Starting phenix.real_space_refine on Sat Aug 23 10:21:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r0c_4692/08_2025/6r0c_4692.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r0c_4692/08_2025/6r0c_4692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r0c_4692/08_2025/6r0c_4692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r0c_4692/08_2025/6r0c_4692.map" model { file = "/net/cci-nas-00/data/ceres_data/6r0c_4692/08_2025/6r0c_4692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r0c_4692/08_2025/6r0c_4692.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 284 5.49 5 S 10 5.16 5 C 6504 2.51 5 N 2186 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11737 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 793 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "G" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 807 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2887 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "J" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2935 Classifications: {'DNA': 142} Link IDs: {'rna3p': 141} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.59, per 1000 atoms: 0.22 Number of scatterers: 11737 At special positions: 0 Unit cell: (118.81, 77.39, 117.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 10 16.00 P 284 15.00 O 2752 8.00 N 2186 7.00 C 6504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 326.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1390 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 74.6% alpha, 1.9% beta 137 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.690A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.549A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.624A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.767A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.582A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.290A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 4.095A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 3.595A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 removed outlier: 3.548A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.614A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 116 " --> pdb=" O ALA C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.844A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.749A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.611A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.614A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.580A pdb=" N ILE E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.573A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.970A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG F 36 " --> pdb=" O PRO F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.233A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.744A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 removed outlier: 3.812A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.752A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.545A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 112 through 116' Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.843A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.748A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.612A pdb=" N SER H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.865A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.734A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.059A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.134A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.561A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 375 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 334 hydrogen bonds 652 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1985 1.33 - 1.45: 4170 1.45 - 1.56: 5783 1.56 - 1.68: 566 1.68 - 1.80: 18 Bond restraints: 12522 Sorted by residual: bond pdb=" C4' DT J -19 " pdb=" O4' DT J -19 " ideal model delta sigma weight residual 1.450 1.537 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C4' DC J -18 " pdb=" O4' DC J -18 " ideal model delta sigma weight residual 1.450 1.526 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C4' DC J -8 " pdb=" O4' DC J -8 " ideal model delta sigma weight residual 1.450 1.511 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C3' DT J 52 " pdb=" O3' DT J 52 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.08e+00 bond pdb=" C3' DA I 47 " pdb=" O3' DA I 47 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.73e+00 ... (remaining 12517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 17080 1.75 - 3.50: 945 3.50 - 5.25: 86 5.25 - 7.00: 15 7.00 - 8.75: 5 Bond angle restraints: 18131 Sorted by residual: angle pdb=" C5' DC J -8 " pdb=" C4' DC J -8 " pdb=" O4' DC J -8 " ideal model delta sigma weight residual 109.40 102.57 6.83 1.50e+00 4.44e-01 2.07e+01 angle pdb=" C3' DA I 47 " pdb=" O3' DA I 47 " pdb=" P DG I 48 " ideal model delta sigma weight residual 120.20 126.04 -5.84 1.50e+00 4.44e-01 1.51e+01 angle pdb=" C5' DT J -20 " pdb=" C4' DT J -20 " pdb=" O4' DT J -20 " ideal model delta sigma weight residual 109.40 103.88 5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C3' DT J 52 " pdb=" O3' DT J 52 " pdb=" P DC J 53 " ideal model delta sigma weight residual 120.20 125.72 -5.52 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C4' DT J -19 " pdb=" O4' DT J -19 " pdb=" C1' DT J -19 " ideal model delta sigma weight residual 109.70 104.19 5.51 1.50e+00 4.44e-01 1.35e+01 ... (remaining 18126 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 5475 35.81 - 71.63: 1353 71.63 - 107.44: 12 107.44 - 143.25: 0 143.25 - 179.07: 6 Dihedral angle restraints: 6846 sinusoidal: 4687 harmonic: 2159 Sorted by residual: dihedral pdb=" CA PHE A 84 " pdb=" C PHE A 84 " pdb=" N GLN A 85 " pdb=" CA GLN A 85 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA ASN B 64 " pdb=" C ASN B 64 " pdb=" N VAL B 65 " pdb=" CA VAL B 65 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ILE B 50 " pdb=" C ILE B 50 " pdb=" N TYR B 51 " pdb=" CA TYR B 51 " ideal model delta harmonic sigma weight residual -180.00 -157.73 -22.27 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 6843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1616 0.054 - 0.107: 379 0.107 - 0.161: 57 0.161 - 0.214: 9 0.214 - 0.268: 4 Chirality restraints: 2065 Sorted by residual: chirality pdb=" C4' DT J -19 " pdb=" C5' DT J -19 " pdb=" O4' DT J -19 " pdb=" C3' DT J -19 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C4' DC J -8 " pdb=" C5' DC J -8 " pdb=" O4' DC J -8 " pdb=" C3' DC J -8 " both_signs ideal model delta sigma weight residual False -2.53 -2.78 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C4' DC J -18 " pdb=" C5' DC J -18 " pdb=" O4' DC J -18 " pdb=" C3' DC J -18 " both_signs ideal model delta sigma weight residual False -2.53 -2.77 0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2062 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.52e+01 pdb=" C GLU B 63 " -0.067 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 60 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.43e+00 pdb=" C VAL B 60 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL B 60 " 0.018 2.00e-02 2.50e+03 pdb=" N PHE B 61 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 57 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.02e+00 pdb=" C VAL B 57 " 0.046 2.00e-02 2.50e+03 pdb=" O VAL B 57 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU B 58 " -0.015 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 33 2.50 - 3.10: 7576 3.10 - 3.70: 19941 3.70 - 4.30: 28089 4.30 - 4.90: 40773 Nonbonded interactions: 96412 Sorted by model distance: nonbonded pdb=" O2 DC I 42 " pdb=" N2 DG J -42 " model vdw 1.900 2.496 nonbonded pdb=" O2 DC I 37 " pdb=" N2 DG J -37 " model vdw 2.083 2.496 nonbonded pdb=" N3 DC I 42 " pdb=" N1 DG J -42 " model vdw 2.204 2.560 nonbonded pdb=" N3 DC I 37 " pdb=" N1 DG J -37 " model vdw 2.251 2.560 nonbonded pdb=" N2 DG I -2 " pdb=" O2 DC J 2 " model vdw 2.275 2.496 ... (remaining 96407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 100) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.570 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 12522 Z= 0.336 Angle : 0.865 8.749 18131 Z= 0.511 Chirality : 0.048 0.268 2065 Planarity : 0.007 0.051 1312 Dihedral : 27.863 179.067 5456 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.35 (0.26), residues: 731 helix: -1.06 (0.18), residues: 523 sheet: None (None), residues: 0 loop : -2.54 (0.38), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 63 TYR 0.019 0.002 TYR F 51 PHE 0.026 0.002 PHE E 104 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00758 (12522) covalent geometry : angle 0.86468 (18131) hydrogen bonds : bond 0.16245 ( 709) hydrogen bonds : angle 5.12258 ( 1771) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.9551 (p) cc_final: 0.9258 (t) REVERT: A 93 GLN cc_start: 0.8725 (tt0) cc_final: 0.8077 (tt0) REVERT: A 94 GLU cc_start: 0.8173 (tp30) cc_final: 0.7776 (tp30) REVERT: A 97 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7909 (mt-10) REVERT: B 34 ILE cc_start: 0.9750 (mt) cc_final: 0.9543 (mm) REVERT: B 58 LEU cc_start: 0.9571 (tp) cc_final: 0.9182 (tt) REVERT: B 88 TYR cc_start: 0.8697 (m-10) cc_final: 0.8395 (m-10) REVERT: C 84 GLN cc_start: 0.9271 (tp40) cc_final: 0.8894 (tp40) REVERT: C 111 ILE cc_start: 0.9037 (mm) cc_final: 0.8688 (tp) REVERT: E 58 THR cc_start: 0.9359 (p) cc_final: 0.9124 (t) REVERT: E 93 GLN cc_start: 0.8507 (tt0) cc_final: 0.8298 (tt0) REVERT: E 107 THR cc_start: 0.9633 (m) cc_final: 0.9369 (p) REVERT: F 43 VAL cc_start: 0.9509 (t) cc_final: 0.9283 (p) REVERT: F 88 TYR cc_start: 0.9076 (m-10) cc_final: 0.7956 (m-10) REVERT: G 84 GLN cc_start: 0.9249 (tp40) cc_final: 0.8931 (tp-100) REVERT: H 42 LEU cc_start: 0.9325 (tp) cc_final: 0.9087 (tp) REVERT: H 49 THR cc_start: 0.8357 (p) cc_final: 0.8059 (p) REVERT: H 79 HIS cc_start: 0.8519 (t70) cc_final: 0.8296 (t70) REVERT: H 80 TYR cc_start: 0.8270 (m-10) cc_final: 0.8039 (m-10) REVERT: H 90 GLU cc_start: 0.9123 (mp0) cc_final: 0.8905 (mp0) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.1596 time to fit residues: 63.8762 Evaluate side-chains 183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.3980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN E 68 GLN E 85 GLN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.057903 restraints weight = 40643.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.059084 restraints weight = 24785.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.059829 restraints weight = 18544.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060252 restraints weight = 15858.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060462 restraints weight = 14616.756| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12522 Z= 0.167 Angle : 0.634 9.994 18131 Z= 0.377 Chirality : 0.037 0.283 2065 Planarity : 0.005 0.035 1312 Dihedral : 31.515 178.426 3991 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.30), residues: 731 helix: 1.04 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -2.19 (0.39), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 42 TYR 0.015 0.001 TYR F 51 PHE 0.009 0.001 PHE H 62 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00353 (12522) covalent geometry : angle 0.63384 (18131) hydrogen bonds : bond 0.06238 ( 709) hydrogen bonds : angle 2.87844 ( 1771) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8772 (tttt) cc_final: 0.8563 (tttm) REVERT: A 93 GLN cc_start: 0.8954 (tt0) cc_final: 0.8425 (tt0) REVERT: A 94 GLU cc_start: 0.8307 (tp30) cc_final: 0.7774 (tp30) REVERT: A 97 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 120 MET cc_start: 0.9125 (mtt) cc_final: 0.8859 (mtp) REVERT: A 133 GLU cc_start: 0.8081 (pm20) cc_final: 0.7378 (pp20) REVERT: C 78 ILE cc_start: 0.8543 (mm) cc_final: 0.8324 (mm) REVERT: C 84 GLN cc_start: 0.9424 (tp40) cc_final: 0.8929 (tp40) REVERT: C 110 ASN cc_start: 0.8888 (t0) cc_final: 0.8445 (p0) REVERT: D 44 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8570 (tm-30) REVERT: D 68 GLU cc_start: 0.8395 (tp30) cc_final: 0.8152 (tp30) REVERT: E 107 THR cc_start: 0.9634 (m) cc_final: 0.9407 (p) REVERT: F 43 VAL cc_start: 0.9359 (t) cc_final: 0.8971 (p) REVERT: F 88 TYR cc_start: 0.8845 (m-10) cc_final: 0.8376 (m-10) REVERT: F 96 THR cc_start: 0.9393 (m) cc_final: 0.8775 (p) REVERT: G 56 GLU cc_start: 0.8470 (tt0) cc_final: 0.8151 (mt-10) REVERT: G 84 GLN cc_start: 0.9309 (tp40) cc_final: 0.8252 (tm-30) REVERT: G 88 ARG cc_start: 0.8656 (mmt180) cc_final: 0.8371 (mpt180) REVERT: H 64 ASN cc_start: 0.9133 (m-40) cc_final: 0.8747 (t0) REVERT: H 85 THR cc_start: 0.9423 (m) cc_final: 0.9093 (p) REVERT: H 90 GLU cc_start: 0.9388 (mp0) cc_final: 0.8993 (mp0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1198 time to fit residues: 41.5020 Evaluate side-chains 191 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS E 68 GLN E 125 GLN F 75 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.083687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.054668 restraints weight = 42282.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.055740 restraints weight = 26788.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.056389 restraints weight = 20579.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.056808 restraints weight = 17856.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.056944 restraints weight = 16476.275| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12522 Z= 0.269 Angle : 0.693 9.899 18131 Z= 0.404 Chirality : 0.038 0.242 2065 Planarity : 0.004 0.038 1312 Dihedral : 31.331 179.484 3991 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.31), residues: 731 helix: 1.68 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -2.31 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.019 0.002 TYR G 50 PHE 0.011 0.002 PHE E 104 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00596 (12522) covalent geometry : angle 0.69266 (18131) hydrogen bonds : bond 0.07078 ( 709) hydrogen bonds : angle 3.30161 ( 1771) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9060 (tt0) cc_final: 0.8802 (tt0) REVERT: A 94 GLU cc_start: 0.8421 (tp30) cc_final: 0.7991 (tp30) REVERT: B 93 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 78 ILE cc_start: 0.8356 (mm) cc_final: 0.8007 (mm) REVERT: C 84 GLN cc_start: 0.9458 (tp40) cc_final: 0.9068 (tp40) REVERT: C 99 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8519 (mttt) REVERT: C 100 VAL cc_start: 0.9652 (t) cc_final: 0.9451 (p) REVERT: C 110 ASN cc_start: 0.8888 (t0) cc_final: 0.8483 (p0) REVERT: D 44 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8710 (tm-30) REVERT: F 43 VAL cc_start: 0.9496 (t) cc_final: 0.9208 (p) REVERT: F 85 ASP cc_start: 0.8781 (m-30) cc_final: 0.8505 (t0) REVERT: F 88 TYR cc_start: 0.8920 (m-10) cc_final: 0.7915 (m-10) REVERT: G 35 ARG cc_start: 0.9274 (mtp85) cc_final: 0.8929 (ttm110) REVERT: G 64 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8286 (tm-30) REVERT: G 84 GLN cc_start: 0.9405 (tp40) cc_final: 0.9132 (tp-100) REVERT: H 65 ASP cc_start: 0.8842 (t70) cc_final: 0.8505 (t0) REVERT: H 80 TYR cc_start: 0.8201 (m-10) cc_final: 0.7874 (m-10) REVERT: H 90 GLU cc_start: 0.9329 (mp0) cc_final: 0.8771 (mp0) REVERT: H 103 LEU cc_start: 0.9318 (mt) cc_final: 0.9113 (mm) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.1191 time to fit residues: 33.1920 Evaluate side-chains 170 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 34 optimal weight: 0.0970 chunk 76 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 50 optimal weight: 0.4980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 75 HIS C 104 GLN E 68 GLN E 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.086655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.057980 restraints weight = 40747.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.059165 restraints weight = 24727.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.059925 restraints weight = 18505.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.060349 restraints weight = 15770.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.060610 restraints weight = 14522.262| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12522 Z= 0.160 Angle : 0.599 6.995 18131 Z= 0.357 Chirality : 0.035 0.206 2065 Planarity : 0.004 0.050 1312 Dihedral : 31.160 178.224 3991 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.16 % Allowed : 2.10 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.31), residues: 731 helix: 2.15 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -2.06 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 67 TYR 0.016 0.001 TYR H 118 PHE 0.021 0.001 PHE H 62 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00344 (12522) covalent geometry : angle 0.59875 (18131) hydrogen bonds : bond 0.05571 ( 709) hydrogen bonds : angle 2.68748 ( 1771) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9333 (mp) cc_final: 0.9086 (mp) REVERT: A 57 SER cc_start: 0.9065 (p) cc_final: 0.8805 (t) REVERT: A 59 GLU cc_start: 0.8298 (mp0) cc_final: 0.7819 (mp0) REVERT: A 93 GLN cc_start: 0.8863 (tt0) cc_final: 0.8022 (tt0) REVERT: A 94 GLU cc_start: 0.8230 (tp30) cc_final: 0.7811 (tp30) REVERT: A 97 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8020 (mt-10) REVERT: B 35 ARG cc_start: 0.9058 (ttm-80) cc_final: 0.8753 (ttm110) REVERT: C 38 ASN cc_start: 0.9282 (m-40) cc_final: 0.9081 (m-40) REVERT: C 78 ILE cc_start: 0.8343 (mm) cc_final: 0.7987 (mm) REVERT: C 84 GLN cc_start: 0.9446 (tp40) cc_final: 0.8967 (tp40) REVERT: C 110 ASN cc_start: 0.8791 (t0) cc_final: 0.8538 (p0) REVERT: D 44 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8657 (tm-30) REVERT: D 49 THR cc_start: 0.8317 (p) cc_final: 0.8096 (p) REVERT: D 56 MET cc_start: 0.9051 (tpp) cc_final: 0.8847 (tpp) REVERT: D 83 ARG cc_start: 0.8836 (tpp80) cc_final: 0.8369 (mmm-85) REVERT: E 50 GLU cc_start: 0.9024 (mp0) cc_final: 0.8805 (mp0) REVERT: F 43 VAL cc_start: 0.9459 (t) cc_final: 0.9182 (p) REVERT: F 84 MET cc_start: 0.8799 (mmt) cc_final: 0.8391 (mmt) REVERT: F 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.8281 (m-10) REVERT: G 39 TYR cc_start: 0.9005 (m-80) cc_final: 0.8768 (m-80) REVERT: G 56 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7765 (mm-30) REVERT: G 84 GLN cc_start: 0.9341 (tp40) cc_final: 0.8796 (tm-30) REVERT: H 65 ASP cc_start: 0.8684 (t70) cc_final: 0.8395 (t0) REVERT: H 80 TYR cc_start: 0.8125 (m-10) cc_final: 0.7924 (m-10) REVERT: H 90 GLU cc_start: 0.9213 (mp0) cc_final: 0.8843 (mp0) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1209 time to fit residues: 36.5491 Evaluate side-chains 183 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 0.0020 chunk 95 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.058027 restraints weight = 41185.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.059236 restraints weight = 25024.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.059981 restraints weight = 18728.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.060444 restraints weight = 16008.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.060683 restraints weight = 14681.275| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12522 Z= 0.162 Angle : 0.586 5.431 18131 Z= 0.350 Chirality : 0.035 0.218 2065 Planarity : 0.004 0.032 1312 Dihedral : 31.048 178.212 3991 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.31), residues: 731 helix: 2.37 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.96 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.013 0.001 TYR H 80 PHE 0.009 0.001 PHE A 78 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00350 (12522) covalent geometry : angle 0.58599 (18131) hydrogen bonds : bond 0.05507 ( 709) hydrogen bonds : angle 2.66926 ( 1771) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9311 (mp) cc_final: 0.9079 (mp) REVERT: A 57 SER cc_start: 0.9065 (p) cc_final: 0.8738 (t) REVERT: A 59 GLU cc_start: 0.8306 (mp0) cc_final: 0.7794 (mp0) REVERT: A 93 GLN cc_start: 0.8865 (tt0) cc_final: 0.7977 (tt0) REVERT: A 94 GLU cc_start: 0.8199 (tp30) cc_final: 0.7749 (tp30) REVERT: A 97 GLU cc_start: 0.8258 (mt-10) cc_final: 0.8021 (mt-10) REVERT: B 84 MET cc_start: 0.8392 (mmm) cc_final: 0.8075 (mmm) REVERT: C 38 ASN cc_start: 0.9303 (m-40) cc_final: 0.9093 (m-40) REVERT: C 84 GLN cc_start: 0.9453 (tp40) cc_final: 0.9005 (tp40) REVERT: C 110 ASN cc_start: 0.8769 (t0) cc_final: 0.8466 (p0) REVERT: D 44 GLN cc_start: 0.9012 (tm-30) cc_final: 0.8717 (tm-30) REVERT: D 83 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8337 (mmm-85) REVERT: F 31 LYS cc_start: 0.8614 (tttt) cc_final: 0.8381 (ttmm) REVERT: F 43 VAL cc_start: 0.9496 (t) cc_final: 0.9232 (p) REVERT: F 84 MET cc_start: 0.8841 (mmt) cc_final: 0.8439 (mmt) REVERT: F 88 TYR cc_start: 0.8996 (m-10) cc_final: 0.7874 (m-10) REVERT: G 56 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7768 (mm-30) REVERT: G 84 GLN cc_start: 0.9381 (tp40) cc_final: 0.8903 (tm-30) REVERT: H 65 ASP cc_start: 0.8719 (t70) cc_final: 0.8387 (t0) REVERT: H 85 THR cc_start: 0.9304 (m) cc_final: 0.8960 (p) REVERT: H 90 GLU cc_start: 0.9196 (mp0) cc_final: 0.8877 (mp0) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1051 time to fit residues: 31.0916 Evaluate side-chains 177 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 71 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.086222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.057618 restraints weight = 41086.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.058808 restraints weight = 24945.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.059574 restraints weight = 18668.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.060003 restraints weight = 15878.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.060250 restraints weight = 14603.233| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12522 Z= 0.184 Angle : 0.615 9.454 18131 Z= 0.363 Chirality : 0.035 0.155 2065 Planarity : 0.004 0.033 1312 Dihedral : 30.984 178.964 3991 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.31), residues: 731 helix: 2.41 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 71 TYR 0.019 0.002 TYR B 88 PHE 0.009 0.001 PHE A 78 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00403 (12522) covalent geometry : angle 0.61499 (18131) hydrogen bonds : bond 0.05688 ( 709) hydrogen bonds : angle 2.80608 ( 1771) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1462 Ramachandran restraints generated. 731 Oldfield, 0 Emsley, 731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9314 (mp) cc_final: 0.9086 (mp) REVERT: A 57 SER cc_start: 0.9073 (p) cc_final: 0.8700 (t) REVERT: A 59 GLU cc_start: 0.8280 (mp0) cc_final: 0.7756 (mp0) REVERT: A 93 GLN cc_start: 0.8900 (tt0) cc_final: 0.8139 (tt0) REVERT: A 94 GLU cc_start: 0.8239 (tp30) cc_final: 0.8012 (tp30) REVERT: A 97 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 120 MET cc_start: 0.8968 (mtt) cc_final: 0.8642 (mtp) REVERT: B 35 ARG cc_start: 0.9093 (ttm-80) cc_final: 0.8811 (ttm110) REVERT: C 36 LYS cc_start: 0.9411 (tmmt) cc_final: 0.9113 (tttt) REVERT: C 38 ASN cc_start: 0.9313 (m-40) cc_final: 0.9105 (m-40) REVERT: C 84 GLN cc_start: 0.9470 (tp40) cc_final: 0.9016 (tp40) REVERT: C 110 ASN cc_start: 0.8712 (t0) cc_final: 0.8465 (p0) REVERT: D 44 GLN cc_start: 0.9026 (tm-30) cc_final: 0.8719 (tm-30) REVERT: E 50 GLU cc_start: 0.9144 (mp0) cc_final: 0.8872 (mp0) REVERT: F 31 LYS cc_start: 0.8594 (tttt) cc_final: 0.8388 (ttmm) REVERT: F 43 VAL cc_start: 0.9511 (t) cc_final: 0.9288 (p) REVERT: F 73 THR cc_start: 0.9597 (m) cc_final: 0.9110 (t) REVERT: F 84 MET cc_start: 0.8785 (mmt) cc_final: 0.8420 (mmt) REVERT: F 85 ASP cc_start: 0.8744 (m-30) cc_final: 0.8407 (t70) REVERT: F 88 TYR cc_start: 0.8981 (m-10) cc_final: 0.7699 (m-10) REVERT: G 35 ARG cc_start: 0.9116 (mtp85) cc_final: 0.8879 (ttm110) REVERT: G 73 ASN cc_start: 0.9300 (m-40) cc_final: 0.9011 (t0) REVERT: G 84 GLN cc_start: 0.9415 (tp40) cc_final: 0.8101 (tm-30) REVERT: H 65 ASP cc_start: 0.8721 (t70) cc_final: 0.8465 (t0) REVERT: H 90 GLU cc_start: 0.9229 (mp0) cc_final: 0.8884 (mp0) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1175 time to fit residues: 34.1515 Evaluate side-chains 176 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.0747 > 50: distance: 6 - 10: 9.660 distance: 10 - 11: 23.118 distance: 11 - 12: 33.009 distance: 11 - 14: 48.805 distance: 12 - 17: 9.544 distance: 14 - 15: 58.732 distance: 14 - 16: 42.032 distance: 17 - 18: 32.925 distance: 18 - 19: 43.709 distance: 18 - 21: 46.062 distance: 19 - 26: 54.166 distance: 21 - 22: 43.249 distance: 22 - 23: 53.886 distance: 23 - 25: 7.951 distance: 26 - 27: 40.151 distance: 27 - 28: 35.221 distance: 27 - 30: 57.253 distance: 28 - 34: 48.786 distance: 30 - 31: 41.303 distance: 31 - 32: 41.825 distance: 31 - 33: 40.237 distance: 34 - 35: 41.223 distance: 35 - 36: 42.039 distance: 35 - 38: 40.296 distance: 36 - 42: 69.672 distance: 38 - 39: 18.596 distance: 39 - 40: 31.135 distance: 39 - 41: 26.836 distance: 42 - 43: 68.725 distance: 43 - 44: 42.586 distance: 43 - 46: 41.456 distance: 44 - 45: 17.807 distance: 44 - 50: 40.205 distance: 46 - 47: 51.673 distance: 46 - 48: 48.534 distance: 47 - 49: 63.364 distance: 50 - 51: 44.340 distance: 51 - 52: 28.997 distance: 51 - 54: 17.169 distance: 52 - 53: 39.581 distance: 52 - 61: 26.132 distance: 54 - 55: 7.979 distance: 55 - 56: 23.227 distance: 56 - 57: 18.440 distance: 57 - 58: 10.027 distance: 58 - 59: 13.479 distance: 58 - 60: 28.340 distance: 61 - 62: 30.707 distance: 62 - 63: 31.124 distance: 62 - 65: 46.366 distance: 63 - 64: 55.335 distance: 63 - 70: 32.348 distance: 64 - 96: 34.588 distance: 65 - 66: 43.060 distance: 68 - 69: 51.610 distance: 70 - 71: 29.643 distance: 71 - 72: 62.497 distance: 71 - 74: 41.638 distance: 72 - 73: 41.263 distance: 72 - 78: 49.869 distance: 73 - 103: 22.288 distance: 74 - 75: 45.425 distance: 75 - 76: 61.721 distance: 78 - 79: 12.238 distance: 78 - 84: 47.447 distance: 79 - 80: 41.795 distance: 79 - 82: 40.113 distance: 80 - 81: 36.744 distance: 80 - 85: 38.851 distance: 81 - 114: 32.219 distance: 82 - 83: 30.550 distance: 83 - 84: 54.282 distance: 85 - 86: 38.335 distance: 86 - 87: 5.683 distance: 86 - 89: 38.274 distance: 87 - 88: 13.336 distance: 87 - 96: 28.921 distance: 88 - 121: 21.960 distance: 89 - 90: 7.335 distance: 90 - 91: 21.742 distance: 90 - 92: 36.621 distance: 91 - 93: 39.406 distance: 92 - 94: 5.807 distance: 93 - 95: 7.062 distance: 94 - 95: 5.522