Starting phenix.real_space_refine on Fri Jul 3 04:00:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f12_50122/07_2026/9f12_50122.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f12_50122/07_2026/9f12_50122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2026/9f12_50122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2026/9f12_50122.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2026/9f12_50122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f12_50122/07_2026/9f12_50122.map" } resolution = 3.42 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= 0.042 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 P 181 5.49 5 Mg 1 5.21 5 S 35 5.16 5 C 7049 2.51 5 N 2214 2.21 5 O 2691 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12171 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1982 Classifications: {'DNA': 96} Link IDs: {'rna3p': 95} Chain: "B" Number of atoms: 1739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1739 Classifications: {'DNA': 85} Link IDs: {'rna3p': 84} Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 764 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "D" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 749 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "F" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 846 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 881 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 4249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4249 Classifications: {'peptide': 564} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 22, 'TRANS': 541} Chain breaks: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 4, 'ASP:plan': 3, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 69 Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12171 At special positions: 0 Unit cell: (94.875, 130.35, 181.5, 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) S 35 16.00 P 181 15.00 Mg 1 11.99 O 2691 8.00 N 2214 7.00 C 7049 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: 0.93 Conformation dependent library (CDL) restraints added in 538.2 milliseconds 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2034 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 45.6% alpha, 17.8% beta 81 base pairs and 154 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 19 through 40 removed outlier: 3.708A pdb=" N ILE C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 92 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 18 through 39 Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'F' and resid 22 through 34 removed outlier: 3.743A pdb=" N LEU F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 52 removed outlier: 3.712A pdb=" N ALA F 41 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 90 removed outlier: 3.651A pdb=" N GLN F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 108 Processing helix chain 'G' and resid 20 through 34 removed outlier: 4.408A pdb=" N LEU G 25 " --> pdb=" O ASP G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 52 Processing helix chain 'G' and resid 75 through 90 removed outlier: 3.597A pdb=" N ALA G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 108 removed outlier: 4.010A pdb=" N ARG G 100 " --> pdb=" O GLU G 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 32 removed outlier: 3.756A pdb=" N SER E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.621A pdb=" N HIS E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 90 removed outlier: 3.545A pdb=" N LEU E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 108 Processing helix chain 'H' and resid 9 through 18 removed outlier: 3.611A pdb=" N ALA H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR H 18 " --> pdb=" O GLY H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 99 through 118 removed outlier: 3.510A pdb=" N ILE H 103 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 192 Processing helix chain 'H' and resid 192 through 211 Processing helix chain 'H' and resid 219 through 222 removed outlier: 3.567A pdb=" N GLY H 222 " --> pdb=" O GLY H 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 219 through 222' Processing helix chain 'H' and resid 229 through 233 Processing helix chain 'H' and resid 235 through 246 Processing helix chain 'H' and resid 250 through 261 Processing helix chain 'H' and resid 269 through 283 removed outlier: 3.636A pdb=" N LYS H 282 " --> pdb=" O MET H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 287 through 302 removed outlier: 3.762A pdb=" N ASP H 300 " --> pdb=" O ASP H 296 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 301 " --> pdb=" O GLN H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 575 through 593 Processing helix chain 'H' and resid 603 through 621 removed outlier: 3.613A pdb=" N ALA H 613 " --> pdb=" O ILE H 609 " (cutoff:3.500A) Processing helix chain 'H' and resid 646 through 650 Processing helix chain 'H' and resid 696 through 698 No H-bonds generated for 'chain 'H' and resid 696 through 698' Processing helix chain 'H' and resid 763 through 767 Processing helix chain 'H' and resid 798 through 806 Processing helix chain 'H' and resid 822 through 827 Processing sheet with id=AA1, first strand: chain 'C' and resid 44 through 46 removed outlier: 3.645A pdb=" N VAL C 44 " --> pdb=" O PHE C 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 43 through 45 Processing sheet with id=AA3, first strand: chain 'D' and resid 59 through 62 Processing sheet with id=AA4, first strand: chain 'F' and resid 13 through 19 removed outlier: 3.582A pdb=" N LEU F 18 " --> pdb=" O LYS F 68 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 13 through 19 Processing sheet with id=AA6, first strand: chain 'E' and resid 13 through 19 Processing sheet with id=AA7, first strand: chain 'H' and resid 2 through 7 removed outlier: 4.051A pdb=" N GLY H 79 " --> pdb=" O VAL H 7 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N GLN H 155 " --> pdb=" O THR H 148 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'H' and resid 122 through 126 Processing sheet with id=AB1, first strand: chain 'H' and resid 166 through 167 Processing sheet with id=AB2, first strand: chain 'H' and resid 216 through 217 Processing sheet with id=AB3, first strand: chain 'H' and resid 775 through 776 removed outlier: 9.038A pdb=" N GLU H 776 " --> pdb=" O SER H 597 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA H 599 " --> pdb=" O GLU H 776 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL H 598 " --> pdb=" O PHE H 789 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N SER H 791 " --> pdb=" O VAL H 598 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN H 600 " --> pdb=" O SER H 791 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL H 788 " --> pdb=" O ARG H 813 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N TYR H 815 " --> pdb=" O VAL H 788 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA H 790 " --> pdb=" O TYR H 815 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU H 814 " --> pdb=" O PRO H 567 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR H 569 " --> pdb=" O LEU H 814 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N SER H 816 " --> pdb=" O THR H 569 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 629 through 636 removed outlier: 3.543A pdb=" N SER H 665 " --> pdb=" O ASN H 660 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N THR H 682 " --> pdb=" O ASP H 672 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL H 674 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER H 680 " --> pdb=" O VAL H 674 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 755 through 759 removed outlier: 6.985A pdb=" N ALA H 744 " --> pdb=" O VAL H 740 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL H 740 " --> pdb=" O ALA H 744 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR H 746 " --> pdb=" O ALA H 738 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN H 736 " --> pdb=" O VAL H 748 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 358 hydrogen bond angles 0 basepair planarities 81 basepair parallelities 154 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.30 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: 2481 1.33 - 1.45: 3591 1.45 - 1.57: 6264 1.57 - 1.69: 360 1.69 - 1.80: 67 Bond restraints: 12763 Sorted by residual: bond pdb=" C3' DT A 88 " pdb=" C2' DT A 88 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.85e+01 bond pdb=" C3' DG A 27 " pdb=" C2' DG A 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG B 85 " pdb=" C2' DG B 85 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT B 82 " pdb=" C2' DT B 82 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG A 17 " pdb=" C2' DG A 17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 12758 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 17029 1.60 - 3.20: 942 3.20 - 4.81: 46 4.81 - 6.41: 7 6.41 - 8.01: 3 Bond angle restraints: 18027 Sorted by residual: angle pdb=" O4' DA B 44 " pdb=" C4' DA B 44 " pdb=" C3' DA B 44 " ideal model delta sigma weight residual 106.00 102.00 4.00 6.00e-01 2.78e+00 4.45e+01 angle pdb=" O4' DT A 46 " pdb=" C4' DT A 46 " pdb=" C3' DT A 46 " ideal model delta sigma weight residual 106.00 102.07 3.93 6.00e-01 2.78e+00 4.28e+01 angle pdb=" O4' DC A 29 " pdb=" C4' DC A 29 " pdb=" C3' DC A 29 " ideal model delta sigma weight residual 106.00 103.19 2.81 6.00e-01 2.78e+00 2.20e+01 angle pdb=" N3 DT B 35 " pdb=" C4 DT B 35 " pdb=" O4 DT B 35 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT A 19 " pdb=" C4 DT A 19 " pdb=" O4 DT A 19 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6504 35.97 - 71.93: 808 71.93 - 107.90: 6 107.90 - 143.86: 1 143.86 - 179.83: 4 Dihedral angle restraints: 7323 sinusoidal: 4182 harmonic: 3141 Sorted by residual: dihedral pdb=" CA ILE F 116 " pdb=" C ILE F 116 " pdb=" N PHE F 117 " pdb=" CA PHE F 117 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA VAL H 229 " pdb=" C VAL H 229 " pdb=" N PRO H 230 " pdb=" CA PRO H 230 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ARG H 807 " pdb=" C ARG H 807 " pdb=" N SER H 808 " pdb=" CA SER H 808 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 7320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1959 0.108 - 0.215: 52 0.215 - 0.323: 0 0.323 - 0.431: 0 0.431 - 0.538: 3 Chirality restraints: 2014 Sorted by residual: chirality pdb=" P DG A 7 " pdb=" OP1 DG A 7 " pdb=" OP2 DG A 7 " pdb=" O5' DG A 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" P DG A 9 " pdb=" OP1 DG A 9 " pdb=" OP2 DG A 9 " pdb=" O5' DG A 9 " both_signs ideal model delta sigma weight residual True 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" P DT A 8 " pdb=" OP1 DT A 8 " pdb=" OP2 DT A 8 " pdb=" O5' DT A 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.82 -0.48 2.00e-01 2.50e+01 5.82e+00 ... (remaining 2011 not shown) Planarity restraints: 1701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT A 13 " 0.024 2.00e-02 2.50e+03 1.19e-02 3.56e+00 pdb=" N1 DT A 13 " -0.026 2.00e-02 2.50e+03 pdb=" C2 DT A 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT A 13 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT A 13 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT A 13 " 0.004 2.00e-02 2.50e+03 pdb=" O4 DT A 13 " 0.010 2.00e-02 2.50e+03 pdb=" C5 DT A 13 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT A 13 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DT A 13 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA A 81 " -0.024 2.00e-02 2.50e+03 1.05e-02 3.02e+00 pdb=" N9 DA A 81 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DA A 81 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA A 81 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA A 81 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA A 81 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA A 81 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA A 81 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA A 81 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DA A 81 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA A 81 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA B 44 " 0.023 2.00e-02 2.50e+03 1.03e-02 2.94e+00 pdb=" N9 DA B 44 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA B 44 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA B 44 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA B 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA B 44 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA B 44 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA B 44 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA B 44 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA B 44 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA B 44 " -0.004 2.00e-02 2.50e+03 ... (remaining 1698 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 47 2.54 - 3.13: 8958 3.13 - 3.72: 20382 3.72 - 4.31: 28765 4.31 - 4.90: 43403 Nonbonded interactions: 101555 Sorted by model distance: nonbonded pdb=" NE2 HIS H 157 " pdb="MG MG H1801 " model vdw 1.944 2.250 nonbonded pdb=" ND1 HIS H 146 " pdb="MG MG H1801 " model vdw 1.952 2.250 nonbonded pdb=" OG SER H 3 " pdb=" OG1 THR H 83 " model vdw 2.129 3.040 nonbonded pdb=" OP2 DA B 46 " pdb=" NH1 ARG C 76 " model vdw 2.146 3.120 nonbonded pdb=" NE2 HIS H 159 " pdb="MG MG H1801 " model vdw 2.184 2.250 ... (remaining 101550 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 'E' and (resid 11 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 53 or (resid 54 and (na \ me N or name CA or name C or name O or name CB )) or resid 55 through 67 or (res \ id 68 and (name N or name CA or name C or name O or name CB )) or resid 69 throu \ gh 76 or (resid 77 and (name N or name CA or name C or name O or name CB )) or r \ esid 78 through 85 or (resid 86 and (name N or name CA or name C or name O or na \ me CB )) or resid 87 through 113)) selection = (chain 'F' and (resid 11 through 16 or (resid 17 through 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 59 or resid 64 through \ 67 or (resid 68 and (name N or name CA or name C or name O or name CB )) or resi \ d 69 through 85 or (resid 86 and (name N or name CA or name C or name O or name \ CB )) or resid 87 through 113)) selection = (chain 'G' and (resid 11 through 59 or resid 64 through 76 or (resid 77 and (nam \ e N or name CA or name C or name O or name CB )) or resid 78 through 113)) } 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 individual isotropic 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: 19.850 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.090 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.006 0.039 12763 Z= 0.483 Angle : 0.715 8.009 18027 Z= 0.618 Chirality : 0.048 0.538 2014 Planarity : 0.003 0.030 1701 Dihedral : 22.834 179.825 5289 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.23 % Allowed : 1.69 % Favored : 98.08 % 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 are not related in a simple way. whole: 0.08 (0.25), residues: 1073 helix: 0.54 (0.22), residues: 474 sheet: 0.27 (0.34), residues: 222 loop : -0.54 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 51 TYR 0.011 0.001 TYR H 669 PHE 0.012 0.001 PHE H 112 TRP 0.010 0.001 TRP F 91 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.48 (12763) covalent geometry : angle 0.71455 / 0.62 (18027) hydrogen bonds : bond 0.15243 / 17.09 ( 623) hydrogen bonds : angle 5.90545 / 7.90 ( 1618) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: D 81 LYS cc_start: 0.8991 (tttt) cc_final: 0.8663 (tttp) REVERT: F 12 LYS cc_start: 0.8758 (mttt) cc_final: 0.8522 (mttp) REVERT: F 46 LYS cc_start: 0.8486 (tttp) cc_final: 0.8174 (ttpp) REVERT: F 60 ASN cc_start: 0.7346 (t0) cc_final: 0.7027 (t0) REVERT: F 103 ASP cc_start: 0.8324 (t70) cc_final: 0.7957 (t0) REVERT: G 43 ILE cc_start: 0.8309 (tp) cc_final: 0.8054 (mt) REVERT: E 8 SER cc_start: 0.9127 (p) cc_final: 0.8758 (m) REVERT: E 46 LYS cc_start: 0.9076 (tttt) cc_final: 0.8758 (tttp) REVERT: H 31 GLU cc_start: 0.7947 (pm20) cc_final: 0.7675 (pm20) REVERT: H 75 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8409 (mmm-85) REVERT: H 202 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7377 (pt0) REVERT: H 573 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7644 (mm-30) REVERT: H 577 ASN cc_start: 0.8584 (t0) cc_final: 0.8380 (t0) REVERT: H 656 MET cc_start: 0.9337 (mmm) cc_final: 0.9111 (mtp) REVERT: H 730 SER cc_start: 0.8573 (t) cc_final: 0.8312 (p) REVERT: H 797 MET cc_start: 0.8229 (mtp) cc_final: 0.7930 (mtt) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.1625 time to fit residues: 53.2182 Evaluate side-chains 154 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 GLN G 79 ASN G 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091449 restraints weight = 21975.879| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.47 r_work: 0.3029 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12763 Z= 0.187 Angle : 0.660 7.022 18027 Z= 0.387 Chirality : 0.045 0.242 2014 Planarity : 0.005 0.038 1701 Dihedral : 27.581 175.944 3269 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.15 % Allowed : 8.25 % Favored : 89.60 % 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 are not related in a simple way. whole: 0.31 (0.24), residues: 1073 helix: 0.98 (0.22), residues: 482 sheet: 0.14 (0.37), residues: 176 loop : -0.57 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 54 TYR 0.019 0.002 TYR D 55 PHE 0.019 0.002 PHE H 16 TRP 0.011 0.001 TRP F 91 HIS 0.003 0.001 HIS H 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.19 (12763) covalent geometry : angle 0.65990 / 0.39 (18027) hydrogen bonds : bond 0.05377 / 5.99 ( 623) hydrogen bonds : angle 4.44570 / 5.87 ( 1618) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: G 16 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8004 (mp) REVERT: G 43 ILE cc_start: 0.8559 (tp) cc_final: 0.8228 (mt) REVERT: H 1 MET cc_start: 0.8564 (tpt) cc_final: 0.8344 (tpt) REVERT: H 29 MET cc_start: 0.6096 (tpt) cc_final: 0.5815 (tpp) REVERT: H 39 GLU cc_start: 0.8332 (tt0) cc_final: 0.8061 (tp30) REVERT: H 182 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8330 (mmtm) REVERT: H 573 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7579 (mm-30) REVERT: H 656 MET cc_start: 0.9052 (mmm) cc_final: 0.8805 (mtp) outliers start: 19 outliers final: 9 residues processed: 167 average time/residue: 0.1410 time to fit residues: 31.9920 Evaluate side-chains 141 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 134 VAL Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 697 SER Chi-restraints excluded: chain H residue 745 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.2980 chunk 0 optimal weight: 20.0000 chunk 97 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 overall best weight: 0.4660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.092383 restraints weight = 21995.196| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.42 r_work: 0.3056 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12763 Z= 0.152 Angle : 0.609 6.068 18027 Z= 0.360 Chirality : 0.043 0.246 2014 Planarity : 0.004 0.037 1701 Dihedral : 27.553 174.294 3269 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.36 % Allowed : 10.96 % Favored : 87.68 % 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 are not related in a simple way. whole: 0.58 (0.25), residues: 1073 helix: 1.29 (0.23), residues: 483 sheet: 0.16 (0.34), residues: 214 loop : -0.58 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 75 TYR 0.021 0.001 TYR F 52 PHE 0.014 0.001 PHE H 16 TRP 0.008 0.001 TRP F 91 HIS 0.003 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (12763) covalent geometry : angle 0.60872 / 0.36 (18027) hydrogen bonds : bond 0.04608 / 5.14 ( 623) hydrogen bonds : angle 4.18275 / 5.47 ( 1618) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.414 Fit side-chains REVERT: G 16 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8380 (mt) REVERT: G 43 ILE cc_start: 0.8529 (tp) cc_final: 0.8172 (mt) REVERT: H 1 MET cc_start: 0.8614 (tpt) cc_final: 0.8331 (tpt) REVERT: H 29 MET cc_start: 0.6083 (tpt) cc_final: 0.5866 (tpp) REVERT: H 573 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7518 (mm-30) REVERT: H 656 MET cc_start: 0.9063 (mmm) cc_final: 0.8822 (mtp) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.1303 time to fit residues: 26.1551 Evaluate side-chains 131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 697 SER Chi-restraints excluded: chain H residue 745 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 119 optimal weight: 0.0010 chunk 37 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 65 optimal weight: 0.0870 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.115081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.091164 restraints weight = 21898.946| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.41 r_work: 0.3055 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12763 Z= 0.154 Angle : 0.603 7.373 18027 Z= 0.352 Chirality : 0.042 0.248 2014 Planarity : 0.004 0.036 1701 Dihedral : 27.624 175.242 3269 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.92 % Allowed : 11.41 % Favored : 86.67 % 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 are not related in a simple way. whole: 0.63 (0.25), residues: 1073 helix: 1.32 (0.23), residues: 484 sheet: 0.25 (0.33), residues: 217 loop : -0.60 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 100 TYR 0.020 0.001 TYR E 52 PHE 0.011 0.001 PHE H 112 TRP 0.007 0.001 TRP G 91 HIS 0.004 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (12763) covalent geometry : angle 0.60306 / 0.35 (18027) hydrogen bonds : bond 0.04407 / 4.93 ( 623) hydrogen bonds : angle 4.04435 / 5.29 ( 1618) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.546 Fit side-chains REVERT: H 29 MET cc_start: 0.6181 (tpt) cc_final: 0.5949 (tpp) REVERT: H 573 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7484 (mm-30) REVERT: H 656 MET cc_start: 0.9037 (mmm) cc_final: 0.8789 (mtp) outliers start: 17 outliers final: 11 residues processed: 151 average time/residue: 0.1168 time to fit residues: 24.6594 Evaluate side-chains 135 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 697 SER Chi-restraints excluded: chain H residue 782 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.114378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090945 restraints weight = 22059.145| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.46 r_work: 0.3035 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12763 Z= 0.160 Angle : 0.596 6.613 18027 Z= 0.349 Chirality : 0.042 0.248 2014 Planarity : 0.004 0.036 1701 Dihedral : 27.661 175.110 3269 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.81 % Allowed : 12.20 % Favored : 85.99 % 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 are not related in a simple way. whole: 0.68 (0.25), residues: 1073 helix: 1.39 (0.23), residues: 484 sheet: 0.20 (0.33), residues: 219 loop : -0.56 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 100 TYR 0.017 0.001 TYR F 52 PHE 0.011 0.001 PHE G 55 TRP 0.008 0.001 TRP G 91 HIS 0.003 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (12763) covalent geometry : angle 0.59623 / 0.35 (18027) hydrogen bonds : bond 0.04310 / 4.81 ( 623) hydrogen bonds : angle 3.98965 / 5.21 ( 1618) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.329 Fit side-chains REVERT: H 29 MET cc_start: 0.6221 (tpt) cc_final: 0.6012 (tpp) REVERT: H 573 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7440 (mm-30) REVERT: H 656 MET cc_start: 0.9040 (mmm) cc_final: 0.8807 (mtp) outliers start: 16 outliers final: 13 residues processed: 147 average time/residue: 0.1348 time to fit residues: 27.3652 Evaluate side-chains 136 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 697 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 102 optimal weight: 0.0970 chunk 9 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 110 optimal weight: 0.0170 chunk 77 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.091944 restraints weight = 21890.016| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.46 r_work: 0.3055 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12763 Z= 0.139 Angle : 0.589 7.822 18027 Z= 0.344 Chirality : 0.041 0.256 2014 Planarity : 0.004 0.053 1701 Dihedral : 27.622 175.241 3269 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.15 % Allowed : 13.22 % Favored : 84.63 % 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 are not related in a simple way. whole: 0.70 (0.26), residues: 1073 helix: 1.46 (0.23), residues: 483 sheet: 0.14 (0.33), residues: 218 loop : -0.57 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 100 TYR 0.015 0.001 TYR F 52 PHE 0.010 0.001 PHE G 55 TRP 0.007 0.001 TRP G 91 HIS 0.004 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12763) covalent geometry : angle 0.58902 / 0.34 (18027) hydrogen bonds : bond 0.04014 / 4.46 ( 623) hydrogen bonds : angle 3.92460 / 5.11 ( 1618) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.387 Fit side-chains REVERT: H 41 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7526 (mp) REVERT: H 297 GLN cc_start: 0.7584 (tp40) cc_final: 0.7311 (tp40) REVERT: H 573 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7409 (mm-30) REVERT: H 577 ASN cc_start: 0.8305 (t0) cc_final: 0.8054 (t0) REVERT: H 656 MET cc_start: 0.9070 (mmm) cc_final: 0.8811 (mtp) outliers start: 19 outliers final: 12 residues processed: 145 average time/residue: 0.1176 time to fit residues: 24.2864 Evaluate side-chains 134 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 697 SER Chi-restraints excluded: chain H residue 782 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 101 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.090961 restraints weight = 21955.920| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.44 r_work: 0.3034 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12763 Z= 0.166 Angle : 0.599 7.211 18027 Z= 0.348 Chirality : 0.041 0.249 2014 Planarity : 0.004 0.038 1701 Dihedral : 27.681 174.853 3269 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.03 % Allowed : 12.99 % Favored : 84.97 % 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 are not related in a simple way. whole: 0.69 (0.26), residues: 1073 helix: 1.50 (0.24), residues: 483 sheet: 0.07 (0.33), residues: 215 loop : -0.61 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 82 TYR 0.014 0.001 TYR F 52 PHE 0.009 0.001 PHE H 112 TRP 0.006 0.001 TRP G 91 HIS 0.004 0.001 HIS H 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (12763) covalent geometry : angle 0.59883 / 0.35 (18027) hydrogen bonds : bond 0.04239 / 4.70 ( 623) hydrogen bonds : angle 3.91877 / 5.10 ( 1618) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2146 Ramachandran restraints generated. 1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.253 Fit side-chains REVERT: H 297 GLN cc_start: 0.7619 (tp40) cc_final: 0.7350 (tp40) REVERT: H 573 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7387 (mm-30) REVERT: H 577 ASN cc_start: 0.8312 (t0) cc_final: 0.8065 (t0) REVERT: H 656 MET cc_start: 0.9047 (mmm) cc_final: 0.8797 (mtp) outliers start: 18 outliers final: 13 residues processed: 137 average time/residue: 0.1173 time to fit residues: 22.6008 Evaluate side-chains 131 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain E residue 6 THR Chi-restraints excluded: chain E residue 33 SER Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 693 VAL Chi-restraints excluded: chain H residue 697 SER Chi-restraints excluded: chain H residue 735 LEU Chi-restraints excluded: chain H residue 782 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1642 > 50: distance: 42 - 216: 34.135 distance: 45 - 213: 32.844 distance: 116 - 206: 32.162 distance: 119 - 203: 32.437 distance: 131 - 136: 34.832 distance: 137 - 138: 40.269 distance: 138 - 142: 21.119 distance: 140 - 141: 69.118 distance: 142 - 143: 18.873 distance: 143 - 146: 57.050 distance: 144 - 153: 38.807 distance: 146 - 147: 41.734 distance: 147 - 148: 40.603 distance: 148 - 149: 6.565 distance: 149 - 150: 40.656 distance: 150 - 151: 51.313 distance: 150 - 152: 8.586 distance: 153 - 154: 41.410 distance: 154 - 155: 55.184 distance: 155 - 156: 41.116 distance: 155 - 161: 41.127 distance: 158 - 159: 39.021 distance: 158 - 160: 41.158 distance: 161 - 162: 55.722 distance: 162 - 165: 57.254 distance: 163 - 170: 38.739 distance: 165 - 166: 40.432 distance: 167 - 168: 39.998 distance: 170 - 171: 57.667 distance: 171 - 172: 41.312 distance: 171 - 174: 55.136 distance: 172 - 173: 57.581 distance: 172 - 179: 39.206 distance: 175 - 176: 57.461 distance: 179 - 180: 39.832 distance: 180 - 181: 38.767 distance: 180 - 183: 41.239 distance: 181 - 182: 41.198 distance: 181 - 186: 40.862 distance: 183 - 184: 39.121 distance: 184 - 185: 39.832 distance: 186 - 187: 33.086 distance: 187 - 188: 39.424 distance: 187 - 190: 40.132 distance: 188 - 195: 40.720 distance: 190 - 191: 70.036 distance: 191 - 192: 39.334 distance: 192 - 193: 39.131 distance: 195 - 196: 40.151 distance: 196 - 197: 56.216 distance: 200 - 201: 40.930 distance: 203 - 204: 39.869 distance: 204 - 205: 68.691 distance: 204 - 207: 57.881 distance: 205 - 206: 32.205 distance: 205 - 213: 64.267 distance: 207 - 208: 40.458 distance: 208 - 209: 55.589 distance: 208 - 210: 56.877 distance: 209 - 211: 41.204 distance: 211 - 212: 40.170 distance: 213 - 214: 11.438 distance: 214 - 217: 40.207 distance: 215 - 216: 41.004 distance: 215 - 220: 34.354 distance: 217 - 218: 39.850 distance: 217 - 219: 39.360