------------------------------------------------------------------------------- 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_723 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: 0.88, per 1000 atoms: 1.89 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 - 1.30: 89 1.30 - 1.44: 129 1.44 - 1.58: 235 1.58 - 1.72: 18 1.72 - 1.85: 2 Bond restraints: 473 Sorted by residual: bond pdb=" CE LYS A 39 " pdb=" NZ LYS A 39 " ideal model delta sigma weight residual 1.489 1.629 -0.140 3.00e-02 1.11e+03 2.18e+01 bond pdb=" CA GLU A 22 " pdb=" C GLU A 22 " ideal model delta sigma weight residual 1.525 1.427 0.098 2.10e-02 2.27e+03 2.17e+01 bond pdb=" CA SER A 21 " pdb=" C SER A 21 " ideal model delta sigma weight residual 1.525 1.437 0.088 2.10e-02 2.27e+03 1.75e+01 bond pdb=" CA ASP A 40 " pdb=" CB ASP A 40 " ideal model delta sigma weight residual 1.530 1.451 0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C LEU A 10 " pdb=" N ALA A 11 " ideal model delta sigma weight residual 1.329 1.274 0.055 1.40e-02 5.10e+03 1.54e+01 ... (remaining 468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 468 3.22 - 6.44: 143 6.44 - 9.66: 22 9.66 - 12.88: 3 12.88 - 16.10: 2 Bond angle restraints: 638 Sorted by residual: angle pdb=" CB LEU A 34 " pdb=" CG LEU A 34 " pdb=" CD1 LEU A 34 " ideal model delta sigma weight residual 110.70 96.44 14.26 3.00e+00 1.11e-01 2.26e+01 angle pdb=" CA LEU A 61 " pdb=" CB LEU A 61 " pdb=" CG LEU A 61 " ideal model delta sigma weight residual 116.30 132.40 -16.10 3.50e+00 8.16e-02 2.12e+01 angle pdb=" CA VAL A 46 " pdb=" CB VAL A 46 " pdb=" CG2 VAL A 46 " ideal model delta sigma weight residual 110.40 103.90 6.50 1.70e+00 3.46e-01 1.46e+01 angle pdb=" CA VAL A 44 " pdb=" CB VAL A 44 " pdb=" CG2 VAL A 44 " ideal model delta sigma weight residual 110.40 116.82 -6.42 1.70e+00 3.46e-01 1.43e+01 angle pdb=" CA LYS A 27 " pdb=" CB LYS A 27 " pdb=" CG LYS A 27 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 ... (remaining 633 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.75: 111 15.75 - 31.49: 31 31.49 - 47.24: 19 47.24 - 62.98: 14 62.98 - 78.72: 2 Dihedral angle restraints: 177 sinusoidal: 118 harmonic: 59 Sorted by residual: dihedral pdb=" N ASP A 29 " pdb=" CA ASP A 29 " pdb=" CB ASP A 29 " pdb=" CG ASP A 29 " ideal model delta sinusoidal sigma weight residual 180.00 -119.73 59.73 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG LYS A 43 " pdb=" CD LYS A 43 " pdb=" CE LYS A 43 " pdb=" NZ LYS A 43 " ideal model delta sinusoidal sigma weight residual 180.00 -121.36 -58.64 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N GLU A 17 " pdb=" CA GLU A 17 " pdb=" CB GLU A 17 " pdb=" CG GLU A 17 " ideal model delta sinusoidal sigma weight residual 180.00 1.49 58.51 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 174 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.088: 31 0.088 - 0.169: 17 0.169 - 0.250: 13 0.250 - 0.331: 6 0.331 - 0.413: 4 Chirality restraints: 71 Sorted by residual: 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 -3.00 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CB THR A 37 " pdb=" CA THR A 37 " pdb=" OG1 THR A 37 " pdb=" CG2 THR A 37 " both_signs ideal model delta sigma weight residual False 2.55 2.15 0.40 2.00e-01 2.50e+01 3.98e+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 -2.22 0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 68 not shown) Planarity restraints: 79 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 49 " -0.041 2.00e-02 2.50e+03 3.85e-02 1.85e+01 pdb=" NE ARG A 49 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 49 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG A 49 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 49 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 15 " 0.031 2.00e-02 2.50e+03 2.97e-02 1.77e+01 pdb=" CG TYR A 15 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 15 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A 15 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 15 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 15 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 15 " 0.055 2.00e-02 2.50e+03 pdb=" OH TYR A 15 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 22 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" CD GLU A 22 " -0.065 2.00e-02 2.50e+03 pdb=" OE1 GLU A 22 " 0.023 2.00e-02 2.50e+03 pdb=" OE2 GLU A 22 " 0.025 2.00e-02 2.50e+03 ... (remaining 76 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 69 2.73 - 3.27: 320 3.27 - 3.81: 641 3.81 - 4.36: 697 4.36 - 4.90: 1190 Nonbonded interactions: 2917 Sorted by model distance: nonbonded pdb=" O SER A 36 " pdb=" OG SER A 36 " model vdw 2.184 2.440 nonbonded pdb=" N LYS A 60 " pdb=" N LEU A 61 " model vdw 2.457 2.560 nonbonded pdb=" O VAL A 53 " pdb=" CA PRO A 54 " model vdw 2.498 2.776 nonbonded pdb=" O THR A 37 " pdb=" CB THR A 37 " model vdw 2.502 2.776 nonbonded pdb=" OG1 THR A 32 " pdb=" NE1 TRP A 41 " model vdw sym.op. 2.514 2.520 -x-1/2,y+1/2,-z+1/4 ... (remaining 2912 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 -0.128 -0.129 -0.113 mtmt none AGLU7 0.041 -0.027 0.228 mt-10 none ALEU8 0.168 0.252 -0.020 mt none AVAL9 -0.113 -0.060 -0.069 m none ALEU10 -0.121 -0.093 -0.324 OUTLIER none AALA11 -0.025 -0.025 None EXCEPTION none ALEU12 0.058 0.065 0.292 OUTLIER none ATYR13 0.097 0.250 -0.090 m-85 none AASP14 0.282 0.354 0.030 t0 none ATYR15 0.044 0.204 -0.156 OUTLIER none AGLN16 0.142 0.233 -0.110 OUTLIER none AGLU17 0.098 0.033 0.168 OUTLIER none ALYS18 0.028 0.140 -0.214 OUTLIER none AGLY19 -0.092 -0.092 None None none AASP20 -0.048 0.033 -0.029 m-20 none ASER21 -0.078 -0.061 -0.420 p none AGLU22 -0.099 -0.023 -0.161 mt-10 none AVAL23 -0.153 -0.071 -0.091 OUTLIER none ATHR24 -0.224 -0.199 -0.236 m none AMET25 -0.053 -0.183 0.005 OUTLIER none ALYS26 -0.009 0.010 0.083 mttt none ALYS27 -0.118 -0.069 0.000 OUTLIER none AGLY28 -0.120 -0.120 None None none AASP29 0.022 0.010 0.096 OUTLIER none AILE30 0.159 0.204 0.051 OUTLIER none ALEU31 0.117 0.177 -0.151 pp none ATHR32 -0.059 -0.083 -0.017 m none ALEU33 -0.242 -0.275 -0.075 tp none ALEU34 -0.109 -0.093 -0.171 mt none AASN35 -0.149 -0.199 0.117 m-20 none ASER36 -0.064 -0.082 0.290 p none ATHR37 -0.147 -0.166 -0.018 p none AASN38 0.081 0.071 0.127 OUTLIER none ALYS39 0.182 0.204 -0.156 OUTLIER none AASP40 0.145 0.142 0.082 t0 none ATRP41 0.153 0.244 0.088 OUTLIER none ATRP42 0.038 0.099 -0.043 m0 none ALYS43 0.267 0.296 0.072 tttt none AVAL44 0.517 0.516 0.410 m none AGLU45 0.205 0.253 0.120 pt-20 none AVAL46 0.018 -0.013 0.106 m none AASN47 0.223 0.260 -0.026 OUTLIER none AASP48 0.148 0.291 -0.220 m-20 none AARG49 0.096 0.176 -0.089 OUTLIER none AGLN50 0.149 0.162 0.061 mp0 none AGLY51 -0.200 -0.200 None None none APHE52 -0.152 -0.076 -0.323 m-30 none AVAL53 0.210 0.190 0.227 m none APRO54 0.079 0.090 0.035 Cg_exo none AALA55 0.349 0.349 None EXCEPTION none AALA56 0.344 0.344 None EXCEPTION none ATYR57 0.187 0.224 0.179 m-85 none AVAL58 0.015 0.037 -0.037 m none ALYS59 -0.109 -0.151 -0.107 ptpt none ALYS60 0.205 0.242 0.218 tmtt? none ALEU61 0.140 0.196 -0.110 OUTLIER none AASP62 0.321 0.311 0.479 m-20 none ------------------------------------------------------------------------------- Start info (overall) ******************** Map CC (whole unit cell): 0.027 Map CC (around atoms): 0.047 rmsd (bonds): 0.0344 rmsd (angles): 3.09 Dist. moved from start: 0.000 Dist. moved from previous: 0.000 All-atom clashscore 12.88 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): 0.069 Map CC (around atoms): 0.100 rmsd (bonds): 0.0602 rmsd (angles): 4.75 Dist. moved from start: 0.997 Dist. moved from previous: 0.997 All-atom clashscore 79.69 Ramachandran plot: outliers: 7.27 % allowed: 29.09 % favored: 63.64 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.100 Map CC (around atoms): 0.144 rmsd (bonds): 0.0870 rmsd (angles): 7.29 Dist. moved from start: 1.675 Dist. moved from previous: 0.755 All-atom clashscore 181.72 Ramachandran plot: outliers: 10.91 % allowed: 32.73 % favored: 56.36 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.102 Map CC (around atoms): 0.149 rmsd (bonds): 0.1068 rmsd (angles): 8.70 Dist. moved from start: 1.980 Dist. moved from previous: 0.471 All-atom clashscore 237.78 Ramachandran plot: outliers: 18.18 % allowed: 30.91 % favored: 50.91 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.103 Map CC (around atoms): 0.151 rmsd (bonds): 0.1210 rmsd (angles): 9.65 Dist. moved from start: 2.123 Dist. moved from previous: 0.347 All-atom clashscore 258.35 Ramachandran plot: outliers: 18.18 % allowed: 36.36 % favored: 45.45 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.111 Map CC (around atoms): 0.169 rmsd (bonds): 0.1250 rmsd (angles): 10.90 Dist. moved from start: 2.233 Dist. moved from previous: 0.397 All-atom clashscore 263.33 Ramachandran plot: outliers: 21.82 % allowed: 38.18 % favored: 40.00 % Rotamer outliers: 33.33 % C-beta deviations: 0 ------------------------------------------------------------------------------- Local refinement **************** Map CC (whole unit cell): 0.167 Map CC (around atoms): 0.257 rmsd (bonds): 0.1250 rmsd (angles): 12.72 Dist. moved from start: 2.703 Dist. moved from previous: 0.151 All-atom clashscore 243.55 Ramachandran plot: outliers: 32.73 % allowed: 36.36 % favored: 30.91 % Rotamer outliers: 11.76 % 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: (0.014897377298072254, -0.05535945911911829, -0.006468021076670346) site_special_frac: (-0.020231040910523017, -0.020231040910523017, 0.0) distance_moved: 2.1837