Starting phenix.real_space_refine on Sun Aug 24 11:43:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwu_27760/08_2025/8dwu_27760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwu_27760/08_2025/8dwu_27760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dwu_27760/08_2025/8dwu_27760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwu_27760/08_2025/8dwu_27760.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwu_27760/08_2025/8dwu_27760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwu_27760/08_2025/8dwu_27760.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.061 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: 4 Type Number sf(0) Gaussians S 182 5.16 5 C 12443 2.51 5 N 3305 2.21 5 O 3760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19690 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2000 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 251, 2000 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 241} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2713 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2713 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2675 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 342, 2675 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 332} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2705 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 335} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 2713 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 344, 2713 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 335} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2703 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1351 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 169} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1410 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 176} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1412 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.26, per 1000 atoms: 0.27 Number of scatterers: 19690 At special positions: 0 Unit cell: (195.847, 191.956, 112.839, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 182 16.00 O 3760 8.00 N 3305 7.00 C 12443 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4820 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 25 sheets defined 44.2% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 185 through 192 removed outlier: 4.061A pdb=" N GLU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 222 Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.508A pdb=" N HIS A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 261 removed outlier: 4.490A pdb=" N GLU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR A 259 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR A 260 " --> pdb=" O CYS A 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 139 through 144 Processing helix chain 'B' and resid 185 through 193 removed outlier: 4.147A pdb=" N GLU B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 222 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.568A pdb=" N GLU B 230 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 261 removed outlier: 4.368A pdb=" N GLU B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR B 260 " --> pdb=" O CYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 280 removed outlier: 3.701A pdb=" N LEU B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 296 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 328 through 333 removed outlier: 4.108A pdb=" N VAL B 332 " --> pdb=" O HIS B 328 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 333' Processing helix chain 'B' and resid 335 through 345 removed outlier: 3.564A pdb=" N LYS B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.498A pdb=" N VAL B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 44 removed outlier: 3.621A pdb=" N CYS C 44 " --> pdb=" O PHE C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 185 through 191 removed outlier: 3.756A pdb=" N GLU C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 222 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.652A pdb=" N HIS C 231 " --> pdb=" O ALA C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 261 removed outlier: 4.409A pdb=" N GLU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR C 259 " --> pdb=" O MET C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.968A pdb=" N LEU C 266 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ASP C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 263 through 267' Processing helix chain 'C' and resid 269 through 280 removed outlier: 3.828A pdb=" N LEU C 273 " --> pdb=" O MET C 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 295 Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.667A pdb=" N VAL C 332 " --> pdb=" O HIS C 328 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 333' Processing helix chain 'C' and resid 335 through 345 removed outlier: 3.504A pdb=" N LYS C 339 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 357 removed outlier: 4.482A pdb=" N VAL C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 350 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 351 " --> pdb=" O HIS C 347 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 44 Processing helix chain 'D' and resid 138 through 144 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 222 through 231 removed outlier: 3.599A pdb=" N GLU D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS D 231 " --> pdb=" O ALA D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 258 removed outlier: 4.288A pdb=" N GLU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 removed outlier: 3.935A pdb=" N LEU D 273 " --> pdb=" O MET D 269 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 296 Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 335 through 345 removed outlier: 3.569A pdb=" N LYS D 339 " --> pdb=" O THR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 removed outlier: 3.822A pdb=" N VAL D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 44 Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 145 through 148 Processing helix chain 'E' and resid 186 through 196 Processing helix chain 'E' and resid 215 through 222 Processing helix chain 'E' and resid 222 through 231 removed outlier: 3.551A pdb=" N GLU E 230 " --> pdb=" O SER E 226 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS E 231 " --> pdb=" O ALA E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 258 removed outlier: 3.746A pdb=" N PHE E 251 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.948A pdb=" N LEU E 273 " --> pdb=" O MET E 269 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 296 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 315 through 328 Processing helix chain 'E' and resid 328 through 333 removed outlier: 4.109A pdb=" N LEU E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 345 removed outlier: 3.781A pdb=" N LYS E 339 " --> pdb=" O THR E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 360 removed outlier: 3.711A pdb=" N ALA E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.601A pdb=" N ARG F 45 " --> pdb=" O PHE F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 81 removed outlier: 3.605A pdb=" N LYS F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 144 Processing helix chain 'F' and resid 145 through 148 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 186 through 192 removed outlier: 3.540A pdb=" N GLY F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 222 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 247 through 258 removed outlier: 4.440A pdb=" N GLU F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 280 removed outlier: 3.939A pdb=" N LEU F 273 " --> pdb=" O MET F 269 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 295 Processing helix chain 'F' and resid 301 through 312 Processing helix chain 'F' and resid 315 through 328 Processing helix chain 'F' and resid 328 through 333 removed outlier: 3.508A pdb=" N VAL F 332 " --> pdb=" O HIS F 328 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 328 through 333' Processing helix chain 'F' and resid 335 through 345 removed outlier: 3.506A pdb=" N LYS F 339 " --> pdb=" O THR F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 358 removed outlier: 3.826A pdb=" N VAL F 349 " --> pdb=" O HIS F 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 192 Processing helix chain 'J' and resid 215 through 222 Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.739A pdb=" N GLU J 230 " --> pdb=" O SER J 226 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS J 231 " --> pdb=" O ALA J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 258 removed outlier: 4.346A pdb=" N GLU J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 280 removed outlier: 3.995A pdb=" N LEU J 273 " --> pdb=" O MET J 269 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA J 275 " --> pdb=" O ASP J 271 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 296 Processing helix chain 'J' and resid 301 through 312 Processing helix chain 'J' and resid 315 through 328 Processing helix chain 'J' and resid 331 through 334 removed outlier: 3.629A pdb=" N GLU J 334 " --> pdb=" O ASP J 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 331 through 334' Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.707A pdb=" N LYS J 339 " --> pdb=" O THR J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 357 removed outlier: 3.800A pdb=" N VAL J 349 " --> pdb=" O HIS J 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 192 removed outlier: 4.275A pdb=" N LEU H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 222 Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.773A pdb=" N HIS H 231 " --> pdb=" O ALA H 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 258 removed outlier: 4.323A pdb=" N GLU H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 280 removed outlier: 4.052A pdb=" N LEU H 273 " --> pdb=" O MET H 269 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 274 " --> pdb=" O ALA H 270 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ALA H 275 " --> pdb=" O ASP H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 282 through 296 removed outlier: 3.522A pdb=" N ASN H 296 " --> pdb=" O ALA H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 312 Processing helix chain 'H' and resid 315 through 328 Processing helix chain 'H' and resid 335 through 345 removed outlier: 3.576A pdb=" N LYS H 339 " --> pdb=" O THR H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 357 removed outlier: 3.754A pdb=" N VAL H 349 " --> pdb=" O HIS H 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 192 removed outlier: 3.706A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 222 Processing helix chain 'I' and resid 222 through 231 removed outlier: 3.603A pdb=" N HIS I 231 " --> pdb=" O ALA I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 261 removed outlier: 4.449A pdb=" N GLU I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR I 259 " --> pdb=" O MET I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 280 removed outlier: 4.140A pdb=" N LEU I 273 " --> pdb=" O MET I 269 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU I 274 " --> pdb=" O ALA I 270 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ALA I 275 " --> pdb=" O ASP I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 295 Processing helix chain 'I' and resid 301 through 312 Processing helix chain 'I' and resid 315 through 328 Processing helix chain 'I' and resid 328 through 333 removed outlier: 3.621A pdb=" N VAL I 332 " --> pdb=" O HIS I 328 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 333' Processing helix chain 'I' and resid 335 through 345 removed outlier: 3.669A pdb=" N LYS I 339 " --> pdb=" O THR I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 358 removed outlier: 3.793A pdb=" N VAL I 349 " --> pdb=" O HIS I 345 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.405A pdb=" N ARG A 99 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 164 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 104 " --> pdb=" O MET C 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.405A pdb=" N ARG A 99 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL A 164 " --> pdb=" O ARG A 99 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 99 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.789A pdb=" N THR A 156 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.837A pdb=" N LYS A 66 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 85 " --> pdb=" O ASN A 72 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 137 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LEU A 86 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS A 135 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU A 88 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE A 133 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU A 90 " --> pdb=" O TRP A 131 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N TRP A 131 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 206 removed outlier: 3.944A pdb=" N PHE A 211 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.638A pdb=" N TYR B 123 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 99 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 101 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL E 163 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 99 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE E 104 " --> pdb=" O MET E 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 123 through 125 removed outlier: 3.638A pdb=" N TYR B 123 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG B 99 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS B 101 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL E 163 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG E 99 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 34 through 39 Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 53 removed outlier: 7.166A pdb=" N LYS B 66 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 84 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 135 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 206 removed outlier: 3.830A pdb=" N PHE B 211 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B 206 " --> pdb=" O GLN B 209 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.612A pdb=" N VAL C 71 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LYS C 66 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER C 85 " --> pdb=" O ASN C 72 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU C 84 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LYS C 135 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 86 " --> pdb=" O PHE C 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 202 through 206 removed outlier: 3.767A pdb=" N CYS C 202 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 213 " --> pdb=" O CYS C 202 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE C 211 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 206 " --> pdb=" O GLN C 209 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 38 removed outlier: 3.918A pdb=" N CYS D 159 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 155 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 69 through 71 Processing sheet with id=AB7, first strand: chain 'D' and resid 202 through 206 removed outlier: 3.547A pdb=" N CYS D 202 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE D 211 " --> pdb=" O LEU D 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 66 through 72 removed outlier: 6.777A pdb=" N LYS E 66 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER E 85 " --> pdb=" O ASN E 72 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU E 86 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS E 135 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU E 88 " --> pdb=" O PHE E 133 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N PHE E 133 " --> pdb=" O LEU E 88 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU E 90 " --> pdb=" O TRP E 131 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N TRP E 131 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 202 through 206 removed outlier: 3.895A pdb=" N CYS E 202 " --> pdb=" O ALA E 213 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA E 213 " --> pdb=" O CYS E 202 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N PHE E 211 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 29 through 39 removed outlier: 3.700A pdb=" N PHE F 32 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 159 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 155 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR F 156 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE F 104 " --> pdb=" O MET F 117 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 29 through 39 removed outlier: 3.700A pdb=" N PHE F 32 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS F 159 " --> pdb=" O TYR F 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F 155 " --> pdb=" O ILE F 38 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG F 99 " --> pdb=" O VAL F 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 57 through 58 removed outlier: 6.827A pdb=" N LYS F 66 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 86 " --> pdb=" O PHE F 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 202 through 206 removed outlier: 3.781A pdb=" N CYS F 202 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA F 213 " --> pdb=" O CYS F 202 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE F 211 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 202 through 206 removed outlier: 4.004A pdb=" N PHE J 211 " --> pdb=" O LEU J 204 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 202 through 206 removed outlier: 3.870A pdb=" N CYS H 202 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA H 213 " --> pdb=" O CYS H 202 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE H 211 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 202 through 206 removed outlier: 3.859A pdb=" N PHE I 211 " --> pdb=" O LEU I 204 " (cutoff:3.500A) 843 hydrogen bonds defined for protein. 2334 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: 3.51 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6236 1.34 - 1.46: 4173 1.46 - 1.58: 9366 1.58 - 1.71: 2 1.71 - 1.83: 274 Bond restraints: 20051 Sorted by residual: bond pdb=" CA SER B 21 " pdb=" CB SER B 21 " ideal model delta sigma weight residual 1.536 1.484 0.052 1.46e-02 4.69e+03 1.28e+01 bond pdb=" CA SER A 21 " pdb=" CB SER A 21 " ideal model delta sigma weight residual 1.537 1.485 0.051 1.67e-02 3.59e+03 9.48e+00 bond pdb=" CG MET I 228 " pdb=" SD MET I 228 " ideal model delta sigma weight residual 1.803 1.736 0.067 2.50e-02 1.60e+03 7.18e+00 bond pdb=" CB ARG C 198 " pdb=" CG ARG C 198 " ideal model delta sigma weight residual 1.520 1.599 -0.079 3.00e-02 1.11e+03 7.00e+00 bond pdb=" N GLU B 20 " pdb=" CA GLU B 20 " ideal model delta sigma weight residual 1.453 1.484 -0.032 1.31e-02 5.83e+03 5.79e+00 ... (remaining 20046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.48: 26361 3.48 - 6.96: 549 6.96 - 10.44: 88 10.44 - 13.92: 27 13.92 - 17.40: 9 Bond angle restraints: 27034 Sorted by residual: angle pdb=" CA MET I 228 " pdb=" CB MET I 228 " pdb=" CG MET I 228 " ideal model delta sigma weight residual 114.10 130.44 -16.34 2.00e+00 2.50e-01 6.67e+01 angle pdb=" N MET I 228 " pdb=" CA MET I 228 " pdb=" CB MET I 228 " ideal model delta sigma weight residual 110.20 121.66 -11.46 1.49e+00 4.50e-01 5.92e+01 angle pdb=" CA MET I 288 " pdb=" CB MET I 288 " pdb=" CG MET I 288 " ideal model delta sigma weight residual 114.10 128.86 -14.76 2.00e+00 2.50e-01 5.45e+01 angle pdb=" N MET C 228 " pdb=" CA MET C 228 " pdb=" CB MET C 228 " ideal model delta sigma weight residual 110.20 120.84 -10.64 1.49e+00 4.50e-01 5.10e+01 angle pdb=" CA MET C 228 " pdb=" CB MET C 228 " pdb=" CG MET C 228 " ideal model delta sigma weight residual 114.10 127.99 -13.89 2.00e+00 2.50e-01 4.82e+01 ... (remaining 27029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 11014 17.64 - 35.27: 1002 35.27 - 52.91: 171 52.91 - 70.55: 34 70.55 - 88.19: 20 Dihedral angle restraints: 12241 sinusoidal: 4861 harmonic: 7380 Sorted by residual: dihedral pdb=" CA SER I 197 " pdb=" C SER I 197 " pdb=" N ARG I 198 " pdb=" CA ARG I 198 " ideal model delta harmonic sigma weight residual 180.00 152.72 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA SER D 197 " pdb=" C SER D 197 " pdb=" N ARG D 198 " pdb=" CA ARG D 198 " ideal model delta harmonic sigma weight residual 180.00 152.74 27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER J 197 " pdb=" C SER J 197 " pdb=" N ARG J 198 " pdb=" CA ARG J 198 " ideal model delta harmonic sigma weight residual 180.00 152.75 27.25 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 12238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2556 0.082 - 0.165: 372 0.165 - 0.247: 56 0.247 - 0.330: 10 0.330 - 0.412: 6 Chirality restraints: 3000 Sorted by residual: chirality pdb=" CB ILE F 52 " pdb=" CA ILE F 52 " pdb=" CG1 ILE F 52 " pdb=" CG2 ILE F 52 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CB ILE D 52 " pdb=" CA ILE D 52 " pdb=" CG1 ILE D 52 " pdb=" CG2 ILE D 52 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" CA MET C 288 " pdb=" N MET C 288 " pdb=" C MET C 288 " pdb=" CB MET C 288 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2997 not shown) Planarity restraints: 3481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 198 " -0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" C ARG C 198 " 0.068 2.00e-02 2.50e+03 pdb=" O ARG C 198 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE C 199 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 324 " -0.017 2.00e-02 2.50e+03 2.54e-02 1.13e+01 pdb=" CG PHE E 324 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE E 324 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE E 324 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE E 324 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 324 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 324 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 198 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C ARG F 198 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG F 198 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE F 199 " -0.019 2.00e-02 2.50e+03 ... (remaining 3478 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2191 2.76 - 3.29: 19697 3.29 - 3.83: 30658 3.83 - 4.36: 36118 4.36 - 4.90: 61570 Nonbonded interactions: 150234 Sorted by model distance: nonbonded pdb=" O LEU E 76 " pdb=" OG SER E 80 " model vdw 2.223 3.040 nonbonded pdb=" OG1 THR E 200 " pdb=" OE1 GLN E 212 " model vdw 2.231 3.040 nonbonded pdb=" NZ LYS E 129 " pdb=" OG1 THR F 25 " model vdw 2.238 3.120 nonbonded pdb=" O CYS C 256 " pdb=" OG1 THR C 260 " model vdw 2.243 3.040 nonbonded pdb=" OE2 GLU E 20 " pdb=" OH TYR F 87 " model vdw 2.248 3.040 ... (remaining 150229 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 'B' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB )) or resid 184 through 357)) selection = (chain 'C' and (resid 17 through 182 or (resid 183 and (name N or name CA or nam \ e C or name O or name CB )) or resid 184 through 357)) selection = (chain 'D' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 357)) selection = (chain 'E' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 through 357)) selection = (chain 'F' and (resid 17 through 172 or (resid 173 through 181 and (name N or na \ me CA or name C or name O or name CB )) or resid 182 or (resid 183 and (name N o \ r name CA or name C or name O or name CB )) or resid 184 through 357)) } ncs_group { reference = (chain 'H' and resid 185 through 357) selection = (chain 'I' and resid 185 through 357) selection = (chain 'J' and resid 185 through 357) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.780 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 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 : 0.005 0.079 20051 Z= 0.272 Angle : 1.260 17.400 27034 Z= 0.667 Chirality : 0.064 0.412 3000 Planarity : 0.006 0.056 3481 Dihedral : 14.455 88.185 7421 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.20 % Favored : 92.28 % Rotamer: Outliers : 0.14 % Allowed : 0.37 % Favored : 99.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.17), residues: 2487 helix: 0.00 (0.17), residues: 940 sheet: -1.76 (0.30), residues: 319 loop : -2.18 (0.17), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG F 198 TYR 0.027 0.002 TYR F 327 PHE 0.057 0.003 PHE E 324 TRP 0.043 0.003 TRP I 338 HIS 0.014 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00538 (20051) covalent geometry : angle 1.26009 (27034) hydrogen bonds : bond 0.18528 ( 789) hydrogen bonds : angle 7.43203 ( 2334) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 169 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.6678 (mtp) cc_final: 0.6420 (mtm) REVERT: B 228 MET cc_start: 0.2223 (ppp) cc_final: 0.1917 (ppp) REVERT: E 176 MET cc_start: 0.4657 (ptm) cc_final: 0.3908 (ppp) REVERT: J 233 MET cc_start: 0.0213 (ptm) cc_final: -0.1667 (ppp) REVERT: I 176 MET cc_start: 0.3514 (ptp) cc_final: 0.0230 (ppp) outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.1658 time to fit residues: 43.5304 Evaluate side-chains 122 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 121 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 216 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN B 120 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN D 177 ASN D 244 ASN E 320 GLN F 40 ASN ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 GLN J 265 ASN ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 HIS I 345 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.064922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.046664 restraints weight = 179163.979| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 4.68 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20051 Z= 0.262 Angle : 0.782 9.789 27034 Z= 0.413 Chirality : 0.046 0.224 3000 Planarity : 0.004 0.049 3481 Dihedral : 5.704 27.838 2662 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.88 % Favored : 91.76 % Rotamer: Outliers : 0.47 % Allowed : 6.33 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.17), residues: 2487 helix: 0.48 (0.17), residues: 970 sheet: -1.61 (0.26), residues: 411 loop : -2.05 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 138 TYR 0.018 0.002 TYR F 327 PHE 0.023 0.002 PHE D 41 TRP 0.016 0.002 TRP F 338 HIS 0.005 0.001 HIS I 345 Details of bonding type rmsd covalent geometry : bond 0.00579 (20051) covalent geometry : angle 0.78182 (27034) hydrogen bonds : bond 0.03288 ( 789) hydrogen bonds : angle 5.23274 ( 2334) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.6381 (mtp) cc_final: 0.5876 (mtp) REVERT: A 254 MET cc_start: 0.7347 (mpp) cc_final: 0.7006 (mpp) REVERT: B 48 MET cc_start: 0.9056 (tpp) cc_final: 0.8573 (tpt) REVERT: B 65 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8693 (pp) REVERT: B 228 MET cc_start: 0.4671 (ppp) cc_final: 0.4308 (ppp) REVERT: B 283 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9273 (pm20) REVERT: B 341 MET cc_start: 0.8261 (ppp) cc_final: 0.8041 (ppp) REVERT: C 228 MET cc_start: 0.6215 (pmm) cc_final: 0.5734 (pmm) REVERT: C 288 MET cc_start: 0.9281 (pmm) cc_final: 0.8973 (pmm) REVERT: D 228 MET cc_start: 0.6815 (tmm) cc_final: 0.6556 (ppp) REVERT: E 176 MET cc_start: 0.3542 (ptm) cc_final: 0.3231 (ppp) REVERT: F 269 MET cc_start: 0.7199 (ppp) cc_final: 0.6898 (ppp) REVERT: F 341 MET cc_start: 0.9020 (ppp) cc_final: 0.8662 (ppp) REVERT: J 228 MET cc_start: 0.6782 (ttt) cc_final: 0.5937 (ppp) REVERT: J 233 MET cc_start: 0.0826 (ptm) cc_final: 0.0437 (ppp) REVERT: J 237 LYS cc_start: 0.7471 (OUTLIER) cc_final: 0.6855 (tmtt) REVERT: H 246 VAL cc_start: -0.0170 (OUTLIER) cc_final: -0.0464 (p) REVERT: H 341 MET cc_start: 0.9464 (tmm) cc_final: 0.8637 (ppp) REVERT: I 176 MET cc_start: 0.1397 (ptp) cc_final: 0.0163 (ppp) REVERT: I 185 ARG cc_start: 0.6720 (tmm160) cc_final: 0.5580 (ptt90) REVERT: I 228 MET cc_start: 0.8332 (pmm) cc_final: 0.7819 (pmm) outliers start: 10 outliers final: 3 residues processed: 132 average time/residue: 0.1571 time to fit residues: 32.4444 Evaluate side-chains 122 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain J residue 237 LYS Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain H residue 246 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 102 optimal weight: 0.0040 chunk 79 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 92 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 186 optimal weight: 0.2980 chunk 171 optimal weight: 0.2980 chunk 240 optimal weight: 8.9990 overall best weight: 0.1850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 214 HIS ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 HIS ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.066081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.048340 restraints weight = 179076.108| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 4.31 r_work: 0.3140 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20051 Z= 0.116 Angle : 0.644 9.469 27034 Z= 0.339 Chirality : 0.043 0.184 3000 Planarity : 0.003 0.053 3481 Dihedral : 5.053 29.074 2660 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.27 % Favored : 93.41 % Rotamer: Outliers : 0.56 % Allowed : 8.23 % Favored : 91.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.17), residues: 2487 helix: 0.81 (0.17), residues: 967 sheet: -1.13 (0.28), residues: 366 loop : -1.93 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 22 TYR 0.014 0.001 TYR B 280 PHE 0.015 0.001 PHE A 199 TRP 0.011 0.001 TRP B 36 HIS 0.004 0.001 HIS I 345 Details of bonding type rmsd covalent geometry : bond 0.00231 (20051) covalent geometry : angle 0.64396 (27034) hydrogen bonds : bond 0.02781 ( 789) hydrogen bonds : angle 4.54215 ( 2334) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.7226 (mtt) cc_final: 0.6742 (mtp) REVERT: A 233 MET cc_start: 0.1383 (tmm) cc_final: 0.1008 (tmm) REVERT: A 254 MET cc_start: 0.7456 (mpp) cc_final: 0.7145 (mpp) REVERT: B 117 MET cc_start: 0.9109 (ttm) cc_final: 0.8818 (ttt) REVERT: B 228 MET cc_start: 0.5138 (ppp) cc_final: 0.4732 (ppp) REVERT: C 228 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5473 (pmm) REVERT: D 228 MET cc_start: 0.6585 (tmm) cc_final: 0.6240 (ppp) REVERT: D 269 MET cc_start: 0.7053 (OUTLIER) cc_final: 0.6842 (ppp) REVERT: E 176 MET cc_start: 0.3879 (ptm) cc_final: 0.3302 (ppp) REVERT: E 233 MET cc_start: 0.3842 (ppp) cc_final: 0.3581 (ppp) REVERT: E 288 MET cc_start: 0.8696 (mtt) cc_final: 0.8412 (ptp) REVERT: E 341 MET cc_start: 0.9502 (tpt) cc_final: 0.9115 (tpp) REVERT: F 178 MET cc_start: 0.7220 (mtt) cc_final: 0.6955 (mtm) REVERT: F 269 MET cc_start: 0.7217 (ppp) cc_final: 0.6931 (ppp) REVERT: F 341 MET cc_start: 0.8969 (ppp) cc_final: 0.8707 (ppp) REVERT: J 228 MET cc_start: 0.6292 (ttt) cc_final: 0.5645 (ppp) REVERT: H 228 MET cc_start: 0.6790 (ppp) cc_final: 0.6577 (ppp) REVERT: I 176 MET cc_start: 0.0396 (ptp) cc_final: -0.0208 (ppp) REVERT: I 341 MET cc_start: 0.9533 (mmm) cc_final: 0.9179 (mmm) outliers start: 12 outliers final: 4 residues processed: 134 average time/residue: 0.1472 time to fit residues: 31.4716 Evaluate side-chains 120 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 114 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain I residue 228 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 171 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 246 optimal weight: 0.5980 chunk 240 optimal weight: 5.9990 chunk 58 optimal weight: 50.0000 chunk 126 optimal weight: 6.9990 chunk 233 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.067991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.049310 restraints weight = 168132.424| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 4.49 r_work: 0.3076 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.95 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20051 Z= 0.239 Angle : 0.704 9.849 27034 Z= 0.371 Chirality : 0.044 0.289 3000 Planarity : 0.004 0.055 3481 Dihedral : 5.277 24.381 2660 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.84 % Favored : 91.84 % Rotamer: Outliers : 0.84 % Allowed : 9.91 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.17), residues: 2487 helix: 0.84 (0.17), residues: 981 sheet: -1.29 (0.27), residues: 412 loop : -1.86 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 22 TYR 0.016 0.002 TYR B 280 PHE 0.019 0.002 PHE D 41 TRP 0.018 0.002 TRP C 67 HIS 0.019 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00528 (20051) covalent geometry : angle 0.70429 (27034) hydrogen bonds : bond 0.02809 ( 789) hydrogen bonds : angle 4.57782 ( 2334) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.0500 (tmm) cc_final: 0.0100 (tmm) REVERT: B 48 MET cc_start: 0.8984 (tpp) cc_final: 0.8497 (tpt) REVERT: B 65 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8782 (pp) REVERT: B 117 MET cc_start: 0.9302 (ttm) cc_final: 0.8832 (ttt) REVERT: B 228 MET cc_start: 0.5258 (ppp) cc_final: 0.4831 (ppp) REVERT: C 228 MET cc_start: 0.6894 (pmm) cc_final: 0.6125 (pmm) REVERT: D 228 MET cc_start: 0.6707 (tmm) cc_final: 0.6224 (ppp) REVERT: E 35 MET cc_start: 0.8844 (tpp) cc_final: 0.8504 (tpp) REVERT: E 178 MET cc_start: 0.7850 (mmm) cc_final: 0.7567 (mmm) REVERT: E 341 MET cc_start: 0.9496 (tpt) cc_final: 0.9210 (tpp) REVERT: F 231 HIS cc_start: 0.8033 (m-70) cc_final: 0.7822 (m-70) REVERT: F 269 MET cc_start: 0.7328 (ppp) cc_final: 0.6995 (ppp) REVERT: F 341 MET cc_start: 0.9107 (ppp) cc_final: 0.8824 (ppp) REVERT: J 228 MET cc_start: 0.6571 (ttt) cc_final: 0.5972 (ppp) REVERT: H 228 MET cc_start: 0.6470 (ppp) cc_final: 0.6160 (ppp) REVERT: H 254 MET cc_start: 0.9054 (ptp) cc_final: 0.8817 (ptp) REVERT: H 341 MET cc_start: 0.9461 (tmm) cc_final: 0.8784 (ppp) REVERT: I 176 MET cc_start: 0.0960 (ptp) cc_final: 0.0128 (ppp) REVERT: I 196 ASN cc_start: 0.8921 (m-40) cc_final: 0.8563 (t0) REVERT: I 233 MET cc_start: -0.0011 (ptm) cc_final: -0.0645 (ptt) REVERT: I 254 MET cc_start: 0.9200 (ppp) cc_final: 0.8889 (ppp) REVERT: I 255 MET cc_start: 0.8595 (ttt) cc_final: 0.8184 (mmm) REVERT: I 341 MET cc_start: 0.9584 (mmm) cc_final: 0.9120 (mmm) outliers start: 18 outliers final: 10 residues processed: 129 average time/residue: 0.1351 time to fit residues: 28.3232 Evaluate side-chains 127 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 244 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 243 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.064251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.045989 restraints weight = 173621.003| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.31 r_work: 0.3113 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20051 Z= 0.133 Angle : 0.632 9.418 27034 Z= 0.330 Chirality : 0.043 0.185 3000 Planarity : 0.003 0.059 3481 Dihedral : 5.003 25.830 2660 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.16 % Favored : 92.52 % Rotamer: Outliers : 0.79 % Allowed : 11.58 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2487 helix: 1.05 (0.17), residues: 979 sheet: -1.09 (0.28), residues: 374 loop : -1.86 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 139 TYR 0.013 0.001 TYR B 280 PHE 0.016 0.001 PHE A 199 TRP 0.008 0.001 TRP F 338 HIS 0.009 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00288 (20051) covalent geometry : angle 0.63180 (27034) hydrogen bonds : bond 0.02475 ( 789) hydrogen bonds : angle 4.37555 ( 2334) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.5200 (mtp) cc_final: 0.4148 (mtp) REVERT: B 48 MET cc_start: 0.8924 (tpp) cc_final: 0.8646 (tpt) REVERT: B 65 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8718 (pp) REVERT: B 228 MET cc_start: 0.5556 (ppp) cc_final: 0.5099 (ppp) REVERT: C 228 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6515 (pmm) REVERT: D 269 MET cc_start: 0.7082 (ppp) cc_final: 0.6819 (ppp) REVERT: E 35 MET cc_start: 0.8761 (tpp) cc_final: 0.8481 (tpp) REVERT: E 288 MET cc_start: 0.8791 (mtt) cc_final: 0.8493 (ptp) REVERT: E 341 MET cc_start: 0.9554 (tpt) cc_final: 0.9218 (tpp) REVERT: F 231 HIS cc_start: 0.7831 (m-70) cc_final: 0.7574 (m-70) REVERT: F 233 MET cc_start: 0.0335 (ttt) cc_final: -0.0023 (ptm) REVERT: F 341 MET cc_start: 0.9209 (ppp) cc_final: 0.8914 (ppp) REVERT: J 228 MET cc_start: 0.6628 (ttt) cc_final: 0.6039 (ppp) REVERT: J 255 MET cc_start: 0.9522 (mmm) cc_final: 0.9309 (mmm) REVERT: H 228 MET cc_start: 0.6411 (ppp) cc_final: 0.6115 (ppp) REVERT: H 341 MET cc_start: 0.9468 (tmm) cc_final: 0.8674 (ppp) REVERT: I 176 MET cc_start: 0.1351 (ptp) cc_final: 0.0748 (ppp) REVERT: I 196 ASN cc_start: 0.8888 (m-40) cc_final: 0.8555 (t0) REVERT: I 228 MET cc_start: 0.8866 (pmm) cc_final: 0.8579 (pmm) REVERT: I 233 MET cc_start: -0.0529 (ptm) cc_final: -0.0926 (ptt) REVERT: I 254 MET cc_start: 0.9317 (ppp) cc_final: 0.8983 (ppp) REVERT: I 255 MET cc_start: 0.8490 (ttt) cc_final: 0.8075 (mmm) REVERT: I 341 MET cc_start: 0.9624 (mmm) cc_final: 0.9143 (mmm) outliers start: 17 outliers final: 12 residues processed: 129 average time/residue: 0.1382 time to fit residues: 29.5147 Evaluate side-chains 128 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 57 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 198 optimal weight: 40.0000 chunk 86 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 68 optimal weight: 0.0770 overall best weight: 4.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.062561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.043452 restraints weight = 172935.817| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.84 r_work: 0.3026 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 20051 Z= 0.273 Angle : 0.737 14.386 27034 Z= 0.385 Chirality : 0.045 0.183 3000 Planarity : 0.004 0.063 3481 Dihedral : 5.430 24.774 2660 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.52 % Favored : 91.19 % Rotamer: Outliers : 1.58 % Allowed : 11.63 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.17), residues: 2487 helix: 0.86 (0.17), residues: 989 sheet: -1.16 (0.26), residues: 427 loop : -1.91 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 198 TYR 0.015 0.002 TYR E 34 PHE 0.022 0.002 PHE D 41 TRP 0.017 0.002 TRP C 67 HIS 0.009 0.001 HIS B 345 Details of bonding type rmsd covalent geometry : bond 0.00608 (20051) covalent geometry : angle 0.73667 (27034) hydrogen bonds : bond 0.03024 ( 789) hydrogen bonds : angle 4.68256 ( 2334) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.5852 (mtp) cc_final: 0.5026 (mtp) REVERT: A 233 MET cc_start: 0.3785 (tmm) cc_final: 0.3434 (tmm) REVERT: A 254 MET cc_start: 0.6349 (mmt) cc_final: 0.5980 (mpp) REVERT: B 65 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8731 (pp) REVERT: B 228 MET cc_start: 0.6151 (ppp) cc_final: 0.5163 (ppp) REVERT: C 228 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7188 (pmm) REVERT: C 233 MET cc_start: 0.2840 (ptp) cc_final: 0.2482 (ptp) REVERT: D 254 MET cc_start: 0.8827 (ppp) cc_final: 0.8613 (ppp) REVERT: E 35 MET cc_start: 0.8866 (tpp) cc_final: 0.8394 (tpp) REVERT: E 341 MET cc_start: 0.9523 (tpt) cc_final: 0.9092 (tpp) REVERT: F 231 HIS cc_start: 0.8355 (m-70) cc_final: 0.7944 (m-70) REVERT: F 341 MET cc_start: 0.8999 (ppp) cc_final: 0.8756 (ppp) REVERT: J 228 MET cc_start: 0.7207 (ttt) cc_final: 0.6675 (ppp) REVERT: J 233 MET cc_start: 0.1875 (ppp) cc_final: 0.1625 (ppp) REVERT: H 341 MET cc_start: 0.9491 (tmm) cc_final: 0.8870 (ppp) REVERT: I 176 MET cc_start: 0.0600 (ptp) cc_final: 0.0366 (ppp) REVERT: I 228 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8632 (pmm) REVERT: I 233 MET cc_start: 0.0890 (ptm) cc_final: 0.0467 (ptt) REVERT: I 341 MET cc_start: 0.9599 (mmm) cc_final: 0.9087 (mmm) outliers start: 34 outliers final: 15 residues processed: 141 average time/residue: 0.1393 time to fit residues: 31.6872 Evaluate side-chains 132 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 20 optimal weight: 20.0000 chunk 247 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 197 optimal weight: 20.0000 chunk 69 optimal weight: 0.9990 chunk 140 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 228 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS ** H 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.063168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.046341 restraints weight = 181574.838| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 5.11 r_work: 0.3040 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20051 Z= 0.180 Angle : 0.678 12.920 27034 Z= 0.349 Chirality : 0.043 0.193 3000 Planarity : 0.004 0.066 3481 Dihedral : 5.220 25.250 2660 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.56 % Favored : 92.16 % Rotamer: Outliers : 1.21 % Allowed : 12.79 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.17), residues: 2487 helix: 1.01 (0.17), residues: 988 sheet: -1.17 (0.27), residues: 389 loop : -1.94 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.013 0.001 TYR B 280 PHE 0.015 0.001 PHE A 199 TRP 0.014 0.001 TRP F 338 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00399 (20051) covalent geometry : angle 0.67833 (27034) hydrogen bonds : bond 0.02646 ( 789) hydrogen bonds : angle 4.51620 ( 2334) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.5663 (mtp) cc_final: 0.4990 (mtp) REVERT: B 65 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8832 (pp) REVERT: B 117 MET cc_start: 0.9109 (ttm) cc_final: 0.8880 (ttt) REVERT: B 228 MET cc_start: 0.7256 (ppp) cc_final: 0.6895 (ppp) REVERT: C 228 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6449 (pmm) REVERT: D 255 MET cc_start: 0.8919 (tpp) cc_final: 0.8712 (tpp) REVERT: E 35 MET cc_start: 0.8811 (tpp) cc_final: 0.8564 (tpp) REVERT: E 288 MET cc_start: 0.8839 (mtt) cc_final: 0.8399 (ptp) REVERT: E 341 MET cc_start: 0.9505 (tpt) cc_final: 0.9038 (tpp) REVERT: F 86 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8847 (tp) REVERT: F 231 HIS cc_start: 0.8326 (m-70) cc_final: 0.7837 (m-70) REVERT: F 341 MET cc_start: 0.8892 (ppp) cc_final: 0.8630 (ppp) REVERT: J 228 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6624 (ppp) REVERT: I 176 MET cc_start: 0.0912 (ptp) cc_final: 0.0465 (ppp) REVERT: I 228 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8627 (pmm) REVERT: I 233 MET cc_start: 0.0681 (ptm) cc_final: 0.0252 (ptt) REVERT: I 255 MET cc_start: 0.8587 (ttt) cc_final: 0.8139 (mmm) REVERT: I 341 MET cc_start: 0.9606 (mmm) cc_final: 0.9132 (mmm) outliers start: 26 outliers final: 13 residues processed: 132 average time/residue: 0.1418 time to fit residues: 30.6114 Evaluate side-chains 129 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 64 optimal weight: 2.9990 chunk 198 optimal weight: 40.0000 chunk 85 optimal weight: 9.9990 chunk 169 optimal weight: 0.5980 chunk 151 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 229 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.063056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.045486 restraints weight = 180076.382| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 4.13 r_work: 0.3073 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20051 Z= 0.157 Angle : 0.679 15.270 27034 Z= 0.349 Chirality : 0.043 0.362 3000 Planarity : 0.003 0.061 3481 Dihedral : 5.097 23.468 2660 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.96 % Favored : 91.76 % Rotamer: Outliers : 1.26 % Allowed : 13.16 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.17), residues: 2487 helix: 1.04 (0.17), residues: 993 sheet: -1.01 (0.28), residues: 382 loop : -1.93 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 198 TYR 0.011 0.001 TYR B 280 PHE 0.015 0.001 PHE A 199 TRP 0.010 0.001 TRP F 338 HIS 0.006 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00347 (20051) covalent geometry : angle 0.67907 (27034) hydrogen bonds : bond 0.02610 ( 789) hydrogen bonds : angle 4.46100 ( 2334) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.5656 (mtp) cc_final: 0.4907 (mtp) REVERT: A 233 MET cc_start: 0.2557 (tmm) cc_final: 0.2299 (tmm) REVERT: B 65 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8839 (pp) REVERT: B 117 MET cc_start: 0.8981 (ttm) cc_final: 0.8708 (ttt) REVERT: B 228 MET cc_start: 0.7005 (ppp) cc_final: 0.6639 (ppp) REVERT: C 228 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7134 (pmm) REVERT: D 254 MET cc_start: 0.8823 (ppp) cc_final: 0.8535 (ppp) REVERT: E 35 MET cc_start: 0.8770 (tpp) cc_final: 0.8506 (tpp) REVERT: E 255 MET cc_start: 0.8453 (mmm) cc_final: 0.8242 (mmm) REVERT: E 288 MET cc_start: 0.8936 (mtt) cc_final: 0.8617 (ptp) REVERT: E 341 MET cc_start: 0.9517 (tpt) cc_final: 0.9068 (tpp) REVERT: F 231 HIS cc_start: 0.8250 (m-70) cc_final: 0.8043 (m-70) REVERT: F 233 MET cc_start: 0.0714 (ttt) cc_final: -0.0077 (ptm) REVERT: F 341 MET cc_start: 0.8957 (ppp) cc_final: 0.8685 (ppp) REVERT: J 228 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6596 (ppp) REVERT: I 176 MET cc_start: 0.1026 (ptp) cc_final: 0.0734 (ppp) REVERT: I 228 MET cc_start: 0.8949 (OUTLIER) cc_final: 0.8654 (pmm) REVERT: I 233 MET cc_start: 0.0677 (ptm) cc_final: 0.0219 (ptt) REVERT: I 254 MET cc_start: 0.9056 (ppp) cc_final: 0.8687 (ppp) REVERT: I 255 MET cc_start: 0.8515 (ttt) cc_final: 0.8136 (mmm) REVERT: I 341 MET cc_start: 0.9635 (mmm) cc_final: 0.9169 (mmm) outliers start: 27 outliers final: 13 residues processed: 135 average time/residue: 0.1333 time to fit residues: 29.6547 Evaluate side-chains 131 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 131 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 234 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 8 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 193 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.077648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.039389 restraints weight = 135419.955| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 9.01 r_work: 0.2842 rms_B_bonded: 6.58 restraints_weight: 2.0000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20051 Z= 0.264 Angle : 0.775 14.374 27034 Z= 0.397 Chirality : 0.045 0.356 3000 Planarity : 0.004 0.061 3481 Dihedral : 5.506 24.539 2660 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.60 % Favored : 91.11 % Rotamer: Outliers : 1.21 % Allowed : 13.67 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.03 (0.17), residues: 2487 helix: 0.86 (0.17), residues: 991 sheet: -1.22 (0.26), residues: 423 loop : -1.94 (0.18), residues: 1073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 198 TYR 0.011 0.002 TYR J 259 PHE 0.020 0.002 PHE D 41 TRP 0.016 0.002 TRP F 338 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00586 (20051) covalent geometry : angle 0.77450 (27034) hydrogen bonds : bond 0.03049 ( 789) hydrogen bonds : angle 4.76905 ( 2334) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8721 (pp) REVERT: B 117 MET cc_start: 0.9291 (ttm) cc_final: 0.8982 (ttt) REVERT: B 228 MET cc_start: 0.7615 (ppp) cc_final: 0.7323 (ppp) REVERT: C 228 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7381 (pmm) REVERT: D 254 MET cc_start: 0.9001 (ppp) cc_final: 0.8718 (ppp) REVERT: D 255 MET cc_start: 0.9189 (tpp) cc_final: 0.8971 (tpp) REVERT: D 341 MET cc_start: 0.8842 (ppp) cc_final: 0.8548 (ppp) REVERT: E 35 MET cc_start: 0.9116 (tpp) cc_final: 0.8715 (tpp) REVERT: E 288 MET cc_start: 0.9030 (mtt) cc_final: 0.8759 (ptp) REVERT: E 341 MET cc_start: 0.9662 (tpt) cc_final: 0.9316 (tpp) REVERT: F 341 MET cc_start: 0.9257 (ppp) cc_final: 0.8908 (ppp) REVERT: J 228 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7209 (ppp) REVERT: J 233 MET cc_start: 0.5164 (ppp) cc_final: 0.4876 (ppp) REVERT: J 254 MET cc_start: 0.9525 (ptp) cc_final: 0.9248 (ptp) REVERT: H 341 MET cc_start: 0.9380 (tmm) cc_final: 0.9042 (ppp) REVERT: I 176 MET cc_start: 0.1281 (ptp) cc_final: 0.1001 (ppp) REVERT: I 233 MET cc_start: 0.3073 (ptm) cc_final: 0.2854 (ptt) REVERT: I 254 MET cc_start: 0.9239 (ppp) cc_final: 0.8990 (ppp) REVERT: I 255 MET cc_start: 0.8548 (ttt) cc_final: 0.8270 (mmm) REVERT: I 341 MET cc_start: 0.9675 (mmm) cc_final: 0.9363 (mmm) outliers start: 26 outliers final: 18 residues processed: 134 average time/residue: 0.1438 time to fit residues: 31.5261 Evaluate side-chains 132 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 247 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain F residue 254 MET Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 112 optimal weight: 30.0000 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 195 optimal weight: 0.4980 chunk 208 optimal weight: 20.0000 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.076219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.039534 restraints weight = 141114.160| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 9.44 r_work: 0.2837 rms_B_bonded: 7.12 restraints_weight: 2.0000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20051 Z= 0.199 Angle : 0.741 15.686 27034 Z= 0.378 Chirality : 0.044 0.319 3000 Planarity : 0.004 0.065 3481 Dihedral : 5.356 23.873 2660 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 0.88 % Allowed : 14.09 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.17), residues: 2487 helix: 0.93 (0.17), residues: 987 sheet: -1.26 (0.26), residues: 403 loop : -1.98 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 198 TYR 0.010 0.001 TYR B 280 PHE 0.015 0.001 PHE A 199 TRP 0.013 0.001 TRP F 338 HIS 0.005 0.001 HIS C 231 Details of bonding type rmsd covalent geometry : bond 0.00444 (20051) covalent geometry : angle 0.74139 (27034) hydrogen bonds : bond 0.02877 ( 789) hydrogen bonds : angle 4.73741 ( 2334) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 MET cc_start: 0.6549 (tmm) cc_final: 0.6345 (tmm) REVERT: B 65 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8750 (pp) REVERT: B 117 MET cc_start: 0.9298 (ttm) cc_final: 0.8997 (ttt) REVERT: B 228 MET cc_start: 0.7780 (ppp) cc_final: 0.7420 (ppp) REVERT: C 228 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7516 (pmm) REVERT: D 254 MET cc_start: 0.9098 (ppp) cc_final: 0.8810 (ppp) REVERT: D 255 MET cc_start: 0.9203 (tpp) cc_final: 0.8972 (tpp) REVERT: D 341 MET cc_start: 0.8739 (ppp) cc_final: 0.8416 (ppp) REVERT: E 35 MET cc_start: 0.9137 (tpp) cc_final: 0.8745 (tpp) REVERT: E 288 MET cc_start: 0.8991 (mtt) cc_final: 0.8710 (ptp) REVERT: E 341 MET cc_start: 0.9649 (tpt) cc_final: 0.9321 (tpp) REVERT: F 233 MET cc_start: 0.3934 (ttt) cc_final: 0.3003 (ptm) REVERT: F 341 MET cc_start: 0.9283 (ppp) cc_final: 0.8926 (ppp) REVERT: J 228 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7121 (ppp) REVERT: J 233 MET cc_start: 0.5343 (ppp) cc_final: 0.4999 (ppp) REVERT: H 228 MET cc_start: 0.6331 (ppp) cc_final: 0.6040 (ppp) REVERT: H 341 MET cc_start: 0.9410 (tmm) cc_final: 0.8989 (ppp) REVERT: I 176 MET cc_start: 0.1318 (ptp) cc_final: 0.0906 (ppp) REVERT: I 254 MET cc_start: 0.9280 (ppp) cc_final: 0.8992 (ppp) REVERT: I 255 MET cc_start: 0.8570 (ttt) cc_final: 0.8268 (mmm) REVERT: I 341 MET cc_start: 0.9705 (mmm) cc_final: 0.9346 (mmm) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.1372 time to fit residues: 28.7373 Evaluate side-chains 131 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 178 MET Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 96 optimal weight: 0.6980 chunk 161 optimal weight: 8.9990 chunk 75 optimal weight: 0.0050 chunk 98 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 242 optimal weight: 20.0000 chunk 190 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 213 optimal weight: 40.0000 overall best weight: 2.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.076140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.038514 restraints weight = 141191.920| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 7.95 r_work: 0.2855 rms_B_bonded: 6.88 restraints_weight: 2.0000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20051 Z= 0.178 Angle : 0.747 15.546 27034 Z= 0.380 Chirality : 0.044 0.302 3000 Planarity : 0.004 0.071 3481 Dihedral : 5.277 23.412 2660 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.88 % Favored : 91.84 % Rotamer: Outliers : 0.79 % Allowed : 14.51 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.17), residues: 2487 helix: 0.92 (0.17), residues: 994 sheet: -1.03 (0.27), residues: 389 loop : -1.96 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 198 TYR 0.010 0.001 TYR B 280 PHE 0.020 0.001 PHE D 229 TRP 0.011 0.001 TRP E 194 HIS 0.005 0.001 HIS F 231 Details of bonding type rmsd covalent geometry : bond 0.00395 (20051) covalent geometry : angle 0.74660 (27034) hydrogen bonds : bond 0.02896 ( 789) hydrogen bonds : angle 4.77702 ( 2334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8701.67 seconds wall clock time: 149 minutes 2.89 seconds (8942.89 seconds total)