------------------------------------------------------------------------------- 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_63 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: 1.03, per 1000 atoms: 2.22 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: 0.83 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: 79 1.29 - 1.42: 117 1.42 - 1.56: 225 1.56 - 1.69: 50 1.69 - 1.82: 2 Bond restraints: 473 Sorted by residual: bond pdb=" CG LEU A 10 " pdb=" CD2 LEU A 10 " ideal model delta sigma weight residual 1.521 1.337 0.184 3.30e-02 9.18e+02 3.10e+01 bond pdb=" CG ASP A 20 " pdb=" OD1 ASP A 20 " ideal model delta sigma weight residual 1.249 1.352 -0.103 1.90e-02 2.77e+03 2.97e+01 bond pdb=" CA SER A 36 " pdb=" C SER A 36 " ideal model delta sigma weight residual 1.525 1.635 -0.110 2.10e-02 2.27e+03 2.75e+01 bond pdb=" C SER A 21 " pdb=" O SER A 21 " ideal model delta sigma weight residual 1.231 1.333 -0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" CB LEU A 10 " pdb=" CG LEU A 10 " ideal model delta sigma weight residual 1.530 1.440 0.090 2.00e-02 2.50e+03 2.01e+01 ... (remaining 468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 368 2.28 - 4.55: 182 4.55 - 6.83: 59 6.83 - 9.10: 20 9.10 - 11.38: 9 Bond angle restraints: 638 Sorted by residual: angle pdb=" CA GLU A 7 " pdb=" CB GLU A 7 " pdb=" CG GLU A 7 " ideal model delta sigma weight residual 114.10 125.48 -11.38 2.00e+00 2.50e-01 3.24e+01 angle pdb=" N PRO A 54 " pdb=" CD PRO A 54 " pdb=" CG PRO A 54 " ideal model delta sigma weight residual 103.20 96.35 6.85 1.50e+00 4.44e-01 2.08e+01 angle pdb=" CA SER A 21 " pdb=" CB SER A 21 " pdb=" OG SER A 21 " ideal model delta sigma weight residual 111.10 119.96 -8.86 2.00e+00 2.50e-01 1.96e+01 angle pdb=" O ASN A 47 " pdb=" C ASN A 47 " pdb=" N ASP A 48 " ideal model delta sigma weight residual 123.00 116.05 6.95 1.60e+00 3.91e-01 1.88e+01 angle pdb=" CG1 VAL A 46 " pdb=" CB VAL A 46 " pdb=" CG2 VAL A 46 " ideal model delta sigma weight residual 110.80 101.42 9.38 2.20e+00 2.07e-01 1.82e+01 ... (remaining 633 not shown) Histogram of dihedral angle deviations from ideal: 0.09 - 15.38: 97 15.38 - 30.68: 50 30.68 - 45.97: 20 45.97 - 61.27: 8 61.27 - 76.56: 2 Dihedral angle restraints: 177 sinusoidal: 118 harmonic: 59 Sorted by residual: dihedral pdb=" CA THR A 32 " pdb=" C THR A 32 " pdb=" N LEU A 33 " pdb=" CA LEU A 33 " ideal model delta harmonic sigma weight residual 180.00 -150.85 -29.15 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA LYS A 39 " pdb=" C LYS A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta harmonic sigma weight residual 180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA ASP A 48 " pdb=" C ASP A 48 " pdb=" N ARG A 49 " pdb=" CA ARG A 49 " ideal model delta harmonic sigma weight residual 180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 174 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.143: 46 0.143 - 0.284: 17 0.284 - 0.426: 7 0.426 - 0.568: 0 0.568 - 0.709: 1 Chirality restraints: 71 Sorted by residual: chirality pdb=" CG LEU A 31 " pdb=" CB LEU A 31 " pdb=" CD1 LEU A 31 " pdb=" CD2 LEU A 31 " both_signs ideal model delta sigma weight residual True 2.59 -3.30 -0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CB VAL A 46 " pdb=" CA VAL A 46 " pdb=" CG1 VAL A 46 " pdb=" CG2 VAL A 46 " both_signs ideal model delta sigma weight residual True 2.63 -3.05 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA LEU A 12 " pdb=" N LEU A 12 " pdb=" C LEU A 12 " pdb=" CB LEU A 12 " both_signs ideal model delta sigma weight residual False 2.50 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 68 not shown) Planarity restraints: 79 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 14 " -0.024 2.00e-02 2.50e+03 5.05e-02 2.55e+01 pdb=" CG ASP A 14 " 0.087 2.00e-02 2.50e+03 pdb=" OD1 ASP A 14 " -0.032 2.00e-02 2.50e+03 pdb=" OD2 ASP A 14 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 41 " -0.022 2.00e-02 2.50e+03 3.11e-02 2.42e+01 pdb=" CG TRP A 41 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 41 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 41 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 41 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP A 41 " 0.053 2.00e-02 2.50e+03 pdb=" CE3 TRP A 41 " -0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 41 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 41 " 0.036 2.00e-02 2.50e+03 pdb=" CH2 TRP A 41 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 15 " -0.017 2.00e-02 2.50e+03 3.47e-02 2.41e+01 pdb=" CG TYR A 15 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 15 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 15 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR A 15 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR A 15 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A 15 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR A 15 " 0.033 2.00e-02 2.50e+03 ... (remaining 76 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 67 2.74 - 3.28: 346 3.28 - 3.82: 611 3.82 - 4.36: 685 4.36 - 4.90: 1161 Nonbonded interactions: 2870 Sorted by model distance: nonbonded pdb=" OE1 GLU A 7 " pdb=" NZ LYS A 60 " model vdw 2.200 2.520 nonbonded pdb=" N ASP A 20 " pdb=" OD2 ASP A 20 " model vdw 2.241 2.520 nonbonded pdb=" N LYS A 26 " pdb=" O LYS A 26 " model vdw 2.497 2.496 nonbonded pdb=" N ALA A 55 " pdb=" N ALA A 56 " model vdw 2.537 2.560 nonbonded pdb=" O ALA A 55 " pdb=" CA ALA A 56 " model vdw 2.590 2.776 ... (remaining 2865 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 -0.094 -0.034 -0.225 OUTLIER none AGLU7 -0.094 -0.162 0.101 mt-10 none ALEU8 -0.154 -0.146 -0.210 OUTLIER none AVAL9 -0.159 -0.116 -0.192 OUTLIER none ALEU10 0.133 0.176 -0.026 tp none AALA11 0.393 0.393 None EXCEPTION none ALEU12 0.040 0.072 -0.062 OUTLIER none ATYR13 -0.021 0.015 -0.084 m-85 none AASP14 0.003 0.029 -0.056 m-20 none ATYR15 0.009 0.089 -0.103 t80 none AGLN16 0.098 0.118 0.123 tp60 none AGLU17 0.145 0.039 0.411 OUTLIER none ALYS18 -0.050 0.111 -0.010 mttm none AGLY19 -0.272 -0.272 None None none AASP20 -0.157 -0.111 -0.424 OUTLIER none ASER21 -0.053 -0.138 0.251 t none AGLU22 -0.149 -0.244 0.051 pm0 none AVAL23 -0.217 -0.231 -0.119 OUTLIER none ATHR24 -0.054 -0.010 -0.307 m none AMET25 0.011 -0.087 0.093 mmt none ALYS26 0.056 0.080 0.108 OUTLIER none ALYS27 0.048 0.099 0.202 ttpt none AGLY28 -0.043 -0.043 None None none AASP29 -0.009 -0.022 0.075 t0 none AILE30 0.245 0.245 0.178 mm none ALEU31 0.320 0.430 -0.039 OUTLIER none ATHR32 0.123 0.117 0.097 m none ALEU33 -0.085 -0.125 0.112 mt none ALEU34 -0.126 -0.112 -0.099 OUTLIER none AASN35 -0.041 0.014 -0.109 p30 none ASER36 0.078 0.069 0.104 p none ATHR37 0.037 0.099 -0.075 m none AASN38 -0.083 -0.136 0.032 t-20 none ALYS39 -0.161 -0.190 -0.015 OUTLIER none AASP40 0.002 -0.057 0.101 t70 none ATRP41 -0.080 -0.045 -0.119 m95 none ATRP42 -0.158 -0.132 -0.163 m0 none ALYS43 0.015 -0.045 0.305 tttp none AVAL44 -0.042 -0.057 0.030 m none AGLU45 0.001 -0.048 0.110 mt-10 none AVAL46 -0.219 -0.225 -0.169 t none AASN47 0.007 -0.031 0.013 m-20 none AASP48 -0.034 -0.032 -0.078 t0 none AARG49 -0.022 -0.003 0.035 mmt-85 none AGLN50 -0.022 -0.057 -0.062 mt-30 none AGLY51 -0.417 -0.417 None None none APHE52 -0.102 -0.093 -0.089 OUTLIER none AVAL53 0.335 0.333 0.201 m none APRO54 0.302 0.368 0.297 Cg_exo none AALA55 0.269 0.269 None EXCEPTION none AALA56 0.397 0.397 None EXCEPTION none ATYR57 0.127 0.082 0.107 m-85 none AVAL58 0.033 0.149 0.010 t none ALYS59 -0.013 -0.037 0.080 pttt none ALYS60 -0.043 0.019 -0.066 OUTLIER none ALEU61 -0.176 -0.092 -0.301 OUTLIER none AASP62 -0.066 -0.139 0.131 t0 none ------------------------------------------------------------------------------- Start info (overall) ******************** Map CC (whole unit cell): 0.006 Map CC (around atoms): 0.006 rmsd (bonds): 0.0381 rmsd (angles): 3.20 Dist. moved from start: 0.000 Dist. moved from previous: 0.000 All-atom clashscore 8.58 Ramachandran plot: outliers: 7.27 % allowed: 23.64 % favored: 69.09 % Rotamer outliers: 27.45 % C-beta deviations: 0 ------------------------------------------------------------------------------- Set refinery object ******************* ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.070 Map CC (around atoms): 0.103 rmsd (bonds): 0.0695 rmsd (angles): 4.72 Dist. moved from start: 1.092 Dist. moved from previous: 1.092 All-atom clashscore 99.34 Ramachandran plot: outliers: 16.36 % allowed: 16.36 % favored: 67.27 % Rotamer outliers: 27.45 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.104 Map CC (around atoms): 0.148 rmsd (bonds): 0.0935 rmsd (angles): 6.31 Dist. moved from start: 1.659 Dist. moved from previous: 0.740 All-atom clashscore 184.90 Ramachandran plot: outliers: 12.73 % allowed: 20.00 % favored: 67.27 % Rotamer outliers: 27.45 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.114 Map CC (around atoms): 0.161 rmsd (bonds): 0.1160 rmsd (angles): 7.50 Dist. moved from start: 1.948 Dist. moved from previous: 0.427 All-atom clashscore 216.48 Ramachandran plot: outliers: 12.73 % allowed: 21.82 % favored: 65.45 % Rotamer outliers: 27.45 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.111 Map CC (around atoms): 0.156 rmsd (bonds): 0.1373 rmsd (angles): 8.28 Dist. moved from start: 2.143 Dist. moved from previous: 0.322 All-atom clashscore 258.03 Ramachandran plot: outliers: 18.18 % allowed: 21.82 % favored: 60.00 % Rotamer outliers: 27.45 % C-beta deviations: 0 ------------------------------------------------------------------------------- Morphing ******** Map CC (whole unit cell): 0.104 Map CC (around atoms): 0.148 rmsd (bonds): 0.1546 rmsd (angles): 9.14 Dist. moved from start: 2.337 Dist. moved from previous: 0.328 All-atom clashscore 323.73 Ramachandran plot: outliers: 18.18 % allowed: 27.27 % favored: 54.55 % Rotamer outliers: 27.45 % C-beta deviations: 0 ------------------------------------------------------------------------------- Local refinement **************** Map CC (whole unit cell): 0.165 Map CC (around atoms): 0.249 rmsd (bonds): 0.1546 rmsd (angles): 10.88 Dist. moved from start: 2.691 Dist. moved from previous: 0.064 All-atom clashscore 375.00 Ramachandran plot: outliers: 27.27 % allowed: 23.64 % favored: 49.09 % 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: (-0.15477106798182527, -0.09965976314862807, 0.01145795302078807) site_special_frac: (-0.12721541556522667, -0.12721541556522667, 0.0) distance_moved: 1.96467