------------------------------------------------------------------------------- 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_26 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: 0.92, per 1000 atoms: 1.98 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: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 74 1.28 - 1.41: 109 1.41 - 1.54: 207 1.54 - 1.67: 81 1.67 - 1.81: 2 Bond restraints: 473 Sorted by residual: bond pdb=" CA ASP A 29 " pdb=" CB ASP A 29 " ideal model delta sigma weight residual 1.530 1.430 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N LEU A 34 " pdb=" CA LEU A 34 " ideal model delta sigma weight residual 1.458 1.546 -0.088 1.90e-02 2.77e+03 2.17e+01 bond pdb=" N LYS A 27 " pdb=" CA LYS A 27 " ideal model delta sigma weight residual 1.458 1.546 -0.088 1.90e-02 2.77e+03 2.14e+01 bond pdb=" CG LEU A 31 " pdb=" CD2 LEU A 31 " ideal model delta sigma weight residual 1.521 1.371 0.150 3.30e-02 9.18e+02 2.06e+01 bond pdb=" N LYS A 59 " pdb=" CA LYS A 59 " ideal model delta sigma weight residual 1.458 1.544 -0.086 1.90e-02 2.77e+03 2.06e+01 ... (remaining 468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 401 2.44 - 4.87: 178 4.87 - 7.30: 38 7.30 - 9.73: 19 9.73 - 12.16: 2 Bond angle restraints: 638 Sorted by residual: angle pdb=" N LYS A 39 " pdb=" CA LYS A 39 " pdb=" CB LYS A 39 " ideal model delta sigma weight residual 110.50 118.34 -7.84 1.70e+00 3.46e-01 2.13e+01 angle pdb=" C ASN A 38 " pdb=" N LYS A 39 " pdb=" CA LYS A 39 " ideal model delta sigma weight residual 121.70 114.03 7.67 1.80e+00 3.09e-01 1.82e+01 angle pdb=" O LYS A 18 " pdb=" C LYS A 18 " pdb=" N GLY A 19 " ideal model delta sigma weight residual 123.00 129.78 -6.78 1.60e+00 3.91e-01 1.80e+01 angle pdb=" CA LYS A 18 " pdb=" CB LYS A 18 " pdb=" CG LYS A 18 " ideal model delta sigma weight residual 114.10 122.44 -8.34 2.00e+00 2.50e-01 1.74e+01 angle pdb=" C GLU A 22 " pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta sigma weight residual 121.70 114.22 7.48 1.80e+00 3.09e-01 1.73e+01 ... (remaining 633 not shown) Histogram of dihedral angle deviations from ideal: 0.16 - 11.82: 92 11.82 - 23.49: 33 23.49 - 35.15: 24 35.15 - 46.81: 14 46.81 - 58.47: 14 Dihedral angle restraints: 177 sinusoidal: 118 harmonic: 59 Sorted by residual: dihedral pdb=" CA ALA A 11 " pdb=" C ALA A 11 " pdb=" N LEU A 12 " pdb=" CA LEU A 12 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+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 -24.17 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA LEU A 61 " pdb=" C LEU A 61 " pdb=" N ASP A 62 " pdb=" CA ASP A 62 " ideal model delta harmonic sigma weight residual 180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 174 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.094: 33 0.094 - 0.186: 23 0.186 - 0.278: 8 0.278 - 0.370: 4 0.370 - 0.462: 3 Chirality restraints: 71 Sorted by residual: chirality pdb=" CB VAL A 53 " pdb=" CA VAL A 53 " pdb=" CG1 VAL A 53 " pdb=" CG2 VAL A 53 " both_signs ideal model delta sigma weight residual True 2.63 -2.17 0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA ASP A 29 " pdb=" N ASP A 29 " pdb=" C ASP A 29 " pdb=" CB ASP A 29 " both_signs ideal model delta sigma weight residual False 2.50 2.07 0.43 2.00e-01 2.50e+01 4.68e+00 chirality pdb=" CG LEU A 34 " pdb=" CB LEU A 34 " pdb=" CD1 LEU A 34 " pdb=" CD2 LEU A 34 " both_signs ideal model delta sigma weight residual True 2.59 -2.17 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 68 not shown) Planarity restraints: 79 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 49 " 0.057 2.00e-02 2.50e+03 4.83e-02 2.91e+01 pdb=" NE ARG A 49 " -0.074 2.00e-02 2.50e+03 pdb=" CZ ARG A 49 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 49 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 49 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 41 " 0.028 2.00e-02 2.50e+03 3.07e-02 2.36e+01 pdb=" CG TRP A 41 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 41 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A 41 " 0.045 2.00e-02 2.50e+03 pdb=" NE1 TRP A 41 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP A 41 " -0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 41 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 41 " 0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 41 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP A 41 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 57 " -0.011 2.00e-02 2.50e+03 3.11e-02 1.94e+01 pdb=" CG TYR A 57 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 57 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR A 57 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 57 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 57 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 57 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 57 " 0.013 2.00e-02 2.50e+03 ... (remaining 76 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 23 2.64 - 3.21: 348 3.21 - 3.77: 609 3.77 - 4.34: 718 4.34 - 4.90: 1188 Nonbonded interactions: 2886 Sorted by model distance: nonbonded pdb=" OD2 ASP A 29 " pdb=" OG1 THR A 37 " model vdw sym.op. 2.076 2.440 -x-1/2,y+1/2,-z+1/4 nonbonded pdb=" OD1 ASP A 29 " pdb=" ND2 ASN A 38 " model vdw sym.op. 2.261 2.520 -x-1/2,y+1/2,-z+1/4 nonbonded pdb=" ND2 ASN A 38 " pdb=" OD1 ASP A 29 " model vdw sym.op. 2.261 2.520 -x-1/2,y-1/2,-z+1/4 nonbonded pdb=" N ASP A 14 " pdb=" OD2 ASP A 14 " model vdw 2.397 2.520 nonbonded pdb=" N ASP A 48 " pdb=" N ARG A 49 " model vdw 2.434 2.560 ... (remaining 2881 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 -0.130 -0.130 0.046 OUTLIER none AGLU7 -0.337 -0.289 -0.224 OUTLIER none ALEU8 -0.114 -0.103 -0.116 mt none AVAL9 -0.210 -0.200 -0.246 m none ALEU10 -0.169 -0.146 -0.198 tp none AALA11 0.171 0.171 None EXCEPTION none ALEU12 0.141 0.131 0.193 tp none ATYR13 -0.005 0.094 -0.125 m-85 none AASP14 0.054 0.054 -0.036 OUTLIER none ATYR15 0.175 0.189 0.103 OUTLIER none AGLN16 0.076 0.073 0.029 mt-30 none AGLU17 0.116 0.117 0.256 OUTLIER none ALYS18 0.020 -0.157 0.311 ttpp none AGLY19 -0.051 -0.051 None None none AASP20 0.049 0.003 0.095 p30 none ASER21 -0.211 -0.206 0.054 m none AGLU22 -0.279 -0.278 -0.148 mp0 none AVAL23 -0.151 -0.038 -0.075 p none ATHR24 -0.028 0.057 -0.134 m none AMET25 -0.215 -0.251 -0.189 mtm none ALYS26 0.040 0.023 -0.033 OUTLIER none ALYS27 0.033 0.000 0.093 tttp none AGLY28 -0.174 -0.174 None None none AASP29 -0.134 -0.113 -0.287 OUTLIER none AILE30 -0.005 -0.046 0.094 OUTLIER none ALEU31 0.147 0.169 -0.019 OUTLIER none ATHR32 0.034 0.061 -0.203 OUTLIER none ALEU33 0.003 0.012 0.022 OUTLIER none ALEU34 -0.118 -0.119 -0.083 OUTLIER none AASN35 -0.110 -0.117 -0.013 p30 none ASER36 -0.088 -0.144 -0.090 p none ATHR37 -0.202 -0.189 -0.146 p none AASN38 0.013 -0.015 0.217 t-20 none ALYS39 -0.065 -0.071 -0.140 OUTLIER none AASP40 0.099 0.050 0.239 OUTLIER none ATRP41 0.034 0.051 -0.030 OUTLIER none ATRP42 0.015 -0.033 0.079 m0 none ALYS43 -0.072 -0.112 0.067 OUTLIER none AVAL44 0.120 0.119 0.205 m none AGLU45 -0.018 0.051 -0.210 tt0 none AVAL46 0.028 -0.020 0.265 t none AASN47 0.273 0.311 0.170 m120 none AASP48 0.263 0.280 0.160 t0 none AARG49 0.079 0.032 0.198 OUTLIER none AGLN50 -0.133 -0.181 -0.121 pt20 none AGLY51 -0.263 -0.263 None None none APHE52 -0.130 -0.202 -0.026 m-85 none AVAL53 -0.060 -0.077 -0.094 OUTLIER none APRO54 0.027 0.050 -0.295 Cg_exo none AALA55 0.251 0.251 None EXCEPTION none AALA56 0.341 0.341 None EXCEPTION none ATYR57 -0.029 0.077 -0.191 m-85 none AVAL58 0.041 0.154 -0.189 OUTLIER none ALYS59 -0.088 -0.120 0.036 pmtp? none ALYS60 -0.058 -0.042 0.135 mmtp none ALEU61 -0.180 -0.240 0.037 tp none AASP62 -0.198 -0.221 -0.138 t70 none ------------------------------------------------------------------------------- Start info (overall) ******************** Map CC (whole unit cell): 0.007 Map CC (around atoms): -0.011 rmsd (bonds): 0.0400 rmsd (angles): 3.00 Dist. moved from start: 0.000 Dist. moved from previous: 0.000 All-atom clashscore 10.73 Ramachandran plot: outliers: 9.09 % allowed: 27.27 % favored: 63.64 % Rotamer outliers: 37.25 % C-beta deviations: 0 ------------------------------------------------------------------------------- Set refinery object ******************* ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.073 Map CC (around atoms): 0.097 rmsd (bonds): 0.0637 rmsd (angles): 4.49 Dist. moved from start: 0.925 Dist. moved from previous: 0.925 All-atom clashscore 89.62 Ramachandran plot: outliers: 12.73 % allowed: 29.09 % favored: 58.18 % Rotamer outliers: 37.25 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.109 Map CC (around atoms): 0.152 rmsd (bonds): 0.0844 rmsd (angles): 6.11 Dist. moved from start: 1.526 Dist. moved from previous: 0.660 All-atom clashscore 232.20 Ramachandran plot: outliers: 14.55 % allowed: 29.09 % favored: 56.36 % Rotamer outliers: 37.25 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.109 Map CC (around atoms): 0.149 rmsd (bonds): 0.0982 rmsd (angles): 7.17 Dist. moved from start: 1.807 Dist. moved from previous: 0.408 All-atom clashscore 261.83 Ramachandran plot: outliers: 20.00 % allowed: 29.09 % favored: 50.91 % Rotamer outliers: 37.25 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.103 Map CC (around atoms): 0.139 rmsd (bonds): 0.1099 rmsd (angles): 8.45 Dist. moved from start: 2.042 Dist. moved from previous: 0.327 All-atom clashscore 255.25 Ramachandran plot: outliers: 25.45 % allowed: 23.64 % favored: 50.91 % Rotamer outliers: 39.22 % C-beta deviations: 1 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.098 Map CC (around atoms): 0.133 rmsd (bonds): 0.1229 rmsd (angles): 10.32 Dist. moved from start: 2.167 Dist. moved from previous: 0.246 All-atom clashscore 317.07 Ramachandran plot: outliers: 25.45 % allowed: 25.45 % favored: 49.09 % Rotamer outliers: 39.22 % C-beta deviations: 1 ------------------------------------------------------------------------------- Local refinement **************** Map CC (whole unit cell): 0.166 Map CC (around atoms): 0.252 rmsd (bonds): 0.1232 rmsd (angles): 11.04 Dist. moved from start: 2.628 Dist. moved from previous: 0.030 All-atom clashscore 378.35 Ramachandran plot: outliers: 30.91 % allowed: 25.45 % favored: 43.64 % Rotamer outliers: 9.80 % C-beta deviations: 1 ------------------------------------------------------------------------------- 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: (-0.14228160051460406, -0.07082944528909693, 0.010216407111444241) site_special_frac: (-0.1065555229018505, -0.1065555229018505, 0.0) distance_moved: 2.33841