------------------------------------------------------------------------------- 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_856 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: 0.80, per 1000 atoms: 1.72 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: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 77 1.28 - 1.42: 109 1.42 - 1.56: 242 1.56 - 1.70: 43 1.70 - 1.84: 2 Bond restraints: 473 Sorted by residual: bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.555 -0.097 1.90e-02 2.77e+03 2.58e+01 bond pdb=" C PRO A 54 " pdb=" O PRO A 54 " ideal model delta sigma weight residual 1.231 1.329 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" CA SER A 36 " pdb=" CB SER A 36 " ideal model delta sigma weight residual 1.530 1.623 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C TRP A 42 " pdb=" O TRP A 42 " ideal model delta sigma weight residual 1.231 1.141 0.090 2.00e-02 2.50e+03 2.05e+01 bond pdb=" CG GLU A 7 " pdb=" CD GLU A 7 " ideal model delta sigma weight residual 1.516 1.618 -0.102 2.50e-02 1.60e+03 1.66e+01 ... (remaining 468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 452 2.88 - 5.76: 152 5.76 - 8.64: 26 8.64 - 11.51: 7 11.51 - 14.39: 1 Bond angle restraints: 638 Sorted by residual: angle pdb=" C ASP A 40 " pdb=" N TRP A 41 " pdb=" CA TRP A 41 " ideal model delta sigma weight residual 121.70 129.87 -8.17 1.80e+00 3.09e-01 2.06e+01 angle pdb=" CD LYS A 39 " pdb=" CE LYS A 39 " pdb=" NZ LYS A 39 " ideal model delta sigma weight residual 111.90 126.29 -14.39 3.20e+00 9.77e-02 2.02e+01 angle pdb=" C GLU A 17 " pdb=" N LYS A 18 " pdb=" CA LYS A 18 " ideal model delta sigma weight residual 121.70 114.17 7.53 1.80e+00 3.09e-01 1.75e+01 angle pdb=" CB ASP A 48 " pdb=" CG ASP A 48 " pdb=" OD2 ASP A 48 " ideal model delta sigma weight residual 118.40 108.90 9.50 2.30e+00 1.89e-01 1.71e+01 angle pdb=" CA LYS A 18 " pdb=" CB LYS A 18 " pdb=" CG LYS A 18 " ideal model delta sigma weight residual 114.10 122.29 -8.19 2.00e+00 2.50e-01 1.68e+01 ... (remaining 633 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.93: 113 16.93 - 33.85: 33 33.85 - 50.77: 18 50.77 - 67.69: 11 67.69 - 84.62: 2 Dihedral angle restraints: 177 sinusoidal: 118 harmonic: 59 Sorted by residual: dihedral pdb=" CA GLU A 7 " pdb=" C GLU A 7 " pdb=" N LEU A 8 " pdb=" CA LEU A 8 " ideal model delta harmonic sigma weight residual 180.00 -157.36 -22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA THR A 37 " pdb=" C THR A 37 " pdb=" N ASN A 38 " pdb=" CA ASN A 38 " ideal model delta harmonic sigma weight residual 180.00 -158.19 -21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ASP A 29 " pdb=" C ASP A 29 " pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 174 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.079: 31 0.079 - 0.153: 19 0.153 - 0.226: 14 0.226 - 0.299: 4 0.299 - 0.373: 3 Chirality restraints: 71 Sorted by residual: chirality pdb=" CA THR A 24 " pdb=" N THR A 24 " pdb=" C THR A 24 " pdb=" CB THR A 24 " both_signs ideal model delta sigma weight residual False 2.52 2.15 0.37 2.00e-01 2.50e+01 3.47e+00 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 -2.24 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA PRO A 54 " pdb=" N PRO A 54 " pdb=" C PRO A 54 " pdb=" CB PRO A 54 " both_signs ideal model delta sigma weight residual False 2.73 3.06 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 68 not shown) Planarity restraints: 79 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 39 " 0.024 2.00e-02 2.50e+03 4.81e-02 2.31e+01 pdb=" C LYS A 39 " -0.083 2.00e-02 2.50e+03 pdb=" O LYS A 39 " 0.031 2.00e-02 2.50e+03 pdb=" N ASP A 40 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 42 " 0.002 2.00e-02 2.50e+03 2.97e-02 2.21e+01 pdb=" CG TRP A 42 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 42 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TRP A 42 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 42 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP A 42 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP A 42 " -0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 42 " -0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 42 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 42 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 52 " 0.049 2.00e-02 2.50e+03 3.18e-02 1.77e+01 pdb=" CG PHE A 52 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 52 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 52 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 52 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 52 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 52 " 0.018 2.00e-02 2.50e+03 ... (remaining 76 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 92 2.77 - 3.30: 334 3.30 - 3.83: 649 3.83 - 4.37: 674 4.37 - 4.90: 1231 Nonbonded interactions: 2980 Sorted by model distance: nonbonded pdb=" N ASP A 14 " pdb=" OD1 ASP A 14 " model vdw 2.237 2.520 nonbonded pdb=" N GLY A 51 " pdb=" O GLY A 51 " model vdw 2.468 2.496 nonbonded pdb=" O LEU A 34 " pdb=" ND2 ASN A 35 " model vdw 2.531 2.520 nonbonded pdb=" CA ASP A 14 " pdb=" OD1 ASP A 14 " model vdw 2.545 2.776 nonbonded pdb=" N ALA A 56 " pdb=" N TYR A 57 " model vdw 2.552 2.560 ... (remaining 2975 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 -0.117 -0.046 -0.259 mttm none AGLU7 -0.316 -0.286 -0.395 OUTLIER none ALEU8 -0.106 -0.099 -0.069 OUTLIER none AVAL9 -0.047 -0.062 0.232 m none ALEU10 0.096 0.100 0.055 OUTLIER none AALA11 0.330 0.330 None EXCEPTION none ALEU12 0.342 0.313 0.468 mt none ATYR13 0.062 0.088 0.042 m-85 none AASP14 0.016 -0.058 0.326 OUTLIER none ATYR15 0.224 0.249 0.236 t80 none AGLN16 -0.028 -0.008 -0.254 mp0 none AGLU17 0.023 0.082 0.072 pt-20 none ALYS18 -0.064 -0.051 0.173 OUTLIER none AGLY19 0.072 0.072 None None none AASP20 0.038 0.131 -0.251 t0 none ASER21 0.184 0.200 0.626 t none AGLU22 -0.186 -0.046 -0.318 mt-10 none AVAL23 -0.186 -0.161 0.029 OUTLIER none ATHR24 -0.013 -0.065 -0.008 OUTLIER none AMET25 0.052 -0.089 0.154 ptt? none ALYS26 0.004 -0.002 -0.092 OUTLIER none ALYS27 -0.111 -0.053 -0.189 ttmt none AGLY28 -0.086 -0.086 None None none AASP29 0.016 -0.039 0.048 m-20 none AILE30 0.223 0.273 0.086 pt none ALEU31 0.328 0.436 -0.151 mt none ATHR32 0.185 0.214 0.143 OUTLIER none ALEU33 -0.047 -0.097 0.096 tp none ALEU34 -0.026 0.022 0.059 OUTLIER none AASN35 -0.009 -0.012 -0.019 m-80 none ASER36 0.100 0.112 -0.072 m none ATHR37 -0.065 -0.061 -0.226 m none AASN38 -0.020 -0.105 0.085 t-20 none ALYS39 0.023 0.011 0.024 tptp none AASP40 0.014 0.007 -0.065 m-20 none ATRP41 0.008 -0.042 0.069 OUTLIER none ATRP42 0.010 -0.028 0.116 m-90 none ALYS43 0.133 0.155 0.171 ptpt none AVAL44 0.029 0.041 0.082 m none AGLU45 0.063 -0.017 0.179 tt0 none AVAL46 -0.005 0.022 -0.001 t none AASN47 0.010 -0.065 0.145 m120 none AASP48 0.073 0.041 0.159 p30 none AARG49 0.212 0.257 0.214 ptp180 none AGLN50 0.019 -0.068 0.060 pt20 none AGLY51 -0.068 -0.068 None None none APHE52 -0.043 0.055 -0.248 m-85 none AVAL53 0.318 0.297 -0.012 m none APRO54 0.388 0.357 0.338 Cg_exo none AALA55 0.208 0.208 None EXCEPTION none AALA56 0.243 0.243 None EXCEPTION none ATYR57 0.166 0.263 0.064 OUTLIER none AVAL58 0.067 0.087 0.029 OUTLIER none ALYS59 0.115 0.107 0.262 tttp none ALYS60 0.105 0.299 -0.048 mttt none ALEU61 0.011 0.046 -0.141 OUTLIER none AASP62 0.005 0.074 -0.071 OUTLIER none ------------------------------------------------------------------------------- Start info (overall) ******************** Map CC (whole unit cell): 0.053 Map CC (around atoms): 0.064 rmsd (bonds): 0.0369 rmsd (angles): 2.97 Dist. moved from start: 0.000 Dist. moved from previous: 0.000 All-atom clashscore 13.95 Ramachandran plot: outliers: 5.45 % allowed: 27.27 % favored: 67.27 % Rotamer outliers: 29.41 % C-beta deviations: 0 ------------------------------------------------------------------------------- Set refinery object ******************* ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.093 Map CC (around atoms): 0.125 rmsd (bonds): 0.0589 rmsd (angles): 4.64 Dist. moved from start: 0.866 Dist. moved from previous: 0.866 All-atom clashscore 93.58 Ramachandran plot: outliers: 9.09 % allowed: 23.64 % favored: 67.27 % Rotamer outliers: 29.41 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.134 Map CC (around atoms): 0.198 rmsd (bonds): 0.0756 rmsd (angles): 6.51 Dist. moved from start: 1.479 Dist. moved from previous: 0.704 All-atom clashscore 164.11 Ramachandran plot: outliers: 9.09 % allowed: 27.27 % favored: 63.64 % Rotamer outliers: 29.41 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.137 Map CC (around atoms): 0.205 rmsd (bonds): 0.0926 rmsd (angles): 7.42 Dist. moved from start: 1.828 Dist. moved from previous: 0.426 All-atom clashscore 208.15 Ramachandran plot: outliers: 7.27 % allowed: 29.09 % favored: 63.64 % Rotamer outliers: 29.41 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.134 Map CC (around atoms): 0.200 rmsd (bonds): 0.1054 rmsd (angles): 8.00 Dist. moved from start: 2.052 Dist. moved from previous: 0.352 All-atom clashscore 230.43 Ramachandran plot: outliers: 10.91 % allowed: 30.91 % favored: 58.18 % Rotamer outliers: 29.41 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.129 Map CC (around atoms): 0.192 rmsd (bonds): 0.1162 rmsd (angles): 8.85 Dist. moved from start: 2.135 Dist. moved from previous: 0.206 All-atom clashscore 274.14 Ramachandran plot: outliers: 14.55 % allowed: 29.09 % favored: 56.36 % Rotamer outliers: 29.41 % C-beta deviations: 0 ------------------------------------------------------------------------------- Local refinement **************** Map CC (whole unit cell): 0.172 Map CC (around atoms): 0.268 rmsd (bonds): 0.1162 rmsd (angles): 9.67 Dist. moved from start: 2.495 Dist. moved from previous: 0.000 All-atom clashscore 220.00 Ramachandran plot: outliers: 14.55 % allowed: 30.91 % favored: 54.55 % Rotamer outliers: 17.65 % 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: (0.015257174817964667, 0.0738414962022828, -0.01830130776626122) site_special_frac: (0.04454933551012373, 0.04454933551012373, 0.0) distance_moved: 2.44915