Starting phenix.real_space_refine on Thu Sep 18 07:35:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oa8_70275/09_2025/9oa8_70275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oa8_70275/09_2025/9oa8_70275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oa8_70275/09_2025/9oa8_70275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oa8_70275/09_2025/9oa8_70275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oa8_70275/09_2025/9oa8_70275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oa8_70275/09_2025/9oa8_70275.map" } resolution = 3.59 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= 0.000 sd= 1.000 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: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 K 3 8.98 5 S 104 5.16 5 Cl 8 4.86 5 C 9753 2.51 5 N 2713 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15255 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2758 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2754 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2754 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2754 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 7, 'TRANS': 352} Chain breaks: 1 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "F" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "G" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "H" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1042 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 143} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 6, 'GLN:plan1': 1, 'GLU:plan': 8, 'ASN:plan1': 2, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 16 Unusual residues: {' CA': 2, '1KP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.39, per 1000 atoms: 0.29 Number of scatterers: 15255 At special positions: 0 Unit cell: (141.04, 141.9, 106.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 K 3 19.00 Cl 8 17.00 S 104 16.00 O 2666 8.00 N 2713 7.00 C 9753 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: 1.33 Conformation dependent library (CDL) restraints added in 740.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 49 removed outlier: 4.086A pdb=" N LYS A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 32 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N HIS A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 71 removed outlier: 3.815A pdb=" N VAL A 61 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 67 " --> pdb=" O CYS A 63 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 92 removed outlier: 4.029A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 84 " --> pdb=" O HIS A 80 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 removed outlier: 4.007A pdb=" N ALA A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 155 Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.894A pdb=" N ARG A 159 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 161 through 172 removed outlier: 4.581A pdb=" N ARG A 165 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ARG A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.577A pdb=" N ASN A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 removed outlier: 3.831A pdb=" N VAL A 195 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 removed outlier: 3.959A pdb=" N LEU A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.662A pdb=" N ALA A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 249 removed outlier: 3.821A pdb=" N LEU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 265 through 289 removed outlier: 3.747A pdb=" N CYS A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 330 removed outlier: 3.541A pdb=" N GLN A 306 " --> pdb=" O MET A 302 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 368 removed outlier: 3.552A pdb=" N ALA A 346 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN A 364 " --> pdb=" O LYS A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 386 Processing helix chain 'B' and resid 10 through 50 removed outlier: 4.227A pdb=" N LYS B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ARG B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LEU B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU B 32 " --> pdb=" O TRP B 28 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA B 33 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N HIS B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 81 removed outlier: 3.833A pdb=" N VAL B 61 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS B 63 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N SER B 66 " --> pdb=" O LYS B 62 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE B 67 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR B 69 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.518A pdb=" N PHE B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 removed outlier: 4.259A pdb=" N ALA B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU B 100 " --> pdb=" O TRP B 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 100' Processing helix chain 'B' and resid 101 through 115 removed outlier: 4.008A pdb=" N ALA B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 155 Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.940A pdb=" N ARG B 159 " --> pdb=" O MET B 156 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 156 through 160' Processing helix chain 'B' and resid 161 through 169 removed outlier: 4.518A pdb=" N ARG B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 183 Processing helix chain 'B' and resid 191 through 203 removed outlier: 3.551A pdb=" N VAL B 195 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B 203 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 219 removed outlier: 3.648A pdb=" N LEU B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.508A pdb=" N ALA B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 3.537A pdb=" N THR B 240 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 265 through 289 removed outlier: 3.707A pdb=" N CYS B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 279 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 331 removed outlier: 3.968A pdb=" N ILE B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 369 removed outlier: 3.566A pdb=" N ALA B 346 " --> pdb=" O ARG B 342 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASN B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 361 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 386 Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.580A pdb=" N LYS C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER C 24 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 60 through 92 removed outlier: 3.967A pdb=" N ILE C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N SER C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 67 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 69 " --> pdb=" O ILE C 65 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 83 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL C 84 " --> pdb=" O HIS C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.940A pdb=" N ALA C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 156 through 160 removed outlier: 3.907A pdb=" N ARG C 159 " --> pdb=" O MET C 156 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 160' Processing helix chain 'C' and resid 161 through 168 removed outlier: 4.574A pdb=" N ARG C 165 " --> pdb=" O TYR C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.535A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.836A pdb=" N LEU C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 209 " --> pdb=" O GLY C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.574A pdb=" N GLU C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 3.542A pdb=" N THR C 240 " --> pdb=" O HIS C 236 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 260 through 289 removed outlier: 3.691A pdb=" N LYS C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N CYS C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 289 " --> pdb=" O VAL C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 328 removed outlier: 3.653A pdb=" N GLN C 306 " --> pdb=" O MET C 302 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 309 " --> pdb=" O ILE C 305 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 312 " --> pdb=" O THR C 308 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 317 " --> pdb=" O GLU C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 367 removed outlier: 3.664A pdb=" N ARG C 352 " --> pdb=" O ILE C 348 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN C 353 " --> pdb=" O ASN C 349 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 386 Processing helix chain 'D' and resid 10 through 26 removed outlier: 3.538A pdb=" N SER D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 50 removed outlier: 4.116A pdb=" N VAL D 31 " --> pdb=" O GLY D 27 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU D 32 " --> pdb=" O TRP D 28 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA D 33 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET D 40 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 68 removed outlier: 3.710A pdb=" N ILE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 92 Processing helix chain 'D' and resid 95 through 100 removed outlier: 4.170A pdb=" N ALA D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 100 " --> pdb=" O TRP D 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 100' Processing helix chain 'D' and resid 103 through 115 Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 156 through 160 removed outlier: 3.928A pdb=" N ARG D 159 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 156 through 160' Processing helix chain 'D' and resid 161 through 169 removed outlier: 4.544A pdb=" N ARG D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 185 removed outlier: 3.553A pdb=" N ALA D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 203 removed outlier: 3.550A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 227 removed outlier: 3.816A pdb=" N LEU D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU D 217 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TRP D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU D 227 " --> pdb=" O LEU D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 249 removed outlier: 3.938A pdb=" N LEU D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 260 through 289 removed outlier: 3.864A pdb=" N LYS D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE D 265 " --> pdb=" O MET D 261 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ALA D 279 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU D 280 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 281 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 289 " --> pdb=" O VAL D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 330 removed outlier: 4.017A pdb=" N ILE D 305 " --> pdb=" O PHE D 301 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 317 " --> pdb=" O GLU D 313 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TRP D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 369 removed outlier: 3.604A pdb=" N LEU D 345 " --> pdb=" O GLN D 341 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA D 346 " --> pdb=" O ARG D 342 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 367 " --> pdb=" O GLU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.501A pdb=" N ILE E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU E 18 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 40 removed outlier: 3.524A pdb=" N LEU E 32 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 54 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.112A pdb=" N THR E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET E 71 " --> pdb=" O GLU E 67 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG E 74 " --> pdb=" O THR E 70 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS E 75 " --> pdb=" O MET E 71 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 91 removed outlier: 3.648A pdb=" N ALA E 88 " --> pdb=" O GLU E 84 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE E 89 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E 90 " --> pdb=" O ARG E 86 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 110 Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 137 through 147 Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.761A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 39 removed outlier: 3.669A pdb=" N LEU F 32 " --> pdb=" O THR F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 56 removed outlier: 4.060A pdb=" N VAL F 55 " --> pdb=" O MET F 51 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.874A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG F 74 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS F 75 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET F 76 " --> pdb=" O MET F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 101 through 109 removed outlier: 4.037A pdb=" N LEU F 105 " --> pdb=" O SER F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 129 Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.738A pdb=" N MET F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.653A pdb=" N PHE G 19 " --> pdb=" O ALA G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 39 removed outlier: 3.603A pdb=" N LEU G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 54 Processing helix chain 'G' and resid 64 through 73 removed outlier: 3.930A pdb=" N THR G 70 " --> pdb=" O PRO G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 91 removed outlier: 3.597A pdb=" N ALA G 88 " --> pdb=" O GLU G 84 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE G 89 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG G 90 " --> pdb=" O ARG G 86 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 110 removed outlier: 3.854A pdb=" N LEU G 105 " --> pdb=" O SER G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 129 Processing helix chain 'G' and resid 137 through 146 Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.757A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 40 removed outlier: 3.928A pdb=" N LEU H 32 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 54 Processing helix chain 'H' and resid 64 through 76 removed outlier: 4.202A pdb=" N ARG H 74 " --> pdb=" O THR H 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS H 75 " --> pdb=" O MET H 71 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET H 76 " --> pdb=" O MET H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.896A pdb=" N VAL H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 92' Processing helix chain 'H' and resid 101 through 109 removed outlier: 3.574A pdb=" N LEU H 105 " --> pdb=" O SER H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.599A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2676 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: 2.44 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2704 1.32 - 1.45: 3844 1.45 - 1.57: 8784 1.57 - 1.69: 0 1.69 - 1.81: 188 Bond restraints: 15520 Sorted by residual: bond pdb=" CG LEU B 319 " pdb=" CD1 LEU B 319 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.37e-01 bond pdb=" C MET B 302 " pdb=" O MET B 302 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.28e-02 6.10e+03 6.22e-01 bond pdb=" CB ASP H 24 " pdb=" CG ASP H 24 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.18e-01 bond pdb=" C MET D 302 " pdb=" O MET D 302 " ideal model delta sigma weight residual 1.237 1.247 -0.010 1.31e-02 5.83e+03 6.05e-01 bond pdb=" CB TYR A 179 " pdb=" CG TYR A 179 " ideal model delta sigma weight residual 1.512 1.496 0.016 2.20e-02 2.07e+03 5.15e-01 ... (remaining 15515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20567 1.29 - 2.59: 371 2.59 - 3.88: 64 3.88 - 5.17: 22 5.17 - 6.47: 5 Bond angle restraints: 21029 Sorted by residual: angle pdb=" C THR G 26 " pdb=" N ILE G 27 " pdb=" CA ILE G 27 " ideal model delta sigma weight residual 121.95 126.97 -5.02 1.53e+00 4.27e-01 1.08e+01 angle pdb=" N VAL D 98 " pdb=" CA VAL D 98 " pdb=" C VAL D 98 " ideal model delta sigma weight residual 113.39 109.65 3.74 1.47e+00 4.63e-01 6.46e+00 angle pdb=" C ILE C 244 " pdb=" CA ILE C 244 " pdb=" CB ILE C 244 " ideal model delta sigma weight residual 114.00 110.95 3.05 1.31e+00 5.83e-01 5.42e+00 angle pdb=" C LEU C 243 " pdb=" N ILE C 244 " pdb=" CA ILE C 244 " ideal model delta sigma weight residual 120.33 122.17 -1.84 8.00e-01 1.56e+00 5.31e+00 angle pdb=" C ARG H 106 " pdb=" N HIS H 107 " pdb=" CA HIS H 107 " ideal model delta sigma weight residual 121.92 117.97 3.95 1.73e+00 3.34e-01 5.20e+00 ... (remaining 21024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8250 17.92 - 35.84: 719 35.84 - 53.76: 141 53.76 - 71.67: 25 71.67 - 89.59: 20 Dihedral angle restraints: 9155 sinusoidal: 3351 harmonic: 5804 Sorted by residual: dihedral pdb=" CA ASP H 93 " pdb=" CB ASP H 93 " pdb=" CG ASP H 93 " pdb=" OD1 ASP H 93 " ideal model delta sinusoidal sigma weight residual -30.00 -86.62 56.62 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU C 111 " pdb=" CG GLU C 111 " pdb=" CD GLU C 111 " pdb=" OE1 GLU C 111 " ideal model delta sinusoidal sigma weight residual 0.00 89.59 -89.59 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU H 87 " pdb=" CG GLU H 87 " pdb=" CD GLU H 87 " pdb=" OE1 GLU H 87 " ideal model delta sinusoidal sigma weight residual 0.00 -88.79 88.79 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 9152 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1539 0.032 - 0.063: 737 0.063 - 0.095: 149 0.095 - 0.127: 34 0.127 - 0.159: 1 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA ILE G 27 " pdb=" N ILE G 27 " pdb=" C ILE G 27 " pdb=" CB ILE G 27 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.29e-01 chirality pdb=" CB VAL A 369 " pdb=" CA VAL A 369 " pdb=" CG1 VAL A 369 " pdb=" CG2 VAL A 369 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA PHE H 65 " pdb=" N PHE H 65 " pdb=" C PHE H 65 " pdb=" CB PHE H 65 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 2457 not shown) Planarity restraints: 2641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 92 " 0.009 2.00e-02 2.50e+03 1.01e-02 1.80e+00 pdb=" CG PHE H 92 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE H 92 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE H 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 92 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 92 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE H 92 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 141 " -0.012 2.00e-02 2.50e+03 9.00e-03 1.42e+00 pdb=" CG PHE E 141 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE E 141 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE E 141 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 141 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 141 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS D 118 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.18e+00 pdb=" N PRO D 119 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " -0.015 5.00e-02 4.00e+02 ... (remaining 2638 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.24: 12 2.24 - 2.97: 6983 2.97 - 3.69: 25119 3.69 - 4.42: 37370 4.42 - 5.14: 64069 Nonbonded interactions: 133553 Sorted by model distance: nonbonded pdb=" OD1 ASP H 22 " pdb=" OE2 GLU H 31 " model vdw 1.515 3.040 nonbonded pdb=" C THR G 26 " pdb="CA CA G 202 " model vdw 1.696 2.740 nonbonded pdb=" O THR G 26 " pdb="CA CA G 202 " model vdw 1.718 2.510 nonbonded pdb=" OD1 ASP F 56 " pdb=" OD1 ASP F 58 " model vdw 2.010 3.040 nonbonded pdb=" OD2 ASP F 56 " pdb=" O THR F 62 " model vdw 2.013 3.040 ... (remaining 133548 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 9 through 365 or (resid 366 and (name N or name CA or name \ C or name O or name CB )) or resid 367 through 385 or (resid 386 and (name N or \ name CA or name C or name O or name CB )))) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.460 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: 0.030 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.230 Find NCS groups from input model: 0.330 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: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 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 : 0.003 0.026 15520 Z= 0.132 Angle : 0.465 6.467 21029 Z= 0.250 Chirality : 0.036 0.159 2460 Planarity : 0.003 0.027 2641 Dihedral : 14.791 89.593 5395 Min Nonbonded Distance : 1.515 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.20), residues: 2000 helix: 1.06 (0.15), residues: 1468 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.017 0.001 TYR A 179 PHE 0.022 0.001 PHE H 92 TRP 0.010 0.001 TRP C 54 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00292 (15520) covalent geometry : angle 0.46484 (21029) hydrogen bonds : bond 0.07879 ( 892) hydrogen bonds : angle 3.36540 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4000 Ramachandran restraints generated. 2000 Oldfield, 0 Emsley, 2000 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 324 MET cc_start: 0.6929 (mmp) cc_final: 0.6621 (ttm) REVERT: B 326 TYR cc_start: 0.7638 (t80) cc_final: 0.7323 (t80) REVERT: C 40 MET cc_start: 0.8177 (tmm) cc_final: 0.7717 (ttp) REVERT: F 42 ASN cc_start: 0.8296 (p0) cc_final: 0.8093 (p0) REVERT: G 78 ASP cc_start: 0.8544 (t70) cc_final: 0.8216 (t0) REVERT: H 50 ASP cc_start: 0.7597 (t70) cc_final: 0.7157 (t0) REVERT: H 78 ASP cc_start: 0.8743 (t70) cc_final: 0.8515 (t0) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1539 time to fit residues: 62.3722 Evaluate side-chains 215 residues out of total 1704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/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-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.4314 > 50: distance: 46 - 52: 9.302 distance: 52 - 53: 15.217 distance: 53 - 54: 20.864 distance: 53 - 56: 24.679 distance: 54 - 55: 15.963 distance: 54 - 58: 20.667 distance: 56 - 57: 29.201 distance: 58 - 59: 38.280 distance: 59 - 60: 59.904 distance: 59 - 62: 22.217 distance: 60 - 61: 32.420 distance: 60 - 67: 44.479 distance: 61 - 93: 40.988 distance: 62 - 63: 13.015 distance: 63 - 64: 7.002 distance: 64 - 65: 7.004 distance: 64 - 66: 7.162 distance: 67 - 68: 31.701 distance: 68 - 69: 45.146 distance: 68 - 71: 28.324 distance: 69 - 70: 25.251 distance: 69 - 76: 42.720 distance: 70 - 104: 23.463 distance: 71 - 72: 27.735 distance: 72 - 73: 19.369 distance: 73 - 74: 36.823 distance: 73 - 75: 22.061 distance: 76 - 77: 19.813 distance: 77 - 78: 38.677 distance: 77 - 80: 32.808 distance: 78 - 79: 20.174 distance: 78 - 85: 30.313 distance: 80 - 81: 25.723 distance: 81 - 82: 27.996 distance: 82 - 83: 20.316 distance: 82 - 84: 18.363 distance: 85 - 86: 27.048 distance: 86 - 87: 47.380 distance: 86 - 89: 52.936 distance: 87 - 88: 40.739 distance: 87 - 93: 49.350 distance: 89 - 90: 50.636 distance: 89 - 91: 42.723 distance: 90 - 92: 31.081 distance: 93 - 94: 50.700 distance: 94 - 95: 57.777 distance: 94 - 97: 44.936 distance: 95 - 96: 18.151 distance: 95 - 104: 36.452 distance: 97 - 98: 24.455 distance: 98 - 99: 18.704 distance: 99 - 100: 16.397 distance: 100 - 101: 50.317 distance: 101 - 102: 41.146 distance: 101 - 103: 42.779 distance: 104 - 105: 36.603 distance: 105 - 106: 29.559 distance: 105 - 108: 39.423 distance: 106 - 107: 12.497 distance: 106 - 113: 41.562 distance: 108 - 109: 40.084 distance: 109 - 110: 36.121 distance: 110 - 111: 32.355 distance: 110 - 112: 37.259 distance: 113 - 114: 23.118 distance: 114 - 115: 38.240 distance: 114 - 117: 42.496 distance: 115 - 116: 35.933 distance: 115 - 118: 29.790 distance: 118 - 119: 22.503 distance: 119 - 120: 17.828 distance: 119 - 122: 21.381 distance: 120 - 121: 23.180 distance: 120 - 129: 18.258 distance: 122 - 123: 16.535 distance: 123 - 124: 20.789 distance: 123 - 125: 15.114 distance: 124 - 126: 14.052 distance: 125 - 127: 8.425 distance: 126 - 128: 8.493 distance: 127 - 128: 3.725 distance: 129 - 130: 23.328 distance: 130 - 131: 22.675 distance: 130 - 133: 41.835 distance: 131 - 132: 37.584 distance: 131 - 140: 30.533 distance: 133 - 134: 14.747 distance: 134 - 135: 25.560 distance: 135 - 136: 11.619 distance: 136 - 137: 4.265 distance: 137 - 138: 4.010 distance: 137 - 139: 13.644