GLU A 17 " pdb=" C GLU A 17 " pdb=" O GLU A 17 " ideal model delta sigma weight residual 120.80 113.88 6.92 1.70e+00 3.46e-01 1.66e+01 ... (remaining 633 not shown) Histogram of dihedral angle deviations from ideal: 0.05 - 17.55: 119 17.55 - 35.05: 25 35.05 - 52.55: 24 52.55 - 70.05: 7 70.05 - 87.55: 2 Dihedral angle restraints: 177 sinusoidal: 118 harmonic: 59 Sorted by residual: dihedral pdb=" CA LEU A 33 " pdb=" C LEU A 33 " pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA ASN A 38 " pdb=" C ASN A 38 " pdb=" N LYS A 39 " pdb=" CA LYS A 39 " ideal model delta harmonic sigma weight residual 180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" N VAL A 46 " pdb=" CA VAL A 46 " pdb=" CB VAL A 46 " pdb=" CG2 VAL A 46 " ideal model delta sinusoidal sigma weight residual 180.00 0.48 59.52 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 174 not shown) Histogram of chiral volume deviations from ideal: 0.009 - 0.079: 23 0.079 - 0.149: 24 0.149 - 0.218: 12 0.218 - 0.288: 6 0.288 - 0.358: 6 Chirality restraints: 71 Sorted by residual: chirality pdb=" CA VAL A 58 " pdb=" N VAL A 58 " pdb=" C VAL A 58 " pdb=" CB VAL A 58 " both_signs ideal model delta sigma weight residual False 2.52 2.88 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB VAL A 9 " pdb=" CA VAL A 9 " pdb=" CG1 VAL A 9 " pdb=" CG2 VAL A 9 " both_signs ideal model delta sigma weight residual True 2.63 -2.28 0.35 2.00e-01 2.50e+01 3.08e+00 chirality pdb=" CA TYR A 13 " pdb=" N TYR A 13 " pdb=" C TYR A 13 " pdb=" CB TYR A 13 " both_signs ideal model delta sigma weight residual False 2.50 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 68 not shown) Planarity restraints: 79 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 42 " -0.023 2.00e-02 2.50e+03 2.72e-02 1.85e+01 pdb=" CG TRP A 42 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 42 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 42 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 42 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 42 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 42 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 42 " -0.032 2.00e-02 2.50e+03 pdb=" CH2 TRP A 42 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 41 " -0.012 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" CG TRP A 41 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 41 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 41 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 41 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 41 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP A 41 " 0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 41 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 41 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP A 41 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 13 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C TYR A 13 " -0.054 2.00e-02 2.50e+03 pdb=" O TYR A 13 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 14 " 0.019 2.00e-02 2.50e+03 ... (remaining 76 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 38 2.69 - 3.24: 318 3.24 - 3.79: 625 3.79 - 4.35: 706 4.35 - 4.90: 1117 Nonbonded interactions: 2804 Sorted by model distance: nonbonded pdb=" O ASP A 20 " pdb=" N GLU A 22 " model vdw 2.133 2.520 nonbonded pdb=" O THR A 37 " pdb=" OG1 THR A 37 " model vdw 2.324 2.440 nonbonded pdb=" CB ARG A 49 " pdb=" NE ARG A 49 " model vdw 2.372 2.816 nonbonded pdb=" ND2 ASN A 38 " pdb=" O TRP A 41 " model vdw 2.405 2.520 nonbonded pdb=" N LYS A 27 " pdb=" CG LYS A 27 " model vdw 2.442 2.816 ... (remaining 2799 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 -0.143 -0.263 0.128 OUTLIER none AGLU7 -0.060 -0.051 -0.020 mt-10 none ALEU8 -0.097 -0.125 -0.006 OUTLIER none AVAL9 -0.149 -0.174 -0.033 m none ALEU10 -0.109 -0.155 0.005 OUTLIER none AALA11 -0.148 -0.148 None EXCEPTION none ALEU12 -0.115 -0.176 -0.088 OUTLIER none ATYR13 0.109 0.082 0.109 m-30 none AASP14 0.318 0.341 0.278 m-20 none ATYR15 0.269 0.349 0.212 OUTLIER none AGLN16 0.228 0.168 0.335 mm-40 none AGLU17 -0.095 -0.073 -0.074 pt-20 none ALYS18 -0.056 -0.125 0.192 OUTLIER none AGLY19 -0.271 -0.271 None None none AASP20 0.120 0.118 0.168 OUTLIER none ASER21 0.003 0.006 0.090 OUTLIER none AGLU22 -0.317 -0.358 -0.185 OUTLIER none AVAL23 -0.126 -0.047 -0.075 OUTLIER none ATHR24 0.092 0.196 -0.123 m none AMET25 0.095 0.047 0.154 OUTLIER none ALYS26 -0.038 0.023 -0.134 mtmt none ALYS27 0.053 0.106 0.107 OUTLIER none AGLY28 0.215 0.215 None None none AASP29 0.209 0.231 0.011 t0 none AILE30 -0.069 -0.085 -0.009 tp none ALEU31 -0.100 -0.143 -0.077 mt none ATHR32 0.015 0.010 -0.020 p none ALEU33 -0.131 -0.173 -0.042 tp none ALEU34 -0.176 -0.139 -0.301 mt none AASN35 -0.245 -0.341 0.077 t-20 none ASER36 -0.077 -0.081 -0.213 m none ATHR37 -0.063 -0.087 0.052 p none AASN38 0.011 -0.022 0.205 t30 none ALYS39 -0.007 -0.004 -0.115 OUTLIER none AASP40 0.097 0.126 0.103 OUTLIER none ATRP41 0.289 0.244 0.384 m95 none ATRP42 0.103 0.191 -0.048 m0 none ALYS43 -0.010 -0.037 0.074 tttp none AVAL44 -0.099 -0.128 0.156 m none AGLU45 0.161 0.091 0.367 tt0 none AVAL46 0.081 0.038 0.120 OUTLIER none AASN47 -0.000 0.009 -0.008 m-20 none AASP48 0.070 0.107 -0.137 p30 none AARG49 0.011 -0.037 -0.019 OUTLIER none AGLN50 0.124 0.114 0.139 pm0 none AGLY51 -0.233 -0.233 None None none APHE52 0.075 0.243 -0.242 m-85 none AVAL53 0.433 0.425 0.301 m none APRO54 0.079 0.094 0.214 Cg_endo none AALA55 0.002 0.002 None EXCEPTION none AALA56 0.092 0.092 None EXCEPTION none ATYR57 0.006 0.214 -0.233 OUTLIER none AVAL58 -0.028 -0.038 -0.142 t none ALYS59 -0.122 -0.195 0.200 ptmt none ALYS60 -0.004 -0.009 -0.026 tptm none ALEU61 0.107 0.127 -0.157 mt none AASP62 0.264 0.215 0.469 m-20 none ------------------------------------------------------------------------------- Start info (overall) ******************** Map CC (whole unit cell): 0.025 Map CC (around atoms): 0.024 rmsd (bonds): 0.0381 rmsd (angles): 3.01 Dist. moved from start: 0.000 Dist. moved from previous: 0.000 All-atom clashscore 9.66 Ramachandran plot: outliers: 3.64 % allowed: 34.55 % favored: 61.82 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Set refinery object ******************* ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.097 Map CC (around atoms): 0.146 rmsd (bonds): 0.0659 rmsd (angles): 4.24 Dist. moved from start: 0.911 Dist. moved from previous: 0.911 All-atom clashscore 64.20 Ramachandran plot: outliers: 5.45 % allowed: 30.91 % favored: 63.64 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.107 Map CC (around atoms): 0.169 rmsd (bonds): 0.0884 rmsd (angles): 5.79 Dist. moved from start: 1.440 Dist. moved from previous: 0.613 All-atom clashscore 139.25 Ramachandran plot: outliers: 7.27 % allowed: 30.91 % favored: 61.82 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.109 Map CC (around atoms): 0.168 rmsd (bonds): 0.1090 rmsd (angles): 7.12 Dist. moved from start: 1.685 Dist. moved from previous: 0.408 All-atom clashscore 162.07 Ramachandran plot: outliers: 9.09 % allowed: 36.36 % favored: 54.55 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.107 Map CC (around atoms): 0.161 rmsd (bonds): 0.1249 rmsd (angles): 8.02 Dist. moved from start: 1.813 Dist. moved from previous: 0.363 All-atom clashscore 136.36 Ramachandran plot: outliers: 12.73 % allowed: 38.18 % favored: 49.09 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.100 Map CC (around atoms): 0.147 rmsd (bonds): 0.1507 rmsd (angles): 9.29 Dist. moved from start: 1.900 Dist. moved from previous: 0.385 All-atom clashscore 189.10 Ramachandran plot: outliers: 21.82 % allowed: 30.91 % favored: 47.27 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Local refinement **************** Map CC (whole unit cell): 0.161 Map CC (around atoms): 0.256 rmsd (bonds): 0.1510 rmsd (angles): 11.12 Dist. moved from start: 2.387 Dist. moved from previous: 0.000 All-atom clashscore 222.97 Ramachandran plot: outliers: 23.64 % allowed: 29.09 % favored: 47.27 % Rotamer outliers: 7.84 % 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: (-0.1360966647235329, -0.1281312598416741, 0.0187647939971323) site_special_frac: (-0.1321139622826035, -0.1321139622826035, 0.0) distance_moved: 1.77344