Starting phenix.real_space_refine on Wed Feb 4 18:05:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zrl_74626/02_2026/9zrl_74626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zrl_74626/02_2026/9zrl_74626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zrl_74626/02_2026/9zrl_74626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zrl_74626/02_2026/9zrl_74626.map" model { file = "/net/cci-nas-00/data/ceres_data/9zrl_74626/02_2026/9zrl_74626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zrl_74626/02_2026/9zrl_74626.cif" } resolution = 3.38 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: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 80 5.16 5 C 7716 2.51 5 N 2136 2.21 5 O 2063 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s 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: 11999 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2558 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2562 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2562 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "D" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2573 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 335} Chain breaks: 1 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 9, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "E" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 435 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "F" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 435 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "G" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 435 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 435 Classifications: {'peptide': 67} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'TRANS': 66} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 84 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 71 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' K': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.82, per 1000 atoms: 0.24 Number of scatterers: 11999 At special positions: 0 Unit cell: (125.56, 127.28, 101.48, 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) K 4 19.00 S 80 16.00 O 2063 8.00 N 2136 7.00 C 7716 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: 1.03 Conformation dependent library (CDL) restraints added in 576.0 milliseconds 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3040 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 1 sheets defined 77.4% alpha, 0.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 28 through 50 removed outlier: 3.915A pdb=" N LEU A 32 " --> pdb=" O TRP A 28 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 92 removed outlier: 4.053A pdb=" N VAL A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 78 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N HIS A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 148 through 155 removed outlier: 3.678A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.551A pdb=" N LEU A 160 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR A 161 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 172 removed outlier: 3.633A pdb=" N ALA A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 removed outlier: 3.583A pdb=" N ILE A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 203 Processing helix chain 'A' and resid 203 through 214 removed outlier: 3.761A pdb=" N LEU A 207 " --> pdb=" O HIS A 203 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 236 through 249 removed outlier: 4.810A pdb=" N TRP A 242 " --> pdb=" O SER A 238 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 262 through 288 removed outlier: 4.145A pdb=" N VAL A 266 " --> pdb=" O TRP A 262 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 271 " --> pdb=" O CYS A 267 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 327 removed outlier: 3.644A pdb=" N LEU A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 369 removed outlier: 3.967A pdb=" N ARG A 339 " --> pdb=" O HIS A 335 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 removed outlier: 4.391A pdb=" N GLU B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 50 removed outlier: 3.582A pdb=" N LEU B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET B 40 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 88 removed outlier: 3.918A pdb=" N LYS B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA B 78 " --> pdb=" O CYS B 74 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 Processing helix chain 'B' and resid 146 through 155 removed outlier: 3.830A pdb=" N LEU B 151 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.585A pdb=" N LEU B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.469A pdb=" N ARG B 165 " --> pdb=" O TYR B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 176 through 187 Processing helix chain 'B' and resid 193 through 203 Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.660A pdb=" N LEU B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'B' and resid 208 through 227 removed outlier: 4.024A pdb=" N THR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA B 220 " --> pdb=" O TRP B 216 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TRP B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL B 222 " --> pdb=" O THR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 249 removed outlier: 4.870A pdb=" N TRP B 242 " --> pdb=" O SER B 238 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix Processing helix chain 'B' and resid 262 through 288 removed outlier: 4.114A pdb=" N VAL B 266 " --> pdb=" O TRP B 262 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N CYS B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 271 " --> pdb=" O CYS B 267 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 273 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 331 removed outlier: 3.721A pdb=" N LEU B 319 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 369 Processing helix chain 'C' and resid 13 through 51 removed outlier: 3.704A pdb=" N ALA C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 88 removed outlier: 3.907A pdb=" N VAL C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA C 78 " --> pdb=" O CYS C 74 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N PHE C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 115 removed outlier: 3.836A pdb=" N ALA C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA C 106 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 removed outlier: 3.890A pdb=" N LEU C 151 " --> pdb=" O GLN C 147 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 161 removed outlier: 3.552A pdb=" N LEU C 160 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR C 161 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 171 removed outlier: 3.572A pdb=" N ALA C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 191 through 203 removed outlier: 3.808A pdb=" N VAL C 195 " --> pdb=" O ARG C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.642A pdb=" N LEU C 207 " --> pdb=" O HIS C 203 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 203 through 208' Processing helix chain 'C' and resid 208 through 227 removed outlier: 3.536A pdb=" N LEU C 213 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY C 214 " --> pdb=" O GLY C 210 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 220 " --> pdb=" O TRP C 216 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TRP C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL C 222 " --> pdb=" O THR C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 removed outlier: 4.802A pdb=" N TRP C 242 " --> pdb=" O SER C 238 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 244 " --> pdb=" O THR C 240 " (cutoff:3.500A) Proline residue: C 245 - end of helix Processing helix chain 'C' and resid 262 through 288 removed outlier: 4.132A pdb=" N VAL C 266 " --> pdb=" O TRP C 262 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS C 267 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLY C 271 " --> pdb=" O CYS C 267 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 327 removed outlier: 3.655A pdb=" N TRP C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 369 removed outlier: 4.343A pdb=" N ARG C 339 " --> pdb=" O HIS C 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 25 removed outlier: 3.894A pdb=" N GLU D 22 " --> pdb=" O LEU D 18 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 50 removed outlier: 3.660A pdb=" N TRP D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 92 removed outlier: 4.017A pdb=" N VAL D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ALA D 78 " --> pdb=" O CYS D 74 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N HIS D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 removed outlier: 3.529A pdb=" N VAL D 98 " --> pdb=" O ASP D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 116 removed outlier: 3.818A pdb=" N ALA D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 106 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 109 " --> pdb=" O ALA D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 155 removed outlier: 3.668A pdb=" N LEU D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 removed outlier: 3.548A pdb=" N LEU D 160 " --> pdb=" O LEU D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 171 removed outlier: 4.545A pdb=" N ARG D 165 " --> pdb=" O TYR D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 Processing helix chain 'D' and resid 191 through 203 removed outlier: 3.916A pdb=" N VAL D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.614A pdb=" N LEU D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 203 through 208' Processing helix chain 'D' and resid 208 through 227 removed outlier: 4.026A pdb=" N THR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 214 " --> pdb=" O GLY D 210 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D 220 " --> pdb=" O TRP D 216 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 249 removed outlier: 4.852A pdb=" N TRP D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Proline residue: D 245 - end of helix Processing helix chain 'D' and resid 262 through 288 removed outlier: 4.136A pdb=" N VAL D 266 " --> pdb=" O TRP D 262 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N CYS D 267 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY D 271 " --> pdb=" O CYS D 267 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET D 273 " --> pdb=" O CYS D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 331 removed outlier: 3.555A pdb=" N LYS D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 319 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 369 Processing helix chain 'E' and resid 87 through 92 Processing helix chain 'E' and resid 105 through 110 removed outlier: 4.165A pdb=" N MET E 109 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 110' Processing helix chain 'E' and resid 120 through 128 removed outlier: 4.037A pdb=" N MET E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'F' and resid 101 through 111 Processing helix chain 'F' and resid 117 through 128 removed outlier: 3.924A pdb=" N ASP F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU F 123 " --> pdb=" O GLU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 147 Processing helix chain 'G' and resid 87 through 92 Processing helix chain 'G' and resid 102 through 111 Processing helix chain 'G' and resid 117 through 127 removed outlier: 3.935A pdb=" N ASP G 122 " --> pdb=" O ASP G 118 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLU G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 147 Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 101 through 111 Processing helix chain 'H' and resid 117 through 129 Processing helix chain 'H' and resid 138 through 147 Processing sheet with id=AA1, first strand: chain 'G' and resid 100 through 101 removed outlier: 3.538A pdb=" N VAL G 136 " --> pdb=" O ILE G 100 " (cutoff:3.500A) 804 hydrogen bonds defined for protein. 2391 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: 1.65 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3943 1.34 - 1.46: 2753 1.46 - 1.58: 5384 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 12212 Sorted by residual: bond pdb=" CB LYS B 357 " pdb=" CG LYS B 357 " ideal model delta sigma weight residual 1.520 1.477 0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CD LYS B 357 " pdb=" CE LYS B 357 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" N LEU D 12 " pdb=" CA LEU D 12 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.36e+00 bond pdb=" CB LYS A 357 " pdb=" CG LYS A 357 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB GLN B 364 " pdb=" CG GLN B 364 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 ... (remaining 12207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 16261 1.53 - 3.05: 224 3.05 - 4.58: 65 4.58 - 6.10: 28 6.10 - 7.63: 12 Bond angle restraints: 16590 Sorted by residual: angle pdb=" C ASN D 300 " pdb=" N PHE D 301 " pdb=" CA PHE D 301 " ideal model delta sigma weight residual 121.14 113.88 7.26 1.75e+00 3.27e-01 1.72e+01 angle pdb=" N GLU B 313 " pdb=" CA GLU B 313 " pdb=" CB GLU B 313 " ideal model delta sigma weight residual 110.28 115.99 -5.71 1.55e+00 4.16e-01 1.36e+01 angle pdb=" C LYS B 312 " pdb=" N GLU B 313 " pdb=" CA GLU B 313 " ideal model delta sigma weight residual 120.31 115.46 4.85 1.52e+00 4.33e-01 1.02e+01 angle pdb=" CA MET E 109 " pdb=" CB MET E 109 " pdb=" CG MET E 109 " ideal model delta sigma weight residual 114.10 119.27 -5.17 2.00e+00 2.50e-01 6.68e+00 angle pdb=" C LYS E 94 " pdb=" N ASP E 95 " pdb=" CA ASP E 95 " ideal model delta sigma weight residual 122.08 125.80 -3.72 1.47e+00 4.63e-01 6.39e+00 ... (remaining 16585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 6447 17.56 - 35.12: 580 35.12 - 52.69: 121 52.69 - 70.25: 13 70.25 - 87.81: 11 Dihedral angle restraints: 7172 sinusoidal: 2480 harmonic: 4692 Sorted by residual: dihedral pdb=" CA LYS B 332 " pdb=" C LYS B 332 " pdb=" N GLU B 333 " pdb=" CA GLU B 333 " ideal model delta harmonic sigma weight residual 180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ALA A 26 " pdb=" C ALA A 26 " pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CB GLU H 84 " pdb=" CG GLU H 84 " pdb=" CD GLU H 84 " pdb=" OE1 GLU H 84 " ideal model delta sinusoidal sigma weight residual 0.00 87.01 -87.01 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 7169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1598 0.045 - 0.090: 340 0.090 - 0.136: 47 0.136 - 0.181: 2 0.181 - 0.226: 1 Chirality restraints: 1988 Sorted by residual: chirality pdb=" CG LEU B 361 " pdb=" CB LEU B 361 " pdb=" CD1 LEU B 361 " pdb=" CD2 LEU B 361 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA PHE D 301 " pdb=" N PHE D 301 " pdb=" C PHE D 301 " pdb=" CB PHE D 301 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CB VAL E 108 " pdb=" CA VAL E 108 " pdb=" CG1 VAL E 108 " pdb=" CG2 VAL E 108 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1985 not shown) Planarity restraints: 2069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 301 " -0.015 2.00e-02 2.50e+03 1.05e-02 1.94e+00 pdb=" CG PHE D 301 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 301 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE D 301 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 301 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 301 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE D 301 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 83 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.72e+00 pdb=" C GLU E 83 " -0.023 2.00e-02 2.50e+03 pdb=" O GLU E 83 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU E 84 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 244 " -0.019 5.00e-02 4.00e+02 2.79e-02 1.24e+00 pdb=" N PRO C 245 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO C 245 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 245 " -0.016 5.00e-02 4.00e+02 ... (remaining 2066 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3170 2.81 - 3.39: 13576 3.39 - 3.98: 20201 3.98 - 4.56: 27987 4.56 - 5.14: 39561 Nonbonded interactions: 104495 Sorted by model distance: nonbonded pdb=" O ALA F 103 " pdb=" ND1 HIS F 107 " model vdw 2.230 3.120 nonbonded pdb=" O GLN H 143 " pdb=" OG1 THR H 146 " model vdw 2.292 3.040 nonbonded pdb=" OE2 GLU A 111 " pdb=" NH2 ARG A 165 " model vdw 2.312 3.120 nonbonded pdb=" OD1 ASN C 201 " pdb=" NH2 ARG C 287 " model vdw 2.335 3.120 nonbonded pdb=" O GLN F 143 " pdb=" OG1 THR F 146 " model vdw 2.346 3.040 ... (remaining 104490 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 369) selection = (chain 'B' and (resid 9 through 340 or (resid 341 and (name N or name CA or name \ C or name O or name CB )) or resid 342 through 369)) selection = (chain 'C' and (resid 9 through 340 or (resid 341 and (name N or name CA or name \ C or name O or name CB )) or resid 342 through 369)) selection = (chain 'D' and (resid 9 through 338 or (resid 339 through 341 and (name N or nam \ e CA or name C or name O or name CB )) or resid 342 through 369)) } 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 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: 10.880 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 0.043 12212 Z= 0.127 Angle : 0.553 7.630 16590 Z= 0.280 Chirality : 0.036 0.226 1988 Planarity : 0.003 0.030 2069 Dihedral : 14.254 87.810 4132 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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: 1.28 (0.23), residues: 1616 helix: 1.70 (0.16), residues: 1190 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 106 TYR 0.010 0.001 TYR A 199 PHE 0.021 0.001 PHE D 301 TRP 0.014 0.001 TRP B 242 HIS 0.010 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00284 (12212) covalent geometry : angle 0.55259 (16590) hydrogen bonds : bond 0.09928 ( 804) hydrogen bonds : angle 3.89230 ( 2391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.8355 (tmm) cc_final: 0.7726 (ttp) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1254 time to fit residues: 34.7214 Evaluate side-chains 183 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.0970 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0770 chunk 149 optimal weight: 9.9990 overall best weight: 0.4014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 320 GLN C 328 HIS C 358 HIS D 201 ASN D 320 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.217316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123041 restraints weight = 13750.742| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.30 r_work: 0.3192 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12212 Z= 0.111 Angle : 0.479 9.508 16590 Z= 0.241 Chirality : 0.034 0.164 1988 Planarity : 0.003 0.026 2069 Dihedral : 3.283 25.508 1733 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.18 % Allowed : 7.27 % Favored : 91.55 % 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: 1.40 (0.23), residues: 1616 helix: 1.76 (0.16), residues: 1192 sheet: None (None), residues: 0 loop : -1.52 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 106 TYR 0.006 0.001 TYR D 161 PHE 0.015 0.001 PHE B 291 TRP 0.011 0.001 TRP C 242 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00241 (12212) covalent geometry : angle 0.47867 (16590) hydrogen bonds : bond 0.04176 ( 804) hydrogen bonds : angle 3.27306 ( 2391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 201 ASN cc_start: 0.6699 (m-40) cc_final: 0.6120 (m110) REVERT: D 310 GLU cc_start: 0.8855 (tp30) cc_final: 0.8167 (tp30) REVERT: D 313 GLU cc_start: 0.8762 (tp30) cc_final: 0.8406 (pt0) outliers start: 13 outliers final: 9 residues processed: 187 average time/residue: 0.1078 time to fit residues: 29.0896 Evaluate side-chains 188 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 179 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 91 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 87 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 90 optimal weight: 0.2980 chunk 109 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 320 GLN B 358 HIS C 328 HIS C 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.215399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.122546 restraints weight = 13883.507| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.35 r_work: 0.3171 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12212 Z= 0.123 Angle : 0.470 7.854 16590 Z= 0.239 Chirality : 0.034 0.130 1988 Planarity : 0.003 0.027 2069 Dihedral : 3.278 25.678 1733 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.63 % Allowed : 10.90 % Favored : 87.47 % 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: 1.46 (0.23), residues: 1616 helix: 1.77 (0.16), residues: 1205 sheet: None (None), residues: 0 loop : -1.51 (0.33), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 106 TYR 0.009 0.001 TYR E 138 PHE 0.016 0.001 PHE D 301 TRP 0.013 0.001 TRP C 242 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00289 (12212) covalent geometry : angle 0.46953 (16590) hydrogen bonds : bond 0.04416 ( 804) hydrogen bonds : angle 3.18795 ( 2391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 353 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8853 (tm-30) REVERT: D 201 ASN cc_start: 0.6759 (m-40) cc_final: 0.6286 (m110) REVERT: D 310 GLU cc_start: 0.8838 (tp30) cc_final: 0.8177 (tp30) REVERT: D 313 GLU cc_start: 0.8740 (tp30) cc_final: 0.8401 (pt0) REVERT: G 106 ARG cc_start: 0.7477 (mtm-85) cc_final: 0.7274 (ptp-110) outliers start: 18 outliers final: 11 residues processed: 186 average time/residue: 0.1111 time to fit residues: 29.6133 Evaluate side-chains 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 176 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 358 HIS C 328 HIS C 358 HIS D 320 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.213424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122124 restraints weight = 14000.977| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 3.69 r_work: 0.3113 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12212 Z= 0.149 Angle : 0.495 7.271 16590 Z= 0.254 Chirality : 0.035 0.123 1988 Planarity : 0.003 0.030 2069 Dihedral : 3.385 25.099 1733 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.54 % Allowed : 13.99 % Favored : 84.47 % 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: 1.38 (0.23), residues: 1616 helix: 1.70 (0.16), residues: 1212 sheet: None (None), residues: 0 loop : -1.55 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 106 TYR 0.005 0.001 TYR A 253 PHE 0.016 0.001 PHE B 291 TRP 0.016 0.001 TRP D 242 HIS 0.008 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00369 (12212) covalent geometry : angle 0.49492 (16590) hydrogen bonds : bond 0.04851 ( 804) hydrogen bonds : angle 3.24884 ( 2391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 349 ASN cc_start: 0.9220 (m-40) cc_final: 0.9014 (m110) REVERT: C 40 MET cc_start: 0.8323 (tmm) cc_final: 0.7658 (ttp) REVERT: D 201 ASN cc_start: 0.6679 (m-40) cc_final: 0.6161 (m110) REVERT: D 310 GLU cc_start: 0.8842 (tp30) cc_final: 0.8175 (tp30) REVERT: D 313 GLU cc_start: 0.8758 (tp30) cc_final: 0.8417 (pt0) REVERT: H 145 MET cc_start: 0.7607 (tmm) cc_final: 0.7373 (tmm) outliers start: 17 outliers final: 13 residues processed: 181 average time/residue: 0.1142 time to fit residues: 29.5881 Evaluate side-chains 189 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 145 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 137 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 118 optimal weight: 0.3980 chunk 60 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 320 GLN B 358 HIS C 328 HIS C 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.214626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116420 restraints weight = 13930.860| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.61 r_work: 0.3220 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12212 Z= 0.123 Angle : 0.470 6.899 16590 Z= 0.243 Chirality : 0.034 0.152 1988 Planarity : 0.003 0.029 2069 Dihedral : 3.329 25.614 1733 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 1.73 % Allowed : 15.26 % Favored : 83.02 % 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: 1.41 (0.23), residues: 1616 helix: 1.74 (0.16), residues: 1212 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 106 TYR 0.004 0.001 TYR D 57 PHE 0.019 0.001 PHE D 301 TRP 0.014 0.001 TRP B 242 HIS 0.009 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00287 (12212) covalent geometry : angle 0.47001 (16590) hydrogen bonds : bond 0.04440 ( 804) hydrogen bonds : angle 3.19830 ( 2391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 328 HIS cc_start: 0.5399 (m-70) cc_final: 0.5093 (m-70) REVERT: C 40 MET cc_start: 0.8448 (tmm) cc_final: 0.7645 (ttp) REVERT: C 353 GLN cc_start: 0.9106 (tm-30) cc_final: 0.8808 (tm-30) REVERT: D 201 ASN cc_start: 0.6751 (m-40) cc_final: 0.6247 (m110) REVERT: D 301 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.6989 (p90) REVERT: D 310 GLU cc_start: 0.8812 (tp30) cc_final: 0.8316 (tp30) REVERT: G 82 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7534 (tm-30) outliers start: 19 outliers final: 13 residues processed: 182 average time/residue: 0.1132 time to fit residues: 29.5294 Evaluate side-chains 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 145 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 132 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 113 optimal weight: 0.0670 chunk 127 optimal weight: 0.5980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 358 HIS B 320 GLN B 358 HIS C 328 HIS C 358 HIS D 320 GLN ** G 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.214359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121160 restraints weight = 13932.312| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 3.41 r_work: 0.3106 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12212 Z= 0.131 Angle : 0.486 6.825 16590 Z= 0.250 Chirality : 0.035 0.139 1988 Planarity : 0.003 0.029 2069 Dihedral : 3.347 25.628 1733 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.91 % Allowed : 16.44 % Favored : 81.65 % 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: 1.39 (0.23), residues: 1616 helix: 1.73 (0.16), residues: 1212 sheet: None (None), residues: 0 loop : -1.61 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 106 TYR 0.008 0.001 TYR E 138 PHE 0.020 0.001 PHE D 301 TRP 0.014 0.001 TRP C 242 HIS 0.013 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00314 (12212) covalent geometry : angle 0.48562 (16590) hydrogen bonds : bond 0.04523 ( 804) hydrogen bonds : angle 3.21027 ( 2391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.7500 (tptp) cc_final: 0.7204 (tptp) REVERT: C 40 MET cc_start: 0.8391 (tmm) cc_final: 0.7668 (ttp) REVERT: C 207 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7677 (tt) REVERT: C 353 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8782 (tm-30) REVERT: C 357 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7357 (tptp) REVERT: D 201 ASN cc_start: 0.6698 (m-40) cc_final: 0.6203 (m110) REVERT: D 301 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7020 (p90) REVERT: D 310 GLU cc_start: 0.8831 (tp30) cc_final: 0.8163 (tp30) REVERT: D 313 GLU cc_start: 0.8781 (tp30) cc_final: 0.8433 (pt0) REVERT: G 82 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7553 (tm-30) outliers start: 21 outliers final: 14 residues processed: 182 average time/residue: 0.1105 time to fit residues: 28.8442 Evaluate side-chains 190 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 145 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.1980 chunk 5 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 112 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 358 HIS B 358 HIS C 328 HIS C 358 HIS G 107 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.214732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121631 restraints weight = 13804.270| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 3.42 r_work: 0.3148 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12212 Z= 0.126 Angle : 0.489 7.405 16590 Z= 0.251 Chirality : 0.034 0.140 1988 Planarity : 0.003 0.028 2069 Dihedral : 3.327 25.620 1733 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.27 % Allowed : 16.71 % Favored : 81.02 % 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: 1.41 (0.23), residues: 1616 helix: 1.75 (0.16), residues: 1212 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 106 TYR 0.007 0.001 TYR E 138 PHE 0.020 0.001 PHE D 301 TRP 0.013 0.001 TRP D 242 HIS 0.012 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00298 (12212) covalent geometry : angle 0.48899 (16590) hydrogen bonds : bond 0.04397 ( 804) hydrogen bonds : angle 3.18496 ( 2391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7212 (tptp) REVERT: B 199 TYR cc_start: 0.6887 (m-80) cc_final: 0.6685 (m-80) REVERT: C 40 MET cc_start: 0.8364 (tmm) cc_final: 0.7621 (ttp) REVERT: C 207 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7690 (tt) REVERT: C 353 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8763 (tm-30) REVERT: C 357 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7367 (tptp) REVERT: D 201 ASN cc_start: 0.6699 (m-40) cc_final: 0.6195 (m110) REVERT: D 301 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.7000 (p90) REVERT: D 310 GLU cc_start: 0.8819 (tp30) cc_final: 0.8139 (tp30) REVERT: D 313 GLU cc_start: 0.8744 (tp30) cc_final: 0.8399 (pt0) REVERT: G 82 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7495 (tm-30) outliers start: 25 outliers final: 17 residues processed: 182 average time/residue: 0.1070 time to fit residues: 28.2611 Evaluate side-chains 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 145 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 0 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.2980 chunk 151 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 358 HIS B 320 GLN B 358 HIS C 328 HIS C 358 HIS D 320 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.213145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117557 restraints weight = 13829.020| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.43 r_work: 0.3181 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12212 Z= 0.125 Angle : 0.499 6.901 16590 Z= 0.255 Chirality : 0.034 0.140 1988 Planarity : 0.003 0.028 2069 Dihedral : 3.327 25.283 1733 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 2.09 % Allowed : 17.35 % Favored : 80.56 % 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: 1.44 (0.23), residues: 1616 helix: 1.77 (0.16), residues: 1212 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 106 TYR 0.007 0.001 TYR E 138 PHE 0.021 0.001 PHE D 301 TRP 0.013 0.001 TRP C 242 HIS 0.010 0.001 HIS A 358 Details of bonding type rmsd covalent geometry : bond 0.00295 (12212) covalent geometry : angle 0.49895 (16590) hydrogen bonds : bond 0.04340 ( 804) hydrogen bonds : angle 3.18883 ( 2391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7155 (tptp) REVERT: C 40 MET cc_start: 0.8263 (tmm) cc_final: 0.7504 (ttp) REVERT: C 207 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7649 (tt) REVERT: C 353 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8732 (tm-30) REVERT: C 357 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7296 (tptp) REVERT: D 201 ASN cc_start: 0.6601 (m-40) cc_final: 0.6125 (m110) REVERT: D 301 PHE cc_start: 0.7344 (OUTLIER) cc_final: 0.6967 (p90) REVERT: D 310 GLU cc_start: 0.8802 (tp30) cc_final: 0.8163 (tp30) REVERT: D 313 GLU cc_start: 0.8759 (tp30) cc_final: 0.8405 (pt0) REVERT: G 82 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7454 (tm-30) outliers start: 23 outliers final: 18 residues processed: 179 average time/residue: 0.1125 time to fit residues: 29.1868 Evaluate side-chains 194 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 145 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 144 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 159 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 358 HIS B 358 HIS C 328 HIS C 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.211257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113592 restraints weight = 13781.985| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.94 r_work: 0.3152 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12212 Z= 0.193 Angle : 0.584 7.182 16590 Z= 0.298 Chirality : 0.037 0.140 1988 Planarity : 0.003 0.030 2069 Dihedral : 3.604 25.052 1733 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.18 % Allowed : 17.89 % Favored : 79.93 % 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: 1.26 (0.23), residues: 1616 helix: 1.61 (0.16), residues: 1210 sheet: None (None), residues: 0 loop : -1.55 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 106 TYR 0.010 0.001 TYR C 253 PHE 0.019 0.002 PHE D 301 TRP 0.018 0.002 TRP D 242 HIS 0.015 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00491 (12212) covalent geometry : angle 0.58403 (16590) hydrogen bonds : bond 0.05505 ( 804) hydrogen bonds : angle 3.39459 ( 2391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7175 (tptp) REVERT: C 40 MET cc_start: 0.8328 (tmm) cc_final: 0.7781 (ttp) REVERT: C 207 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7808 (tt) REVERT: C 353 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8709 (tm-30) REVERT: C 357 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7351 (tptp) REVERT: D 201 ASN cc_start: 0.6740 (m-40) cc_final: 0.6249 (m110) REVERT: D 301 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6981 (p90) REVERT: G 82 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7404 (tm-30) outliers start: 24 outliers final: 17 residues processed: 181 average time/residue: 0.1080 time to fit residues: 28.3042 Evaluate side-chains 196 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain B residue 25 LEU Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 349 ASN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 145 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 39 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 151 optimal weight: 10.0000 chunk 88 optimal weight: 0.0770 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 1 optimal weight: 0.0370 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 320 GLN A 358 HIS B 320 GLN B 358 HIS C 328 HIS C 358 HIS D 320 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.214186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.120375 restraints weight = 13818.947| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 3.38 r_work: 0.3194 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12212 Z= 0.114 Angle : 0.514 7.540 16590 Z= 0.266 Chirality : 0.034 0.232 1988 Planarity : 0.003 0.028 2069 Dihedral : 3.377 25.462 1733 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.00 % Allowed : 17.80 % Favored : 80.20 % 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: 1.40 (0.23), residues: 1616 helix: 1.75 (0.16), residues: 1209 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 106 TYR 0.011 0.001 TYR B 199 PHE 0.021 0.001 PHE D 301 TRP 0.011 0.001 TRP B 242 HIS 0.012 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00247 (12212) covalent geometry : angle 0.51426 (16590) hydrogen bonds : bond 0.04096 ( 804) hydrogen bonds : angle 3.21572 ( 2391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3232 Ramachandran restraints generated. 1616 Oldfield, 0 Emsley, 1616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 207 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7696 (tt) REVERT: C 353 GLN cc_start: 0.9154 (tm-30) cc_final: 0.8738 (tm-30) REVERT: C 357 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7354 (tptp) REVERT: D 201 ASN cc_start: 0.6592 (m-40) cc_final: 0.6144 (m110) REVERT: D 301 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6978 (p90) REVERT: D 310 GLU cc_start: 0.8803 (tp30) cc_final: 0.8160 (tp30) REVERT: D 313 GLU cc_start: 0.8765 (tp30) cc_final: 0.8411 (pt0) REVERT: F 83 GLU cc_start: 0.3833 (tm-30) cc_final: 0.3458 (tm-30) REVERT: G 82 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7407 (tm-30) outliers start: 22 outliers final: 14 residues processed: 176 average time/residue: 0.1081 time to fit residues: 27.7831 Evaluate side-chains 187 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 170 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 CYS Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 301 PHE Chi-restraints excluded: chain B residue 74 CYS Chi-restraints excluded: chain B residue 301 PHE Chi-restraints excluded: chain B residue 357 LYS Chi-restraints excluded: chain C residue 74 CYS Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 301 PHE Chi-restraints excluded: chain C residue 357 LYS Chi-restraints excluded: chain D residue 74 CYS Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 91 ASN Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain E residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 138 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 358 HIS B 358 HIS C 328 HIS C 358 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.209816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.111499 restraints weight = 13855.601| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.87 r_work: 0.3154 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12212 Z= 0.184 Angle : 0.592 9.045 16590 Z= 0.305 Chirality : 0.037 0.194 1988 Planarity : 0.003 0.030 2069 Dihedral : 3.605 24.645 1733 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.00 % Allowed : 17.80 % Favored : 80.20 % 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: 1.25 (0.23), residues: 1616 helix: 1.60 (0.16), residues: 1209 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 106 TYR 0.009 0.001 TYR B 199 PHE 0.020 0.002 PHE D 301 TRP 0.018 0.002 TRP C 242 HIS 0.010 0.001 HIS G 107 Details of bonding type rmsd covalent geometry : bond 0.00465 (12212) covalent geometry : angle 0.59163 (16590) hydrogen bonds : bond 0.05399 ( 804) hydrogen bonds : angle 3.39553 ( 2391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4044.13 seconds wall clock time: 69 minutes 45.99 seconds (4185.99 seconds total)