Starting phenix.real_space_refine on Thu Feb 5 11:22:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zr9_60393/02_2026/8zr9_60393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zr9_60393/02_2026/8zr9_60393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zr9_60393/02_2026/8zr9_60393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zr9_60393/02_2026/8zr9_60393.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zr9_60393/02_2026/8zr9_60393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zr9_60393/02_2026/8zr9_60393.map" } resolution = 2.7 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= 0.004 sd= 0.023 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 72 5.16 5 C 10638 2.51 5 N 2814 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16692 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "B" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "C" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "D" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "E" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "F" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2737 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 14, 'TRANS': 329} Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'4BW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 45 Unusual residues: {'4BW': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.87, per 1000 atoms: 0.23 Number of scatterers: 16692 At special positions: 0 Unit cell: (85.744, 84.812, 169.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 12 15.00 O 3156 8.00 N 2814 7.00 C 10638 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 680.2 milliseconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 12 sheets defined 57.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.855A pdb=" N THR A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.765A pdb=" N TYR A 50 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 51 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 69 Processing helix chain 'A' and resid 74 through 88 removed outlier: 4.018A pdb=" N GLU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 Processing helix chain 'A' and resid 97 through 104 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.547A pdb=" N LEU A 195 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.518A pdb=" N VAL A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 239 through 246 Processing helix chain 'A' and resid 258 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.000A pdb=" N ALA A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 333 removed outlier: 3.516A pdb=" N ALA A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 340 removed outlier: 3.538A pdb=" N ARG A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 21 through 41 removed outlier: 3.865A pdb=" N THR B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.881A pdb=" N TYR B 50 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 51 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 70 Processing helix chain 'B' and resid 72 through 88 removed outlier: 4.563A pdb=" N THR B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 86 " --> pdb=" O ILE B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 109 through 121 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.655A pdb=" N LEU B 129 " --> pdb=" O PHE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.620A pdb=" N ALA B 167 " --> pdb=" O ARG B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 removed outlier: 3.641A pdb=" N LEU B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 258 through 284 removed outlier: 3.674A pdb=" N SER B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.695A pdb=" N GLU B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 333 Processing helix chain 'B' and resid 333 through 340 removed outlier: 3.587A pdb=" N ARG B 337 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 20 No H-bonds generated for 'chain 'C' and resid 18 through 20' Processing helix chain 'C' and resid 21 through 41 removed outlier: 3.529A pdb=" N THR C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.655A pdb=" N TYR C 50 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE C 51 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 70 Processing helix chain 'C' and resid 72 through 88 removed outlier: 4.227A pdb=" N THR C 85 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LYS C 86 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 97 through 102 Processing helix chain 'C' and resid 108 through 121 removed outlier: 4.289A pdb=" N LEU C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.621A pdb=" N LEU C 129 " --> pdb=" O PHE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 Processing helix chain 'C' and resid 192 through 196 Processing helix chain 'C' and resid 200 through 211 removed outlier: 3.563A pdb=" N ILE C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 222 No H-bonds generated for 'chain 'C' and resid 220 through 222' Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 258 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.808A pdb=" N GLU C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 333 Processing helix chain 'C' and resid 333 through 340 removed outlier: 4.206A pdb=" N PHE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 21 through 41 removed outlier: 3.919A pdb=" N THR D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.830A pdb=" N TYR D 50 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 70 Processing helix chain 'D' and resid 72 through 88 removed outlier: 3.597A pdb=" N ILE D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR D 85 " --> pdb=" O GLU D 81 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LYS D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 removed outlier: 3.656A pdb=" N ASN D 95 " --> pdb=" O LYS D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 Processing helix chain 'D' and resid 108 through 120 removed outlier: 4.204A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 Processing helix chain 'D' and resid 192 through 196 removed outlier: 3.637A pdb=" N LEU D 195 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 211 removed outlier: 3.618A pdb=" N VAL D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 222 No H-bonds generated for 'chain 'D' and resid 220 through 222' Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 258 through 284 removed outlier: 3.608A pdb=" N LEU D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.592A pdb=" N GLU D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 333 Processing helix chain 'D' and resid 333 through 340 removed outlier: 3.500A pdb=" N ARG D 337 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 339 " --> pdb=" O GLU D 335 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 20 No H-bonds generated for 'chain 'E' and resid 18 through 20' Processing helix chain 'E' and resid 21 through 41 removed outlier: 3.643A pdb=" N THR E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 removed outlier: 3.962A pdb=" N TYR E 50 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 70 removed outlier: 3.618A pdb=" N GLY E 70 " --> pdb=" O GLY E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 88 removed outlier: 4.374A pdb=" N THR E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 95 Processing helix chain 'E' and resid 97 through 104 Processing helix chain 'E' and resid 108 through 121 removed outlier: 4.235A pdb=" N LEU E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.575A pdb=" N LEU E 129 " --> pdb=" O PHE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 3.735A pdb=" N ALA E 167 " --> pdb=" O ARG E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 196 removed outlier: 3.604A pdb=" N LEU E 195 " --> pdb=" O ASP E 192 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 196 " --> pdb=" O GLY E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 196' Processing helix chain 'E' and resid 200 through 211 Processing helix chain 'E' and resid 220 through 222 No H-bonds generated for 'chain 'E' and resid 220 through 222' Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 258 through 284 removed outlier: 3.530A pdb=" N LEU E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 288 removed outlier: 5.686A pdb=" N LYS E 288 " --> pdb=" O LYS E 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 285 through 288' Processing helix chain 'E' and resid 298 through 305 removed outlier: 3.724A pdb=" N GLU E 304 " --> pdb=" O GLU E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 333 Processing helix chain 'E' and resid 333 through 340 removed outlier: 3.587A pdb=" N ARG E 337 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 339 " --> pdb=" O GLU E 335 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 20 No H-bonds generated for 'chain 'F' and resid 18 through 20' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.560A pdb=" N THR F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.689A pdb=" N PHE F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 70 removed outlier: 3.545A pdb=" N GLY F 70 " --> pdb=" O GLY F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 88 removed outlier: 3.527A pdb=" N ILE F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS F 86 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 104 Processing helix chain 'F' and resid 108 through 120 removed outlier: 4.115A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 129 Processing helix chain 'F' and resid 163 through 172 removed outlier: 3.524A pdb=" N ALA F 167 " --> pdb=" O ARG F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.524A pdb=" N ASN F 198 " --> pdb=" O GLY F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 211 removed outlier: 3.636A pdb=" N ILE F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 239 through 246 Processing helix chain 'F' and resid 258 through 284 removed outlier: 3.520A pdb=" N SER F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 298 through 303 Processing helix chain 'F' and resid 311 through 333 Processing helix chain 'F' and resid 333 through 340 removed outlier: 3.566A pdb=" N ARG F 337 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE F 340 " --> pdb=" O LEU F 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.671A pdb=" N VAL A 138 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASN A 188 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 145 through 149 removed outlier: 3.679A pdb=" N THR A 136 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 11 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N THR A 55 " --> pdb=" O LYS A 11 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU A 13 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE A 10 " --> pdb=" O LYS A 225 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N LEU A 227 " --> pdb=" O ILE A 10 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE A 12 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ILE A 229 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 14 " --> pdb=" O ILE A 229 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL A 291 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N VAL A 226 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ILE A 293 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN A 228 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.785A pdb=" N VAL B 138 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN B 188 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.545A pdb=" N THR B 136 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS B 11 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N THR B 55 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N LEU B 13 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR B 57 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 15 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE B 10 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LEU B 227 " --> pdb=" O ILE B 10 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 12 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 229 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER B 14 " --> pdb=" O ILE B 229 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N VAL B 291 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL B 226 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE B 293 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN B 228 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 145 through 149 removed outlier: 3.643A pdb=" N VAL C 138 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN C 188 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 145 through 149 removed outlier: 3.500A pdb=" N THR C 136 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS C 11 " --> pdb=" O LEU C 53 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR C 55 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU C 13 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE C 10 " --> pdb=" O LYS C 225 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU C 227 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE C 12 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE C 229 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N SER C 14 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N VAL C 291 " --> pdb=" O ILE C 224 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL C 226 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE C 293 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ASN C 228 " --> pdb=" O ILE C 293 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.658A pdb=" N LYS D 11 " --> pdb=" O LEU D 53 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR D 55 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU D 13 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE D 10 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU D 227 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE D 12 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE D 229 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N SER D 14 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL D 291 " --> pdb=" O ILE D 224 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL D 226 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N ILE D 293 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN D 228 " --> pdb=" O ILE D 293 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 149 removed outlier: 3.705A pdb=" N ASN D 188 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.723A pdb=" N VAL E 138 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN E 188 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.560A pdb=" N THR E 136 " --> pdb=" O GLY E 56 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LYS E 11 " --> pdb=" O LEU E 53 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N THR E 55 " --> pdb=" O LYS E 11 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU E 13 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE E 10 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LEU E 227 " --> pdb=" O ILE E 10 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE E 12 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE E 229 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER E 14 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL E 291 " --> pdb=" O ILE E 224 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL E 226 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N ILE E 293 " --> pdb=" O VAL E 226 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN E 228 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.793A pdb=" N VAL F 138 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN F 188 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 145 through 149 removed outlier: 3.564A pdb=" N THR F 136 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS F 11 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR F 55 " --> pdb=" O LYS F 11 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU F 13 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE F 10 " --> pdb=" O LYS F 225 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU F 227 " --> pdb=" O ILE F 10 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE F 12 " --> pdb=" O LEU F 227 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE F 229 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER F 14 " --> pdb=" O ILE F 229 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL F 291 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL F 226 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ILE F 293 " --> pdb=" O VAL F 226 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN F 228 " --> pdb=" O ILE F 293 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 2217 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 5361 1.35 - 1.46: 3793 1.46 - 1.58: 7730 1.58 - 1.70: 24 1.70 - 1.82: 126 Bond restraints: 17034 Sorted by residual: bond pdb=" CB GLU B 184 " pdb=" CG GLU B 184 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.88e+00 bond pdb=" CB GLU B 300 " pdb=" CG GLU B 300 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CB GLU D 312 " pdb=" CG GLU D 312 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CA THR D 231 " pdb=" C THR D 231 " ideal model delta sigma weight residual 1.524 1.538 -0.014 1.47e-02 4.63e+03 9.43e-01 bond pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.59e-02 3.96e+03 7.81e-01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 22803 2.16 - 4.32: 181 4.32 - 6.48: 22 6.48 - 8.64: 8 8.64 - 10.80: 2 Bond angle restraints: 23016 Sorted by residual: angle pdb=" CB MET F 155 " pdb=" CG MET F 155 " pdb=" SD MET F 155 " ideal model delta sigma weight residual 112.70 123.50 -10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " pdb=" CG GLU B 184 " ideal model delta sigma weight residual 114.10 120.65 -6.55 2.00e+00 2.50e-01 1.07e+01 angle pdb=" CB MET D 134 " pdb=" CG MET D 134 " pdb=" SD MET D 134 " ideal model delta sigma weight residual 112.70 103.02 9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N THR D 231 " pdb=" CA THR D 231 " pdb=" C THR D 231 " ideal model delta sigma weight residual 111.71 107.53 4.18 1.34e+00 5.57e-01 9.73e+00 angle pdb=" CA GLN A 97 " pdb=" CB GLN A 97 " pdb=" CG GLN A 97 " ideal model delta sigma weight residual 114.10 119.95 -5.85 2.00e+00 2.50e-01 8.56e+00 ... (remaining 23011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 10175 35.54 - 71.08: 386 71.08 - 106.62: 26 106.62 - 142.16: 1 142.16 - 177.70: 38 Dihedral angle restraints: 10626 sinusoidal: 4632 harmonic: 5994 Sorted by residual: dihedral pdb=" CA LEU B 254 " pdb=" C LEU B 254 " pdb=" N TRP B 255 " pdb=" CA TRP B 255 " ideal model delta harmonic sigma weight residual 180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CAN 4BW A 402 " pdb=" OAV 4BW A 402 " pdb=" PBR 4BW A 402 " pdb=" OAH 4BW A 402 " ideal model delta sinusoidal sigma weight residual -29.82 147.88 -177.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CAN 4BW C 401 " pdb=" OAV 4BW C 401 " pdb=" PBR 4BW C 401 " pdb=" OAH 4BW C 401 " ideal model delta sinusoidal sigma weight residual 330.18 153.03 177.15 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1611 0.029 - 0.058: 629 0.058 - 0.087: 176 0.087 - 0.115: 126 0.115 - 0.144: 20 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA ILE F 297 " pdb=" N ILE F 297 " pdb=" C ILE F 297 " pdb=" CB ILE F 297 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA TYR D 251 " pdb=" N TYR D 251 " pdb=" C TYR D 251 " pdb=" CB TYR D 251 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE D 135 " pdb=" N ILE D 135 " pdb=" C ILE D 135 " pdb=" CB ILE D 135 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2559 not shown) Planarity restraints: 2892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 184 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" CD GLU B 184 " 0.027 2.00e-02 2.50e+03 pdb=" OE1 GLU B 184 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 184 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 99 " 0.012 2.00e-02 2.50e+03 9.83e-03 2.41e+00 pdb=" CG TRP A 99 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP A 99 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 99 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 99 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 99 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 99 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 99 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 297 " 0.025 5.00e-02 4.00e+02 3.84e-02 2.36e+00 pdb=" N PRO F 298 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO F 298 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 298 " 0.021 5.00e-02 4.00e+02 ... (remaining 2889 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 715 2.72 - 3.26: 16802 3.26 - 3.81: 27561 3.81 - 4.35: 37161 4.35 - 4.90: 61716 Nonbonded interactions: 143955 Sorted by model distance: nonbonded pdb=" O ILE C 261 " pdb=" OG1 THR C 265 " model vdw 2.174 3.040 nonbonded pdb=" OH TYR E 107 " pdb=" OD2 ASP E 308 " model vdw 2.189 3.040 nonbonded pdb=" N GLU D 312 " pdb=" OE1 GLU D 312 " model vdw 2.202 3.120 nonbonded pdb=" OH TYR D 107 " pdb=" OD2 ASP D 308 " model vdw 2.206 3.040 nonbonded pdb=" N GLN C 97 " pdb=" OE1 GLN C 97 " model vdw 2.223 3.120 ... (remaining 143950 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 8 through 351) selection = chain 'B' selection = (chain 'C' and resid 8 through 351) selection = (chain 'D' and resid 8 through 351) selection = (chain 'E' and resid 8 through 351) selection = (chain 'F' and resid 8 through 351) } 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: 1.690 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.180 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.002 0.041 17035 Z= 0.081 Angle : 0.482 10.804 23016 Z= 0.237 Chirality : 0.039 0.144 2562 Planarity : 0.003 0.049 2892 Dihedral : 21.007 177.703 6762 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % Rotamer: Outliers : 1.85 % Allowed : 27.44 % Favored : 70.71 % 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: 0.23 (0.19), residues: 2052 helix: 0.60 (0.17), residues: 990 sheet: 0.53 (0.33), residues: 264 loop : -0.40 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 279 TYR 0.006 0.001 TYR B 107 PHE 0.013 0.001 PHE F 156 TRP 0.026 0.003 TRP A 99 HIS 0.002 0.001 HIS F 152 Details of bonding type rmsd covalent geometry : bond 0.00172 (17034) covalent geometry : angle 0.48184 (23016) hydrogen bonds : bond 0.23532 ( 744) hydrogen bonds : angle 7.52366 ( 2217) Misc. bond : bond 0.00235 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.629 Fit side-chains REVERT: A 134 MET cc_start: 0.9162 (ttp) cc_final: 0.8946 (ttp) REVERT: B 158 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.7442 (tmm) REVERT: C 295 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: D 222 GLU cc_start: 0.8769 (tt0) cc_final: 0.8293 (tm-30) REVERT: D 295 GLU cc_start: 0.8829 (pt0) cc_final: 0.8132 (pp20) REVERT: D 325 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9105 (mp) REVERT: E 97 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: E 137 SER cc_start: 0.9371 (t) cc_final: 0.9015 (p) REVERT: E 155 MET cc_start: 0.9202 (mmp) cc_final: 0.8081 (tmt) REVERT: F 97 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7373 (mp10) REVERT: F 251 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7475 (m-80) outliers start: 33 outliers final: 20 residues processed: 136 average time/residue: 0.5156 time to fit residues: 79.6829 Evaluate side-chains 130 residues out of total 1782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 104 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 TYR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 251 TYR Chi-restraints excluded: chain C residue 101 LEU Chi-restraints excluded: chain C residue 251 TYR Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 214 ASN Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 251 TYR Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain F residue 251 TYR Chi-restraints excluded: chain F residue 296 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 50.8291 > 50: distance: 76 - 82: 14.561 distance: 82 - 83: 10.189 distance: 83 - 84: 12.107 distance: 83 - 86: 12.220 distance: 84 - 85: 15.291 distance: 84 - 88: 19.729 distance: 86 - 87: 30.231 distance: 88 - 89: 30.772 distance: 89 - 90: 6.974 distance: 90 - 91: 10.119 distance: 90 - 92: 29.330 distance: 92 - 93: 6.528 distance: 93 - 94: 17.387 distance: 93 - 96: 4.442 distance: 94 - 95: 12.257 distance: 94 - 101: 31.600 distance: 96 - 97: 9.460 distance: 97 - 98: 9.535 distance: 98 - 99: 20.353 distance: 99 - 100: 22.052 distance: 101 - 102: 11.081 distance: 102 - 103: 8.769 distance: 103 - 104: 14.482 distance: 103 - 105: 23.332 distance: 105 - 106: 28.010 distance: 106 - 107: 10.810 distance: 106 - 109: 12.810 distance: 107 - 108: 24.815 distance: 107 - 117: 6.649 distance: 109 - 110: 6.648 distance: 110 - 111: 18.959 distance: 110 - 112: 19.924 distance: 111 - 113: 15.722 distance: 112 - 114: 27.899 distance: 113 - 115: 12.237 distance: 114 - 115: 15.948 distance: 115 - 116: 7.240 distance: 117 - 118: 22.529 distance: 118 - 119: 13.739 distance: 119 - 120: 15.438 distance: 119 - 125: 17.605 distance: 121 - 122: 46.324 distance: 122 - 123: 4.624 distance: 122 - 124: 7.410 distance: 125 - 126: 12.199 distance: 126 - 127: 24.758 distance: 126 - 129: 11.451 distance: 127 - 128: 35.152 distance: 127 - 131: 10.288 distance: 129 - 130: 10.229 distance: 131 - 132: 5.754 distance: 132 - 133: 10.074 distance: 132 - 135: 26.905 distance: 133 - 139: 12.866 distance: 135 - 136: 11.649 distance: 136 - 137: 25.214 distance: 136 - 138: 12.731 distance: 139 - 140: 24.389 distance: 140 - 141: 17.694 distance: 140 - 143: 31.264 distance: 141 - 142: 20.450 distance: 141 - 153: 18.457 distance: 143 - 144: 20.026 distance: 144 - 145: 13.829 distance: 144 - 146: 13.849 distance: 145 - 147: 18.110 distance: 146 - 148: 10.022 distance: 146 - 149: 10.145 distance: 147 - 148: 15.557 distance: 148 - 150: 10.395 distance: 149 - 151: 5.018 distance: 150 - 152: 7.475 distance: 151 - 152: 7.182 distance: 153 - 154: 27.793 distance: 154 - 155: 10.677 distance: 154 - 157: 5.613 distance: 155 - 156: 5.528 distance: 155 - 161: 31.805 distance: 157 - 158: 27.367 distance: 158 - 159: 16.257 distance: 158 - 160: 17.725