Starting phenix.real_space_refine on Tue Jun 17 06:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dwu_27760/06_2025/8dwu_27760.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dwu_27760/06_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_27760/06_2025/8dwu_27760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dwu_27760/06_2025/8dwu_27760.map" model { file = "/net/cci-nas-00/data/ceres_data/8dwu_27760/06_2025/8dwu_27760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dwu_27760/06_2025/8dwu_27760.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 2} 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: 11.64, per 1000 atoms: 0.59 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: 4.67 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.35 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: 5.86 Time building geometry restraints manager: 5.56 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.200 Process input model: 43.600 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.380 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.043 0.003 TRP I 338 HIS 0.014 0.002 HIS B 347 PHE 0.057 0.003 PHE E 324 TYR 0.027 0.002 TYR F 327 ARG 0.017 0.002 ARG F 198 Details of bonding type rmsd hydrogen bonds : bond 0.18528 ( 789) hydrogen bonds : angle 7.43203 ( 2334) covalent geometry : bond 0.00538 (20051) covalent geometry : angle 1.26009 (27034) *********************** 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 : 2.082 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 176 MET cc_start: 0.6678 (mtp) cc_final: 0.6419 (mtm) REVERT: B 228 MET cc_start: 0.2223 (ppp) cc_final: 0.1915 (ppp) REVERT: E 176 MET cc_start: 0.4657 (ptm) cc_final: 0.3907 (ppp) REVERT: J 233 MET cc_start: 0.0213 (ptm) cc_final: -0.1668 (ppp) REVERT: I 176 MET cc_start: 0.3514 (ptp) cc_final: 0.0231 (ppp) outliers start: 3 outliers final: 1 residues processed: 172 average time/residue: 0.3239 time to fit residues: 84.5013 Evaluate side-chains 123 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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 209 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 75 optimal weight: 0.0570 chunk 118 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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 F 40 ASN F 345 HIS 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 = 0.4178 r_free = 0.4178 target = 0.065497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.047317 restraints weight = 178392.795| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 4.71 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20051 Z= 0.224 Angle : 0.752 9.549 27034 Z= 0.398 Chirality : 0.046 0.205 3000 Planarity : 0.004 0.048 3481 Dihedral : 5.561 28.115 2662 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.76 % Favored : 91.92 % Rotamer: Outliers : 0.42 % Allowed : 5.91 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.17), residues: 2487 helix: 0.54 (0.17), residues: 972 sheet: -1.52 (0.27), residues: 411 loop : -2.06 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 338 HIS 0.004 0.001 HIS E 347 PHE 0.022 0.002 PHE I 251 TYR 0.019 0.001 TYR F 327 ARG 0.004 0.001 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.03188 ( 789) hydrogen bonds : angle 5.18918 ( 2334) covalent geometry : bond 0.00494 (20051) covalent geometry : angle 0.75241 (27034) *********************** 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 139 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 2.164 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: symmetry clash REVERT: A 176 MET cc_start: 0.6413 (mtp) cc_final: 0.5923 (mtp) REVERT: A 254 MET cc_start: 0.7564 (mpp) cc_final: 0.7257 (mpp) REVERT: B 48 MET cc_start: 0.8987 (tpp) cc_final: 0.8762 (tpt) REVERT: B 228 MET cc_start: 0.4594 (ppp) cc_final: 0.4237 (ppp) REVERT: B 254 MET cc_start: 0.6862 (ppp) cc_final: 0.6548 (ppp) REVERT: C 48 MET cc_start: 0.7892 (tpp) cc_final: 0.7633 (tpt) REVERT: C 228 MET cc_start: 0.6012 (pmm) cc_final: 0.5513 (pmm) REVERT: C 269 MET cc_start: 0.5471 (ptt) cc_final: 0.4853 (tmm) REVERT: C 288 MET cc_start: 0.9268 (pmm) cc_final: 0.8938 (pmm) REVERT: C 341 MET cc_start: 0.7951 (tmm) cc_final: 0.7742 (tmm) REVERT: D 228 MET cc_start: 0.6856 (tmm) cc_final: 0.6564 (ppp) REVERT: E 176 MET cc_start: 0.3598 (ptm) cc_final: 0.3069 (ppp) REVERT: F 231 HIS cc_start: 0.8151 (m-70) cc_final: 0.7936 (m-70) REVERT: F 269 MET cc_start: 0.7210 (ppp) cc_final: 0.6903 (ppp) REVERT: F 341 MET cc_start: 0.8995 (ppp) cc_final: 0.8652 (ppp) REVERT: J 228 MET cc_start: 0.6738 (ttt) cc_final: 0.5811 (ppp) REVERT: J 233 MET cc_start: 0.0460 (ptm) cc_final: 0.0101 (ppp) REVERT: J 237 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.6511 (tmtt) REVERT: J 288 MET cc_start: 0.9345 (mpp) cc_final: 0.9142 (mpp) REVERT: H 262 LYS cc_start: 0.8785 (mmmt) cc_final: 0.8562 (mmmt) REVERT: H 341 MET cc_start: 0.9456 (tmm) cc_final: 0.8596 (ppp) REVERT: I 176 MET cc_start: 0.1242 (ptp) cc_final: -0.0029 (ppp) REVERT: I 228 MET cc_start: 0.8294 (pmm) cc_final: 0.7798 (pmm) REVERT: I 255 MET cc_start: 0.8606 (mpp) cc_final: 0.8016 (mpp) outliers start: 9 outliers final: 4 residues processed: 134 average time/residue: 0.3163 time to fit residues: 66.1299 Evaluate side-chains 125 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 238 LYS Chi-restraints excluded: chain H residue 239 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 151 optimal weight: 9.9990 chunk 67 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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** E 347 HIS ** 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 = 0.4170 r_free = 0.4170 target = 0.064957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.046990 restraints weight = 177909.492| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.75 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20051 Z= 0.168 Angle : 0.667 9.568 27034 Z= 0.353 Chirality : 0.044 0.185 3000 Planarity : 0.004 0.053 3481 Dihedral : 5.214 27.233 2660 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.20 % Favored : 92.48 % Rotamer: Outliers : 0.74 % Allowed : 8.33 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.17), residues: 2487 helix: 0.77 (0.17), residues: 975 sheet: -1.37 (0.27), residues: 407 loop : -1.93 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 67 HIS 0.005 0.001 HIS I 345 PHE 0.018 0.001 PHE I 251 TYR 0.014 0.001 TYR B 280 ARG 0.004 0.000 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.02882 ( 789) hydrogen bonds : angle 4.65940 ( 2334) covalent geometry : bond 0.00369 (20051) covalent geometry : angle 0.66718 (27034) *********************** 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 140 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 2.108 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: symmetry clash REVERT: A 176 MET cc_start: 0.6349 (mtt) cc_final: 0.5869 (mtp) REVERT: A 254 MET cc_start: 0.7099 (mpp) cc_final: 0.6636 (mpp) REVERT: B 117 MET cc_start: 0.8173 (ttm) cc_final: 0.7575 (ttt) REVERT: B 228 MET cc_start: 0.4858 (ppp) cc_final: 0.4468 (ppp) REVERT: B 341 MET cc_start: 0.8349 (ppp) cc_final: 0.8131 (ppp) REVERT: C 48 MET cc_start: 0.8319 (tpp) cc_final: 0.8000 (tpt) REVERT: C 228 MET cc_start: 0.6209 (OUTLIER) cc_final: 0.5595 (pmm) REVERT: D 228 MET cc_start: 0.6466 (tmm) cc_final: 0.6023 (ppp) REVERT: D 269 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6921 (ppp) REVERT: E 176 MET cc_start: 0.3235 (ptm) cc_final: 0.2829 (ppp) REVERT: E 341 MET cc_start: 0.9154 (tpt) cc_final: 0.8935 (tpp) REVERT: F 48 MET cc_start: 0.8371 (tpp) cc_final: 0.8082 (tpp) REVERT: F 231 HIS cc_start: 0.8088 (m-70) cc_final: 0.7853 (m-70) REVERT: F 255 MET cc_start: 0.8835 (ptm) cc_final: 0.8583 (ptm) REVERT: F 269 MET cc_start: 0.7280 (ppp) cc_final: 0.7008 (ppp) REVERT: F 341 MET cc_start: 0.9053 (ppp) cc_final: 0.8727 (ppp) REVERT: J 228 MET cc_start: 0.6497 (ttt) cc_final: 0.5725 (ppp) REVERT: J 254 MET cc_start: 0.9348 (ptp) cc_final: 0.8960 (ptp) REVERT: J 255 MET cc_start: 0.9350 (mmm) cc_final: 0.9066 (mmm) REVERT: H 176 MET cc_start: -0.5884 (tmm) cc_final: -0.6323 (ptt) REVERT: H 228 MET cc_start: 0.6532 (ppp) cc_final: 0.6100 (ppp) REVERT: I 176 MET cc_start: 0.1768 (ptp) cc_final: 0.0434 (ppp) REVERT: I 228 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8128 (pmm) REVERT: I 254 MET cc_start: 0.9048 (ppp) cc_final: 0.8303 (ppp) REVERT: I 341 MET cc_start: 0.9553 (mmm) cc_final: 0.9200 (mmm) outliers start: 16 outliers final: 6 residues processed: 134 average time/residue: 0.2977 time to fit residues: 63.4884 Evaluate side-chains 126 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET 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 J residue 239 ASN Chi-restraints excluded: chain J residue 341 MET 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 105 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 21 optimal weight: 0.0030 chunk 108 optimal weight: 0.4980 chunk 69 optimal weight: 5.9990 chunk 214 optimal weight: 30.0000 chunk 237 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 112 optimal weight: 30.0000 chunk 178 optimal weight: 0.9990 overall best weight: 1.6996 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.064783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.046347 restraints weight = 174230.762| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 4.55 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3293 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 : 0.627 9.433 27034 Z= 0.330 Chirality : 0.043 0.271 3000 Planarity : 0.003 0.054 3481 Dihedral : 4.985 27.316 2660 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.12 % Favored : 92.56 % Rotamer: Outliers : 0.88 % Allowed : 9.26 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.17), residues: 2487 helix: 0.95 (0.17), residues: 978 sheet: -1.06 (0.28), residues: 372 loop : -1.87 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 338 HIS 0.009 0.001 HIS B 345 PHE 0.017 0.001 PHE A 199 TYR 0.014 0.001 TYR B 280 ARG 0.004 0.000 ARG C 22 Details of bonding type rmsd hydrogen bonds : bond 0.02476 ( 789) hydrogen bonds : angle 4.39803 ( 2334) covalent geometry : bond 0.00286 (20051) covalent geometry : angle 0.62747 (27034) *********************** 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 141 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 2.143 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 176 MET cc_start: 0.6614 (mtt) cc_final: 0.6277 (mtp) REVERT: B 117 MET cc_start: 0.8176 (ttm) cc_final: 0.7596 (ttt) REVERT: B 228 MET cc_start: 0.4942 (ppp) cc_final: 0.4539 (ppp) REVERT: C 48 MET cc_start: 0.8188 (tpp) cc_final: 0.7879 (tpt) REVERT: C 228 MET cc_start: 0.6331 (OUTLIER) cc_final: 0.5765 (pmm) REVERT: D 228 MET cc_start: 0.6414 (tmm) cc_final: 0.6015 (ppp) REVERT: D 254 MET cc_start: 0.8586 (ppp) cc_final: 0.8356 (ppp) REVERT: D 255 MET cc_start: 0.8617 (tpp) cc_final: 0.8213 (tpp) REVERT: E 178 MET cc_start: 0.7791 (mmm) cc_final: 0.7552 (mmm) REVERT: E 341 MET cc_start: 0.9341 (tpt) cc_final: 0.9010 (tpp) REVERT: F 48 MET cc_start: 0.8546 (tpp) cc_final: 0.8325 (tpp) REVERT: F 231 HIS cc_start: 0.7935 (m-70) cc_final: 0.7727 (m-70) REVERT: F 233 MET cc_start: -0.0565 (ttt) cc_final: -0.1078 (ptm) REVERT: F 269 MET cc_start: 0.7300 (ppp) cc_final: 0.6974 (ppp) REVERT: F 341 MET cc_start: 0.9154 (ppp) cc_final: 0.8848 (ppp) REVERT: J 228 MET cc_start: 0.6529 (ttt) cc_final: 0.5731 (ppp) REVERT: J 233 MET cc_start: -0.0142 (ppp) cc_final: -0.0399 (ppp) REVERT: J 254 MET cc_start: 0.9402 (ptp) cc_final: 0.9088 (ptp) REVERT: J 255 MET cc_start: 0.9370 (mmm) cc_final: 0.9096 (mmm) REVERT: H 228 MET cc_start: 0.6325 (ppp) cc_final: 0.5922 (ppp) REVERT: H 288 MET cc_start: 0.8854 (ptp) cc_final: 0.8588 (ptp) REVERT: H 341 MET cc_start: 0.9372 (tmm) cc_final: 0.8614 (ppp) REVERT: I 176 MET cc_start: 0.1333 (ptp) cc_final: 0.0214 (ppp) REVERT: I 196 ASN cc_start: 0.8585 (m-40) cc_final: 0.8168 (t0) REVERT: I 228 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8063 (pmm) REVERT: I 254 MET cc_start: 0.9166 (ppp) cc_final: 0.8768 (ppp) REVERT: I 255 MET cc_start: 0.9196 (mmt) cc_final: 0.8568 (mmt) REVERT: I 341 MET cc_start: 0.9553 (mmm) cc_final: 0.9123 (mmm) outliers start: 19 outliers final: 8 residues processed: 135 average time/residue: 0.2893 time to fit residues: 62.7311 Evaluate side-chains 129 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET 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 F residue 161 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 239 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain I residue 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 74 optimal weight: 8.9990 chunk 187 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 56 optimal weight: 50.0000 chunk 188 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 chunk 225 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 111 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 320 GLN ** F 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.061656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.042463 restraints weight = 177025.108| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.89 r_work: 0.2998 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2970 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2970 r_free = 0.2970 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2970 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 20051 Z= 0.366 Angle : 0.826 10.727 27034 Z= 0.435 Chirality : 0.047 0.206 3000 Planarity : 0.005 0.062 3481 Dihedral : 5.908 26.632 2660 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.85 % Favored : 90.83 % Rotamer: Outliers : 1.35 % Allowed : 11.53 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2487 helix: 0.50 (0.16), residues: 985 sheet: -1.40 (0.26), residues: 430 loop : -2.02 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 67 HIS 0.006 0.001 HIS B 345 PHE 0.030 0.002 PHE D 41 TYR 0.017 0.002 TYR E 34 ARG 0.009 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 789) hydrogen bonds : angle 4.93392 ( 2334) covalent geometry : bond 0.00812 (20051) covalent geometry : angle 0.82635 (27034) *********************** 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 149 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 2.340 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 176 MET cc_start: 0.7212 (mtt) cc_final: 0.7008 (mtp) REVERT: A 233 MET cc_start: 0.2908 (tmm) cc_final: 0.2686 (tmm) REVERT: A 254 MET cc_start: 0.6502 (mmt) cc_final: 0.6107 (mpp) REVERT: B 48 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8420 (tpt) REVERT: B 65 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8899 (pp) REVERT: B 117 MET cc_start: 0.8958 (ttm) cc_final: 0.8737 (ttt) REVERT: B 228 MET cc_start: 0.6442 (ppp) cc_final: 0.5444 (ppp) REVERT: C 35 MET cc_start: 0.9027 (tpp) cc_final: 0.8433 (tpp) REVERT: C 228 MET cc_start: 0.7769 (pmm) cc_final: 0.7244 (pmm) REVERT: E 341 MET cc_start: 0.9479 (tpt) cc_final: 0.9071 (tpp) REVERT: F 231 HIS cc_start: 0.8247 (m-70) cc_final: 0.7954 (m-70) REVERT: F 255 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9105 (ptm) REVERT: F 269 MET cc_start: 0.7345 (ppp) cc_final: 0.7002 (ppp) REVERT: F 341 MET cc_start: 0.8898 (ppp) cc_final: 0.8659 (ppp) REVERT: J 228 MET cc_start: 0.7270 (ttt) cc_final: 0.6760 (ppp) REVERT: J 233 MET cc_start: 0.2328 (ppp) cc_final: 0.1795 (ppp) REVERT: J 255 MET cc_start: 0.9608 (mmm) cc_final: 0.9374 (mmm) REVERT: H 233 MET cc_start: 0.2329 (tmm) cc_final: 0.1957 (tmm) REVERT: H 341 MET cc_start: 0.9529 (tmm) cc_final: 0.8948 (ppp) REVERT: I 176 MET cc_start: 0.0874 (ptp) cc_final: 0.0557 (ppp) REVERT: I 196 ASN cc_start: 0.9204 (m-40) cc_final: 0.8983 (t0) REVERT: I 341 MET cc_start: 0.9577 (mmm) cc_final: 0.9265 (mmm) outliers start: 29 outliers final: 10 residues processed: 138 average time/residue: 0.3304 time to fit residues: 73.9130 Evaluate side-chains 127 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 65 LEU 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 F residue 46 GLU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 255 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 246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 89 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 194 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN E 312 HIS I 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.063615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.046994 restraints weight = 181057.003| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 5.02 r_work: 0.3091 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3065 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3065 r_free = 0.3065 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3065 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20051 Z= 0.123 Angle : 0.655 10.230 27034 Z= 0.339 Chirality : 0.043 0.188 3000 Planarity : 0.003 0.062 3481 Dihedral : 5.176 26.417 2660 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.55 % Favored : 93.12 % Rotamer: Outliers : 1.21 % Allowed : 12.65 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.17), residues: 2487 helix: 0.89 (0.17), residues: 984 sheet: -1.11 (0.27), residues: 397 loop : -1.90 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 194 HIS 0.004 0.001 HIS B 345 PHE 0.016 0.001 PHE A 199 TYR 0.014 0.001 TYR B 280 ARG 0.005 0.000 ARG F 139 Details of bonding type rmsd hydrogen bonds : bond 0.02540 ( 789) hydrogen bonds : angle 4.48615 ( 2334) covalent geometry : bond 0.00264 (20051) covalent geometry : angle 0.65460 (27034) *********************** 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 143 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7866 (tpt) cc_final: 0.7536 (tpt) REVERT: B 48 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8321 (tpp) REVERT: B 117 MET cc_start: 0.9142 (ttm) cc_final: 0.8920 (ttt) REVERT: B 153 ASP cc_start: 0.8592 (OUTLIER) cc_final: 0.8230 (t70) REVERT: B 228 MET cc_start: 0.7311 (ppp) cc_final: 0.6899 (ppp) REVERT: C 35 MET cc_start: 0.9030 (tpp) cc_final: 0.8568 (tpp) REVERT: C 48 MET cc_start: 0.8222 (tpp) cc_final: 0.7997 (tpt) REVERT: C 228 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7212 (pmm) REVERT: D 228 MET cc_start: 0.7134 (tmm) cc_final: 0.6746 (ppp) REVERT: E 341 MET cc_start: 0.9535 (tpt) cc_final: 0.9076 (tpp) REVERT: F 231 HIS cc_start: 0.8127 (m-70) cc_final: 0.7837 (m-70) REVERT: F 233 MET cc_start: 0.0885 (ttt) cc_final: 0.0180 (ppp) REVERT: F 269 MET cc_start: 0.7326 (ppp) cc_final: 0.7121 (ppp) REVERT: F 341 MET cc_start: 0.9137 (ppp) cc_final: 0.8836 (ppp) REVERT: J 228 MET cc_start: 0.7133 (ttt) cc_final: 0.6475 (ppp) REVERT: J 255 MET cc_start: 0.9660 (mmm) cc_final: 0.9318 (mmm) REVERT: H 178 MET cc_start: -0.0211 (pmm) cc_final: -0.2225 (mmp) REVERT: H 255 MET cc_start: 0.8085 (mmm) cc_final: 0.7881 (mmm) REVERT: H 288 MET cc_start: 0.8840 (ptp) cc_final: 0.8516 (ptp) REVERT: H 341 MET cc_start: 0.9500 (tmm) cc_final: 0.8791 (ppp) REVERT: I 176 MET cc_start: 0.1120 (ptp) cc_final: 0.0626 (ppp) REVERT: I 196 ASN cc_start: 0.9137 (m-40) cc_final: 0.8929 (t0) REVERT: I 228 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8744 (pmm) REVERT: I 233 MET cc_start: 0.0411 (ptm) cc_final: -0.0034 (ptt) REVERT: I 254 MET cc_start: 0.9057 (ppp) cc_final: 0.8515 (ppp) REVERT: I 255 MET cc_start: 0.9110 (mmt) cc_final: 0.8707 (mmm) REVERT: I 341 MET cc_start: 0.9644 (mmm) cc_final: 0.9243 (mmm) outliers start: 26 outliers final: 10 residues processed: 136 average time/residue: 0.2853 time to fit residues: 63.3879 Evaluate side-chains 125 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 153 ASP 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 65 LEU Chi-restraints excluded: chain F residue 161 VAL 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 183 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 191 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 65 optimal weight: 0.0870 chunk 137 optimal weight: 4.9990 chunk 200 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN C 231 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.063326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.046367 restraints weight = 179841.058| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.49 r_work: 0.3076 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.99 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20051 Z= 0.139 Angle : 0.653 9.753 27034 Z= 0.337 Chirality : 0.042 0.192 3000 Planarity : 0.003 0.062 3481 Dihedral : 5.038 25.378 2660 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.44 % Favored : 92.28 % Rotamer: Outliers : 1.12 % Allowed : 13.40 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.17), residues: 2487 helix: 1.00 (0.17), residues: 992 sheet: -0.94 (0.27), residues: 391 loop : -1.92 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 338 HIS 0.007 0.001 HIS C 231 PHE 0.016 0.001 PHE A 199 TYR 0.011 0.001 TYR B 280 ARG 0.005 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.02514 ( 789) hydrogen bonds : angle 4.40983 ( 2334) covalent geometry : bond 0.00305 (20051) covalent geometry : angle 0.65277 (27034) *********************** 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 139 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6986 (tpt) REVERT: A 176 MET cc_start: 0.6339 (mtp) cc_final: 0.5983 (mtp) REVERT: A 254 MET cc_start: 0.6157 (mmt) cc_final: 0.5697 (mpp) REVERT: B 48 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8208 (tpp) REVERT: B 117 MET cc_start: 0.9019 (ttm) cc_final: 0.8804 (ttt) REVERT: B 228 MET cc_start: 0.7268 (ppp) cc_final: 0.6887 (ppp) REVERT: C 35 MET cc_start: 0.9012 (tpp) cc_final: 0.8662 (tpp) REVERT: C 48 MET cc_start: 0.8128 (tpp) cc_final: 0.7874 (tpt) REVERT: C 228 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.7330 (pmm) REVERT: D 228 MET cc_start: 0.7066 (tmm) cc_final: 0.6775 (ppp) REVERT: E 341 MET cc_start: 0.9485 (tpt) cc_final: 0.9060 (tpp) REVERT: F 178 MET cc_start: 0.7946 (mtt) cc_final: 0.7655 (mtp) REVERT: F 231 HIS cc_start: 0.8223 (m-70) cc_final: 0.7876 (m-70) REVERT: F 269 MET cc_start: 0.7367 (ppp) cc_final: 0.7146 (ppp) REVERT: F 341 MET cc_start: 0.8973 (ppp) cc_final: 0.8706 (ppp) REVERT: J 228 MET cc_start: 0.7092 (ttt) cc_final: 0.6543 (ppp) REVERT: J 255 MET cc_start: 0.9664 (mmm) cc_final: 0.9438 (mmm) REVERT: H 178 MET cc_start: 0.0004 (pmm) cc_final: -0.1982 (mmp) REVERT: I 176 MET cc_start: 0.1053 (ptp) cc_final: 0.0607 (ppp) REVERT: I 196 ASN cc_start: 0.9232 (m-40) cc_final: 0.9026 (t0) REVERT: I 228 MET cc_start: 0.8937 (OUTLIER) cc_final: 0.8696 (pmm) REVERT: I 233 MET cc_start: 0.0315 (ptm) cc_final: 0.0061 (ptt) REVERT: I 341 MET cc_start: 0.9595 (mmm) cc_final: 0.9203 (mmm) outliers start: 24 outliers final: 11 residues processed: 133 average time/residue: 0.2782 time to fit residues: 60.7307 Evaluate side-chains 127 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 2.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain C residue 161 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 197 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 236 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 139 optimal weight: 2.9990 chunk 238 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 ASN C 231 HIS ** I 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.046183 restraints weight = 179993.684| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 4.66 r_work: 0.3054 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 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 = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4975 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= 0.163 Angle : 0.679 12.952 27034 Z= 0.349 Chirality : 0.043 0.350 3000 Planarity : 0.003 0.061 3481 Dihedral : 5.064 23.381 2660 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.48 % Favored : 92.24 % Rotamer: Outliers : 1.21 % Allowed : 13.91 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.17), residues: 2487 helix: 1.03 (0.17), residues: 990 sheet: -0.93 (0.27), residues: 384 loop : -1.84 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 338 HIS 0.015 0.001 HIS C 231 PHE 0.015 0.001 PHE A 199 TYR 0.010 0.001 TYR B 280 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.02561 ( 789) hydrogen bonds : angle 4.46090 ( 2334) covalent geometry : bond 0.00361 (20051) covalent geometry : angle 0.67926 (27034) *********************** 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 141 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.6974 (tpt) REVERT: A 176 MET cc_start: 0.5922 (mtp) cc_final: 0.5496 (mtp) REVERT: A 233 MET cc_start: 0.2577 (tmm) cc_final: 0.2375 (tmm) REVERT: A 254 MET cc_start: 0.6170 (mmt) cc_final: 0.5714 (mpp) REVERT: B 48 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8185 (tpp) REVERT: B 117 MET cc_start: 0.9028 (ttm) cc_final: 0.8786 (ttt) REVERT: B 228 MET cc_start: 0.7472 (ppp) cc_final: 0.7115 (ppp) REVERT: C 35 MET cc_start: 0.9037 (tpp) cc_final: 0.8693 (tpp) REVERT: C 48 MET cc_start: 0.8229 (tpp) cc_final: 0.7953 (tpt) REVERT: C 228 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.6791 (pmm) REVERT: C 231 HIS cc_start: 0.9033 (m90) cc_final: 0.8825 (p-80) REVERT: C 233 MET cc_start: 0.2769 (ptp) cc_final: 0.2492 (ptt) REVERT: D 228 MET cc_start: 0.7022 (tmm) cc_final: 0.6541 (ppp) REVERT: D 254 MET cc_start: 0.8774 (ppp) cc_final: 0.8475 (ppp) REVERT: E 255 MET cc_start: 0.8501 (mmm) cc_final: 0.8284 (mmm) REVERT: E 341 MET cc_start: 0.9508 (tpt) cc_final: 0.9101 (tpp) REVERT: F 178 MET cc_start: 0.7989 (mtt) cc_final: 0.7671 (mtp) REVERT: F 231 HIS cc_start: 0.8114 (m-70) cc_final: 0.7760 (m-70) REVERT: F 233 MET cc_start: 0.0998 (ttt) cc_final: 0.0161 (ptm) REVERT: F 269 MET cc_start: 0.7443 (ppp) cc_final: 0.7200 (ppp) REVERT: F 341 MET cc_start: 0.8958 (ppp) cc_final: 0.8690 (ppp) REVERT: J 228 MET cc_start: 0.7210 (ttt) cc_final: 0.6578 (ppp) REVERT: I 176 MET cc_start: 0.0778 (ptp) cc_final: 0.0449 (ppp) REVERT: I 228 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8800 (pmm) REVERT: I 233 MET cc_start: 0.0479 (ptm) cc_final: 0.0231 (ptt) REVERT: I 255 MET cc_start: 0.9007 (mmt) cc_final: 0.8734 (mmm) REVERT: I 341 MET cc_start: 0.9601 (mmm) cc_final: 0.9223 (mmm) outliers start: 26 outliers final: 12 residues processed: 134 average time/residue: 0.2771 time to fit residues: 60.8725 Evaluate side-chains 129 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 48 MET 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 161 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 196 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 36 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 198 optimal weight: 50.0000 chunk 137 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 I 312 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.078342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.039874 restraints weight = 135864.679| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 9.22 r_work: 0.2912 rms_B_bonded: 6.89 restraints_weight: 2.0000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.5281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20051 Z= 0.177 Angle : 0.695 11.332 27034 Z= 0.358 Chirality : 0.044 0.329 3000 Planarity : 0.003 0.064 3481 Dihedral : 5.085 23.504 2660 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.76 % Favored : 91.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2487 helix: 1.01 (0.17), residues: 994 sheet: -1.00 (0.27), residues: 402 loop : -1.86 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 338 HIS 0.005 0.001 HIS B 345 PHE 0.015 0.001 PHE A 199 TYR 0.009 0.001 TYR B 280 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 789) hydrogen bonds : angle 4.55721 ( 2334) covalent geometry : bond 0.00392 (20051) covalent geometry : angle 0.69503 (27034) *********************** 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 133 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7071 (tpt) REVERT: A 254 MET cc_start: 0.6206 (mmt) cc_final: 0.5924 (mpp) REVERT: B 48 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8440 (tpp) REVERT: B 117 MET cc_start: 0.9211 (ttm) cc_final: 0.8914 (ttt) REVERT: B 228 MET cc_start: 0.7659 (ppp) cc_final: 0.7350 (ppp) REVERT: C 35 MET cc_start: 0.9285 (tpp) cc_final: 0.8941 (tpp) REVERT: C 48 MET cc_start: 0.8182 (tpp) cc_final: 0.7881 (tpt) REVERT: C 228 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7263 (pmm) REVERT: C 231 HIS cc_start: 0.9410 (m90) cc_final: 0.9199 (p-80) REVERT: D 228 MET cc_start: 0.7354 (tmm) cc_final: 0.6882 (ppp) REVERT: D 254 MET cc_start: 0.9024 (ppp) cc_final: 0.8751 (ppp) REVERT: D 255 MET cc_start: 0.9145 (tpp) cc_final: 0.8929 (tpp) REVERT: D 341 MET cc_start: 0.8804 (ppp) cc_final: 0.8527 (ppp) REVERT: E 341 MET cc_start: 0.9673 (tpt) cc_final: 0.9335 (tpp) REVERT: F 178 MET cc_start: 0.8392 (mtt) cc_final: 0.8031 (mtt) REVERT: F 233 MET cc_start: 0.3125 (ttt) cc_final: 0.1838 (ppp) REVERT: F 269 MET cc_start: 0.7422 (ppp) cc_final: 0.7062 (ppp) REVERT: F 341 MET cc_start: 0.9282 (ppp) cc_final: 0.8945 (ppp) REVERT: J 228 MET cc_start: 0.7122 (ttt) cc_final: 0.6750 (ppp) REVERT: H 341 MET cc_start: 0.9390 (tmm) cc_final: 0.8960 (ppp) REVERT: I 176 MET cc_start: 0.0839 (ptp) cc_final: 0.0582 (ppp) REVERT: I 341 MET cc_start: 0.9675 (mmm) cc_final: 0.9367 (mmm) outliers start: 17 outliers final: 12 residues processed: 125 average time/residue: 0.2878 time to fit residues: 58.5696 Evaluate side-chains 130 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 48 MET 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 D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 37 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 228 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 226 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.076058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.039845 restraints weight = 140098.152| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 10.08 r_work: 0.2835 rms_B_bonded: 7.00 restraints_weight: 2.0000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 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 = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20051 Z= 0.224 Angle : 0.757 16.186 27034 Z= 0.387 Chirality : 0.045 0.299 3000 Planarity : 0.004 0.064 3481 Dihedral : 5.376 23.531 2660 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.16 % Favored : 91.56 % Rotamer: Outliers : 0.93 % Allowed : 14.47 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2487 helix: 0.97 (0.17), residues: 987 sheet: -1.11 (0.26), residues: 414 loop : -1.88 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 338 HIS 0.006 0.001 HIS B 345 PHE 0.018 0.002 PHE D 41 TYR 0.012 0.001 TYR F 24 ARG 0.008 0.001 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 789) hydrogen bonds : angle 4.77487 ( 2334) covalent geometry : bond 0.00499 (20051) covalent geometry : angle 0.75718 (27034) ********************** 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 135 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7085 (tpt) REVERT: A 233 MET cc_start: 0.6872 (tmm) cc_final: 0.6630 (tmm) REVERT: B 48 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8586 (tpp) REVERT: B 117 MET cc_start: 0.9267 (ttm) cc_final: 0.8922 (ttt) REVERT: C 35 MET cc_start: 0.9393 (tpp) cc_final: 0.9106 (tpp) REVERT: C 48 MET cc_start: 0.8310 (tpp) cc_final: 0.7965 (tpt) REVERT: C 228 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7630 (pmm) REVERT: D 228 MET cc_start: 0.7543 (tmm) cc_final: 0.7122 (ppp) REVERT: D 254 MET cc_start: 0.9153 (ppp) cc_final: 0.8888 (ppp) REVERT: D 255 MET cc_start: 0.9242 (tpp) cc_final: 0.9033 (tpp) REVERT: D 341 MET cc_start: 0.8752 (ppp) cc_final: 0.8432 (ppp) REVERT: E 288 MET cc_start: 0.9339 (mpp) cc_final: 0.9033 (pmm) REVERT: E 341 MET cc_start: 0.9653 (tpt) cc_final: 0.9357 (tpp) REVERT: F 178 MET cc_start: 0.8425 (mtt) cc_final: 0.8118 (mtt) REVERT: F 233 MET cc_start: 0.4403 (ttt) cc_final: 0.3467 (ptm) REVERT: F 269 MET cc_start: 0.7455 (ppp) cc_final: 0.7074 (ppp) REVERT: F 341 MET cc_start: 0.9317 (ppp) cc_final: 0.8975 (ppp) REVERT: J 228 MET cc_start: 0.7732 (ttt) cc_final: 0.7348 (ppp) REVERT: J 233 MET cc_start: 0.5508 (ppp) cc_final: 0.5181 (ppp) REVERT: H 341 MET cc_start: 0.9429 (tmm) cc_final: 0.9049 (ppp) REVERT: I 176 MET cc_start: 0.1425 (ptp) cc_final: 0.1025 (ppp) REVERT: I 255 MET cc_start: 0.8585 (mmm) cc_final: 0.8332 (mmm) REVERT: I 341 MET cc_start: 0.9668 (mmm) cc_final: 0.9355 (mmm) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.3141 time to fit residues: 65.6720 Evaluate side-chains 129 residues out of total 2175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 2.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 48 MET 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 D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 25 THR 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 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 246 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 227 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 = 0.4490 r_free = 0.4490 target = 0.076370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.040255 restraints weight = 141633.496| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 10.32 r_work: 0.2860 rms_B_bonded: 7.08 restraints_weight: 2.0000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.030 | | occupancies: max = 1.00 min = 0.98 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20051 Z= 0.149 Angle : 0.714 14.343 27034 Z= 0.365 Chirality : 0.044 0.284 3000 Planarity : 0.003 0.063 3481 Dihedral : 5.129 23.374 2660 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.20 % Favored : 92.52 % Rotamer: Outliers : 0.70 % Allowed : 14.98 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.17), residues: 2487 helix: 1.01 (0.17), residues: 985 sheet: -0.88 (0.27), residues: 386 loop : -1.86 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 338 HIS 0.005 0.001 HIS B 345 PHE 0.015 0.001 PHE D 229 TYR 0.010 0.001 TYR B 280 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd hydrogen bonds : bond 0.02753 ( 789) hydrogen bonds : angle 4.65705 ( 2334) covalent geometry : bond 0.00329 (20051) covalent geometry : angle 0.71440 (27034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16097.46 seconds wall clock time: 274 minutes 41.31 seconds (16481.31 seconds total)