Starting phenix.real_space_refine on Sat Sep 28 15:05:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/09_2024/8dwu_27760.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/09_2024/8dwu_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/09_2024/8dwu_27760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/09_2024/8dwu_27760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/09_2024/8dwu_27760.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dwu_27760/09_2024/8dwu_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.35, per 1000 atoms: 0.58 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: 4.74 Conformation dependent library (CDL) restraints added in 2.5 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: 2.30 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: 6.20 Time building geometry restraints manager: 5.58 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 43.170 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.920 ------------------------------------------------------------------------------- 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= 0.355 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 2.205 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: 0.3390 time to fit residues: 87.8219 Evaluate side-chains 123 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 122 time to evaluate : 2.238 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 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= 0.319 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 *********************** 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 fitting. rotamer outliers: 9 poor density : 130 time to evaluate : 2.402 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 233 MET cc_start: -0.0828 (tmm) cc_final: -0.1595 (tmm) REVERT: B 48 MET cc_start: 0.8134 (tpp) cc_final: 0.7647 (tpt) REVERT: E 176 MET cc_start: 0.4002 (ptm) cc_final: 0.3441 (ppp) REVERT: J 233 MET cc_start: 0.0635 (ptm) cc_final: 0.0153 (ppp) REVERT: I 176 MET cc_start: 0.3198 (ptp) cc_final: 0.0883 (ppp) REVERT: I 228 MET cc_start: 0.6847 (pmm) cc_final: 0.6488 (pmm) outliers start: 9 outliers final: 4 residues processed: 134 average time/residue: 0.3287 time to fit residues: 68.2316 Evaluate side-chains 123 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 269 MET 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 125 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 187 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 225 optimal weight: 8.9990 chunk 243 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 223 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 180 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.2907 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= 0.249 Angle : 0.697 9.531 27034 Z= 0.367 Chirality : 0.044 0.187 3000 Planarity : 0.004 0.053 3481 Dihedral : 5.274 27.148 2660 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.16 % Favored : 92.52 % Rotamer: Outliers : 0.65 % Allowed : 8.47 % Favored : 90.88 % 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: -1.21 (0.17), residues: 2487 helix: 0.69 (0.17), residues: 971 sheet: -1.40 (0.27), residues: 407 loop : -1.94 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 67 HIS 0.004 0.001 HIS I 345 PHE 0.016 0.001 PHE I 251 TYR 0.016 0.001 TYR B 280 ARG 0.004 0.000 ARG C 22 *********************** 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 137 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 123 time to evaluate : 2.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.5472 (mtp) cc_final: 0.5003 (mtp) REVERT: B 48 MET cc_start: 0.7929 (tpp) cc_final: 0.7634 (tpt) REVERT: E 176 MET cc_start: 0.3730 (ptm) cc_final: 0.3138 (ppp) REVERT: J 228 MET cc_start: 0.6256 (ppp) cc_final: 0.5912 (ppp) REVERT: J 233 MET cc_start: 0.0497 (ptm) cc_final: -0.0164 (ppp) REVERT: H 176 MET cc_start: -0.1872 (tmm) cc_final: -0.2569 (ptt) REVERT: I 176 MET cc_start: 0.3532 (ptp) cc_final: 0.1134 (ppp) outliers start: 14 outliers final: 6 residues processed: 132 average time/residue: 0.3056 time to fit residues: 64.0800 Evaluate side-chains 123 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 246 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 222 optimal weight: 50.0000 chunk 169 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 226 optimal weight: 20.0000 chunk 239 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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** ** C 62 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.3937 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= 0.351 Angle : 0.742 10.651 27034 Z= 0.389 Chirality : 0.045 0.267 3000 Planarity : 0.004 0.056 3481 Dihedral : 5.437 25.136 2660 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 8.44 % Favored : 91.19 % Rotamer: Outliers : 0.93 % Allowed : 9.95 % Favored : 89.12 % 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: -1.19 (0.17), residues: 2487 helix: 0.67 (0.17), residues: 976 sheet: -1.37 (0.27), residues: 406 loop : -1.91 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 67 HIS 0.009 0.001 HIS B 345 PHE 0.019 0.002 PHE D 41 TYR 0.018 0.002 TYR B 280 ARG 0.005 0.001 ARG C 22 *********************** 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 fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 MET cc_start: 0.4823 (mtp) cc_final: 0.4486 (mtp) REVERT: A 233 MET cc_start: -0.0494 (tmm) cc_final: -0.0743 (tmm) REVERT: C 35 MET cc_start: 0.6741 (tpp) cc_final: 0.6379 (tpp) REVERT: J 233 MET cc_start: 0.0186 (ptm) cc_final: -0.0463 (ppp) REVERT: H 176 MET cc_start: -0.1671 (tmm) cc_final: -0.2385 (ptt) REVERT: H 228 MET cc_start: 0.5090 (ppp) cc_final: 0.4612 (ppp) REVERT: I 176 MET cc_start: 0.3601 (ptp) cc_final: 0.1879 (ppp) REVERT: I 228 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6754 (pmm) REVERT: I 233 MET cc_start: -0.0292 (ptm) cc_final: -0.0956 (ptt) REVERT: I 254 MET cc_start: 0.5879 (ppp) cc_final: 0.5193 (ppp) outliers start: 20 outliers final: 8 residues processed: 134 average time/residue: 0.2956 time to fit residues: 63.7298 Evaluate side-chains 125 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 MET Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 161 VAL 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 228 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 199 optimal weight: 5.9990 chunk 136 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 178 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 overall best weight: 3.9386 ------------------------------------------------------------------------------- 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** E 312 HIS ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20051 Z= 0.324 Angle : 0.728 11.286 27034 Z= 0.377 Chirality : 0.044 0.189 3000 Planarity : 0.004 0.062 3481 Dihedral : 5.381 25.525 2660 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.44 % Favored : 92.24 % Rotamer: Outliers : 1.30 % Allowed : 11.72 % Favored : 86.98 % 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: -1.13 (0.17), residues: 2487 helix: 0.74 (0.17), residues: 980 sheet: -1.32 (0.26), residues: 418 loop : -1.90 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 338 HIS 0.008 0.001 HIS C 231 PHE 0.015 0.002 PHE A 199 TYR 0.016 0.001 TYR B 280 ARG 0.006 0.001 ARG A 198 *********************** 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 148 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 2.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6014 (tpt) REVERT: A 176 MET cc_start: 0.5308 (mtp) cc_final: 0.5090 (mtp) REVERT: C 35 MET cc_start: 0.6684 (tpp) cc_final: 0.6339 (tpp) REVERT: F 341 MET cc_start: 0.4865 (ppp) cc_final: 0.4656 (ppp) REVERT: H 176 MET cc_start: -0.1129 (tmm) cc_final: -0.1745 (ptt) REVERT: I 176 MET cc_start: 0.3289 (ptp) cc_final: 0.1839 (ppp) REVERT: I 233 MET cc_start: -0.0529 (ptm) cc_final: -0.1071 (ptt) outliers start: 28 outliers final: 13 residues processed: 137 average time/residue: 0.3147 time to fit residues: 70.2663 Evaluate side-chains 129 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 161 VAL 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 239 ASN Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 80 optimal weight: 20.0000 chunk 215 optimal weight: 0.1980 chunk 47 optimal weight: 40.0000 chunk 140 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 199 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 328 HIS ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 HIS ** J 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6280 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 20051 Z= 0.334 Angle : 0.744 11.092 27034 Z= 0.384 Chirality : 0.044 0.181 3000 Planarity : 0.004 0.064 3481 Dihedral : 5.424 24.578 2660 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.44 % Favored : 91.27 % Rotamer: Outliers : 1.53 % Allowed : 12.56 % Favored : 85.91 % 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: -1.17 (0.17), residues: 2487 helix: 0.72 (0.17), residues: 984 sheet: -1.39 (0.26), residues: 405 loop : -1.94 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 67 HIS 0.005 0.001 HIS C 231 PHE 0.017 0.002 PHE D 41 TYR 0.016 0.001 TYR B 280 ARG 0.006 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 119 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.6842 (OUTLIER) cc_final: 0.6136 (tpt) REVERT: B 48 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7254 (tpp) REVERT: H 176 MET cc_start: -0.1389 (tmm) cc_final: -0.2277 (ptt) REVERT: H 178 MET cc_start: -0.0430 (pmm) cc_final: -0.2081 (mmp) REVERT: H 228 MET cc_start: 0.5153 (ppp) cc_final: 0.4918 (ppp) REVERT: I 176 MET cc_start: 0.3169 (ptp) cc_final: 0.2029 (ppp) REVERT: I 228 MET cc_start: 0.6740 (pmm) cc_final: 0.6533 (pmm) REVERT: I 233 MET cc_start: -0.0526 (ptm) cc_final: -0.0805 (ptt) outliers start: 33 outliers final: 13 residues processed: 145 average time/residue: 0.3004 time to fit residues: 69.4297 Evaluate side-chains 129 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 347 HIS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 161 VAL 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 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 231 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 175 optimal weight: 10.0000 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 149 optimal weight: 0.4980 chunk 145 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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** I 312 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20051 Z= 0.192 Angle : 0.715 12.988 27034 Z= 0.364 Chirality : 0.043 0.193 3000 Planarity : 0.003 0.058 3481 Dihedral : 5.173 25.183 2660 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.20 % Favored : 92.52 % Rotamer: Outliers : 1.02 % Allowed : 14.05 % Favored : 84.93 % 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: -0.98 (0.17), residues: 2487 helix: 0.84 (0.17), residues: 981 sheet: -1.04 (0.28), residues: 371 loop : -1.89 (0.18), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 338 HIS 0.005 0.001 HIS D 231 PHE 0.017 0.001 PHE I 225 TYR 0.012 0.001 TYR B 280 ARG 0.005 0.000 ARG A 198 *********************** 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 138 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.7136 (tpp) REVERT: F 341 MET cc_start: 0.4544 (ppp) cc_final: 0.3780 (ppp) REVERT: H 176 MET cc_start: -0.1517 (tmm) cc_final: -0.2237 (ptt) REVERT: H 178 MET cc_start: -0.1016 (pmm) cc_final: -0.2158 (mmp) REVERT: I 176 MET cc_start: 0.3010 (ptp) cc_final: 0.1834 (ppp) REVERT: I 228 MET cc_start: 0.6557 (pmm) cc_final: 0.6312 (pmm) REVERT: I 233 MET cc_start: -0.0628 (ptm) cc_final: -0.1171 (ptt) outliers start: 22 outliers final: 13 residues processed: 134 average time/residue: 0.2743 time to fit residues: 60.2935 Evaluate side-chains 127 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 113 time to evaluate : 2.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 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 199 PHE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain H residue 239 ASN Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 147 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 151 optimal weight: 0.0970 chunk 162 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 187 optimal weight: 10.0000 chunk 217 optimal weight: 50.0000 overall best weight: 3.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 212 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20051 Z= 0.299 Angle : 0.756 13.766 27034 Z= 0.385 Chirality : 0.045 0.382 3000 Planarity : 0.004 0.057 3481 Dihedral : 5.325 23.715 2660 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.12 % Favored : 91.60 % Rotamer: Outliers : 0.98 % Allowed : 14.70 % 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: -1.02 (0.17), residues: 2487 helix: 0.80 (0.17), residues: 992 sheet: -1.10 (0.27), residues: 410 loop : -1.93 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 338 HIS 0.005 0.001 HIS B 345 PHE 0.015 0.002 PHE D 41 TYR 0.012 0.001 TYR B 280 ARG 0.007 0.001 ARG A 198 *********************** 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 138 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 2.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7093 (tpt) REVERT: F 233 MET cc_start: 0.0373 (ppp) cc_final: -0.0258 (ppp) REVERT: F 341 MET cc_start: 0.4516 (ppp) cc_final: 0.3736 (ppp) REVERT: H 176 MET cc_start: -0.1580 (tmm) cc_final: -0.1984 (ptt) REVERT: I 176 MET cc_start: 0.3454 (ptp) cc_final: 0.1875 (ppp) REVERT: I 228 MET cc_start: 0.6741 (pmm) cc_final: 0.6322 (pmm) REVERT: I 233 MET cc_start: -0.0541 (ptm) cc_final: -0.1145 (ptt) outliers start: 21 outliers final: 15 residues processed: 131 average time/residue: 0.3014 time to fit residues: 64.1809 Evaluate side-chains 131 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 246 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 199 PHE 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 Chi-restraints excluded: chain I residue 268 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 228 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 134 optimal weight: 0.0570 chunk 97 optimal weight: 4.9990 chunk 174 optimal weight: 0.0970 chunk 68 optimal weight: 5.9990 chunk 201 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 overall best weight: 3.8302 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.5760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20051 Z= 0.320 Angle : 0.793 15.358 27034 Z= 0.401 Chirality : 0.045 0.351 3000 Planarity : 0.004 0.056 3481 Dihedral : 5.448 24.020 2660 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.04 % Favored : 91.68 % Rotamer: Outliers : 1.30 % Allowed : 14.84 % Favored : 83.86 % 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: -1.20 (0.17), residues: 2487 helix: 0.61 (0.17), residues: 1005 sheet: -1.20 (0.27), residues: 390 loop : -1.99 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 338 HIS 0.005 0.001 HIS B 345 PHE 0.015 0.002 PHE D 41 TYR 0.015 0.001 TYR F 24 ARG 0.008 0.001 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 113 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7030 (tpt) REVERT: C 288 MET cc_start: 0.6614 (pmm) cc_final: 0.6358 (pmm) REVERT: F 233 MET cc_start: 0.0889 (ppp) cc_final: 0.0632 (ppp) REVERT: F 341 MET cc_start: 0.4440 (ppp) cc_final: 0.3922 (ppp) REVERT: H 176 MET cc_start: -0.1220 (tmm) cc_final: -0.1810 (ptt) REVERT: H 228 MET cc_start: 0.5018 (ppp) cc_final: 0.4261 (ppp) REVERT: I 176 MET cc_start: 0.3966 (ptp) cc_final: 0.2060 (ppp) REVERT: I 228 MET cc_start: 0.6700 (pmm) cc_final: 0.6297 (pmm) REVERT: I 233 MET cc_start: -0.0547 (ptm) cc_final: -0.0940 (ptt) outliers start: 28 outliers final: 20 residues processed: 132 average time/residue: 0.2894 time to fit residues: 62.2116 Evaluate side-chains 133 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 112 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 B residue 64 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 211 PHE Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 235 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 247 optimal weight: 7.9990 chunk 227 optimal weight: 7.9990 chunk 196 optimal weight: 30.0000 chunk 20 optimal weight: 50.0000 chunk 151 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6396 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 20051 Z= 0.478 Angle : 0.887 17.378 27034 Z= 0.453 Chirality : 0.047 0.330 3000 Planarity : 0.004 0.059 3481 Dihedral : 5.904 25.265 2660 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.13 % Favored : 90.59 % Rotamer: Outliers : 1.16 % Allowed : 15.02 % Favored : 83.81 % 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: -1.49 (0.17), residues: 2487 helix: 0.39 (0.17), residues: 997 sheet: -1.49 (0.25), residues: 428 loop : -2.10 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 67 HIS 0.005 0.001 HIS D 347 PHE 0.025 0.002 PHE D 41 TYR 0.014 0.002 TYR B 280 ARG 0.011 0.001 ARG A 198 ********************** 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 137 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 48 MET cc_start: 0.8093 (OUTLIER) cc_final: 0.7372 (tpt) REVERT: B 269 MET cc_start: 0.2891 (pmm) cc_final: 0.2147 (pmm) REVERT: F 233 MET cc_start: 0.1196 (ppp) cc_final: 0.0949 (ppp) REVERT: F 341 MET cc_start: 0.4494 (ppp) cc_final: 0.4090 (ppp) REVERT: H 176 MET cc_start: -0.0938 (tmm) cc_final: -0.1812 (ptt) REVERT: I 176 MET cc_start: 0.3804 (ptp) cc_final: 0.1832 (ppp) REVERT: I 228 MET cc_start: 0.6799 (pmm) cc_final: 0.6390 (pmm) REVERT: I 233 MET cc_start: -0.0624 (ptm) cc_final: -0.1198 (ptt) outliers start: 25 outliers final: 22 residues processed: 132 average time/residue: 0.2962 time to fit residues: 62.9882 Evaluate side-chains 134 residues out of total 2175 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 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 B residue 64 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 43 PHE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 251 PHE Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 199 PHE Chi-restraints excluded: chain F residue 246 VAL Chi-restraints excluded: chain J residue 211 PHE Chi-restraints excluded: chain J residue 333 LEU Chi-restraints excluded: chain J residue 341 MET Chi-restraints excluded: chain I residue 246 VAL Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 333 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: chunk 209 optimal weight: 30.0000 chunk 60 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 54 optimal weight: 50.0000 chunk 197 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 202 optimal weight: 6.9990 chunk 24 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.065094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.046086 restraints weight = 168680.631| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.96 r_work: 0.3004 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20051 Z= 0.275 Angle : 0.821 16.778 27034 Z= 0.415 Chirality : 0.045 0.303 3000 Planarity : 0.004 0.057 3481 Dihedral : 5.585 25.401 2660 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.12 % Favored : 91.60 % Rotamer: Outliers : 1.21 % Allowed : 15.53 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.28 (0.17), residues: 2487 helix: 0.61 (0.17), residues: 995 sheet: -1.38 (0.26), residues: 401 loop : -2.02 (0.17), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 338 HIS 0.004 0.001 HIS B 345 PHE 0.016 0.002 PHE B 211 TYR 0.015 0.001 TYR F 24 ARG 0.008 0.001 ARG A 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3937.30 seconds wall clock time: 71 minutes 40.65 seconds (4300.65 seconds total)