Starting phenix.real_space_refine on Sun Aug 24 10:54:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyt_34377/08_2025/8gyt_34377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyt_34377/08_2025/8gyt_34377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gyt_34377/08_2025/8gyt_34377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyt_34377/08_2025/8gyt_34377.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gyt_34377/08_2025/8gyt_34377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyt_34377/08_2025/8gyt_34377.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.050 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 98 5.16 5 C 12718 2.51 5 N 3231 2.21 5 O 3456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19503 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2770 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2774 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2765 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "D" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2774 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2774 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2774 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2774 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 16, 'TRANS': 333} Chain breaks: 2 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.00, per 1000 atoms: 0.26 Number of scatterers: 19503 At special positions: 0 Unit cell: (129.822, 129.822, 127.293, 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 98 16.00 O 3456 8.00 N 3231 7.00 C 12718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 261 " distance=2.04 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 261 " distance=2.04 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 261 " distance=2.04 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 261 " distance=2.04 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 242 " distance=2.02 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 261 " distance=2.04 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 261 " distance=2.04 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 261 " distance=2.04 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 242 " distance=2.03 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 Links applied NAG-ASN " NAG A 401 " - " ASN A 71 " " NAG B 401 " - " ASN B 71 " " NAG C 401 " - " ASN C 71 " " NAG D 401 " - " ASN D 71 " " NAG E 401 " - " ASN E 71 " " NAG F 401 " - " ASN F 71 " " NAG G 401 " - " ASN G 71 " Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 850.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4760 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 7 sheets defined 77.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 33 through 61 removed outlier: 3.809A pdb=" N ILE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 43 " --> pdb=" O LYS A 39 " (cutoff:3.500A) Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 109 through 133 Proline residue: A 124 - end of helix removed outlier: 3.529A pdb=" N VAL A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 157 removed outlier: 3.783A pdb=" N LYS A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.638A pdb=" N PHE A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 202 removed outlier: 3.847A pdb=" N ARG A 201 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 265 through 293 Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 300 through 307 removed outlier: 4.264A pdb=" N MET A 307 " --> pdb=" O SER A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 316 removed outlier: 3.621A pdb=" N LEU A 313 " --> pdb=" O PRO A 309 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 341 removed outlier: 3.836A pdb=" N VAL A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N GLU A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE A 341 " --> pdb=" O ILE A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.639A pdb=" N VAL A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 32 through 60 removed outlier: 3.840A pdb=" N SER B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 73 through 91 removed outlier: 4.321A pdb=" N LEU B 88 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N HIS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 109 through 157 Proline residue: B 124 - end of helix removed outlier: 3.591A pdb=" N VAL B 133 " --> pdb=" O GLN B 129 " (cutoff:3.500A) Proline residue: B 134 - end of helix removed outlier: 3.894A pdb=" N LYS B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 170 through 184 removed outlier: 3.624A pdb=" N PHE B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 265 through 296 Proline residue: B 285 - end of helix removed outlier: 4.205A pdb=" N LEU B 294 " --> pdb=" O ASN B 290 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N CYS B 295 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'B' and resid 308 through 316 removed outlier: 3.733A pdb=" N LEU B 313 " --> pdb=" O PRO B 309 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 320 Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.905A pdb=" N VAL B 328 " --> pdb=" O ASN B 324 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 356 removed outlier: 4.129A pdb=" N VAL B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 374 Processing helix chain 'C' and resid 21 through 28 Processing helix chain 'C' and resid 32 through 61 removed outlier: 3.720A pdb=" N ILE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Proline residue: C 46 - end of helix Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 109 through 133 Proline residue: C 124 - end of helix removed outlier: 3.546A pdb=" N VAL C 133 " --> pdb=" O GLN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 157 removed outlier: 3.930A pdb=" N LYS C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 168 Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.632A pdb=" N PHE C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 265 through 293 Proline residue: C 285 - end of helix Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 300 through 307 removed outlier: 4.426A pdb=" N MET C 307 " --> pdb=" O SER C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 316 removed outlier: 3.703A pdb=" N LEU C 313 " --> pdb=" O PRO C 309 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N LEU C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 320 Processing helix chain 'C' and resid 324 through 341 removed outlier: 3.703A pdb=" N VAL C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 356 removed outlier: 4.593A pdb=" N LEU C 346 " --> pdb=" O SER C 342 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 347 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'D' and resid 21 through 28 Processing helix chain 'D' and resid 32 through 60 removed outlier: 3.730A pdb=" N SER D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) Proline residue: D 46 - end of helix Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 104 through 109 removed outlier: 4.292A pdb=" N LYS D 108 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 133 Proline residue: D 124 - end of helix removed outlier: 3.592A pdb=" N VAL D 133 " --> pdb=" O GLN D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 157 removed outlier: 3.827A pdb=" N LYS D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 168 Processing helix chain 'D' and resid 170 through 184 removed outlier: 3.694A pdb=" N PHE D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 202 removed outlier: 3.860A pdb=" N ARG D 201 " --> pdb=" O ALA D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 248 through 252 removed outlier: 4.389A pdb=" N ASP D 251 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU D 252 " --> pdb=" O LEU D 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 248 through 252' Processing helix chain 'D' and resid 265 through 293 Proline residue: D 285 - end of helix Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 300 through 307 removed outlier: 4.294A pdb=" N MET D 307 " --> pdb=" O SER D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 3.576A pdb=" N LEU D 313 " --> pdb=" O PRO D 309 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 320 Processing helix chain 'D' and resid 324 through 341 removed outlier: 3.719A pdb=" N VAL D 328 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 356 removed outlier: 4.702A pdb=" N LEU D 346 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER D 347 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 374 Processing helix chain 'E' and resid 21 through 28 Processing helix chain 'E' and resid 33 through 61 removed outlier: 4.122A pdb=" N ILE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 38 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 43 " --> pdb=" O LYS E 39 " (cutoff:3.500A) Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 109 through 133 Proline residue: E 124 - end of helix removed outlier: 3.594A pdb=" N VAL E 133 " --> pdb=" O GLN E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 157 removed outlier: 3.839A pdb=" N LYS E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 170 through 184 removed outlier: 3.628A pdb=" N PHE E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 200 Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 265 through 296 Proline residue: E 285 - end of helix removed outlier: 4.198A pdb=" N LEU E 294 " --> pdb=" O ASN E 290 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N CYS E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 307 removed outlier: 4.583A pdb=" N MET E 307 " --> pdb=" O SER E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 313 Processing helix chain 'E' and resid 314 through 320 removed outlier: 4.118A pdb=" N LYS E 317 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N MET E 318 " --> pdb=" O SER E 315 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU E 319 " --> pdb=" O ARG E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 341 removed outlier: 3.834A pdb=" N VAL E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER E 338 " --> pdb=" O ARG E 334 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 356 removed outlier: 4.132A pdb=" N VAL E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 Processing helix chain 'F' and resid 21 through 28 Processing helix chain 'F' and resid 33 through 61 removed outlier: 4.027A pdb=" N ILE F 37 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL F 38 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 104 through 109 removed outlier: 4.276A pdb=" N LYS F 108 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 133 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 133 through 157 removed outlier: 3.787A pdb=" N LYS F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 168 Processing helix chain 'F' and resid 170 through 184 removed outlier: 3.638A pdb=" N PHE F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 Processing helix chain 'F' and resid 203 through 230 Processing helix chain 'F' and resid 265 through 293 Proline residue: F 285 - end of helix Processing helix chain 'F' and resid 294 through 296 No H-bonds generated for 'chain 'F' and resid 294 through 296' Processing helix chain 'F' and resid 300 through 307 removed outlier: 4.487A pdb=" N MET F 307 " --> pdb=" O SER F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 316 removed outlier: 3.753A pdb=" N LEU F 313 " --> pdb=" O PRO F 309 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU F 314 " --> pdb=" O ALA F 310 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 316 " --> pdb=" O ASP F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 341 removed outlier: 3.837A pdb=" N VAL F 328 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 338 " --> pdb=" O ARG F 334 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLU F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE F 341 " --> pdb=" O ILE F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 356 removed outlier: 4.102A pdb=" N VAL F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 374 Processing helix chain 'G' and resid 21 through 28 Processing helix chain 'G' and resid 33 through 61 removed outlier: 4.042A pdb=" N ILE G 37 " --> pdb=" O PRO G 33 " (cutoff:3.500A) Proline residue: G 46 - end of helix Processing helix chain 'G' and resid 73 through 87 Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 109 through 157 Proline residue: G 124 - end of helix removed outlier: 3.535A pdb=" N VAL G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) Proline residue: G 134 - end of helix removed outlier: 3.781A pdb=" N LYS G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 168 Processing helix chain 'G' and resid 170 through 184 removed outlier: 3.640A pdb=" N PHE G 174 " --> pdb=" O ASP G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 200 Processing helix chain 'G' and resid 203 through 230 Processing helix chain 'G' and resid 265 through 293 Proline residue: G 285 - end of helix Processing helix chain 'G' and resid 294 through 296 No H-bonds generated for 'chain 'G' and resid 294 through 296' Processing helix chain 'G' and resid 300 through 306 Processing helix chain 'G' and resid 308 through 316 removed outlier: 3.778A pdb=" N LEU G 313 " --> pdb=" O PRO G 309 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU G 314 " --> pdb=" O ALA G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 341 removed outlier: 3.851A pdb=" N VAL G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER G 338 " --> pdb=" O ARG G 334 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE G 341 " --> pdb=" O ILE G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 343 through 356 removed outlier: 4.119A pdb=" N VAL G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 374 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.542A pdb=" N SER A 65 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG A 262 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.567A pdb=" N SER B 65 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG B 262 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.588A pdb=" N SER C 65 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 262 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.530A pdb=" N SER D 65 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG D 262 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.511A pdb=" N SER E 65 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E 262 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.531A pdb=" N SER F 65 " --> pdb=" O ARG F 262 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG F 262 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.526A pdb=" N SER G 65 " --> pdb=" O ARG G 262 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG G 262 " --> pdb=" O SER G 65 " (cutoff:3.500A) 1251 hydrogen bonds defined for protein. 3711 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.66 Time building geometry restraints manager: 2.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6020 1.35 - 1.47: 4902 1.47 - 1.59: 8889 1.59 - 1.71: 0 1.71 - 1.84: 140 Bond restraints: 19951 Sorted by residual: bond pdb=" C5 NAG D 401 " pdb=" O5 NAG D 401 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C5 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" C5 NAG G 401 " pdb=" O5 NAG G 401 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C5 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" C5 NAG F 401 " pdb=" O5 NAG F 401 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.24e+00 ... (remaining 19946 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 26106 1.38 - 2.77: 764 2.77 - 4.15: 162 4.15 - 5.53: 45 5.53 - 6.92: 11 Bond angle restraints: 27088 Sorted by residual: angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 106.21 109.34 -3.13 1.07e+00 8.73e-01 8.56e+00 angle pdb=" N VAL E 43 " pdb=" CA VAL E 43 " pdb=" C VAL E 43 " ideal model delta sigma weight residual 111.81 109.46 2.35 8.60e-01 1.35e+00 7.45e+00 angle pdb=" C LEU G 340 " pdb=" N ILE G 341 " pdb=" CA ILE G 341 " ideal model delta sigma weight residual 121.97 126.73 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" N VAL F 43 " pdb=" CA VAL F 43 " pdb=" C VAL F 43 " ideal model delta sigma weight residual 111.81 109.55 2.26 8.60e-01 1.35e+00 6.89e+00 angle pdb=" C LEU B 340 " pdb=" N ILE B 341 " pdb=" CA ILE B 341 " ideal model delta sigma weight residual 121.97 126.69 -4.72 1.80e+00 3.09e-01 6.87e+00 ... (remaining 27083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 10260 16.65 - 33.30: 1352 33.30 - 49.95: 427 49.95 - 66.60: 84 66.60 - 83.25: 26 Dihedral angle restraints: 12149 sinusoidal: 4862 harmonic: 7287 Sorted by residual: dihedral pdb=" CB CYS C 66 " pdb=" SG CYS C 66 " pdb=" SG CYS C 261 " pdb=" CB CYS C 261 " ideal model delta sinusoidal sigma weight residual 93.00 39.68 53.32 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS E 66 " pdb=" SG CYS E 66 " pdb=" SG CYS E 261 " pdb=" CB CYS E 261 " ideal model delta sinusoidal sigma weight residual 93.00 40.04 52.96 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CB CYS A 66 " pdb=" SG CYS A 66 " pdb=" SG CYS A 261 " pdb=" CB CYS A 261 " ideal model delta sinusoidal sigma weight residual 93.00 40.04 52.96 1 1.00e+01 1.00e-02 3.82e+01 ... (remaining 12146 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2193 0.028 - 0.056: 617 0.056 - 0.084: 277 0.084 - 0.111: 111 0.111 - 0.139: 7 Chirality restraints: 3205 Sorted by residual: chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 71 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" C1 NAG E 401 " pdb=" ND2 ASN E 71 " pdb=" C2 NAG E 401 " pdb=" O5 NAG E 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 71 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 3202 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 71 " -0.132 2.00e-02 2.50e+03 2.43e-01 7.37e+02 pdb=" CG ASN E 71 " 0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN E 71 " -0.098 2.00e-02 2.50e+03 pdb=" ND2 ASN E 71 " 0.434 2.00e-02 2.50e+03 pdb=" C1 NAG E 401 " -0.273 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 71 " -0.132 2.00e-02 2.50e+03 2.32e-01 6.74e+02 pdb=" CG ASN A 71 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN A 71 " -0.088 2.00e-02 2.50e+03 pdb=" ND2 ASN A 71 " 0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " -0.261 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 71 " -0.146 2.00e-02 2.50e+03 2.28e-01 6.49e+02 pdb=" CG ASN C 71 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN C 71 " -0.065 2.00e-02 2.50e+03 pdb=" ND2 ASN C 71 " 0.404 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.258 2.00e-02 2.50e+03 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 167 2.57 - 3.15: 16492 3.15 - 3.73: 30794 3.73 - 4.32: 38362 4.32 - 4.90: 65794 Nonbonded interactions: 151609 Sorted by model distance: nonbonded pdb=" OH TYR A 224 " pdb=" OG1 THR A 281 " model vdw 1.982 3.040 nonbonded pdb=" OH TYR F 224 " pdb=" OG1 THR F 281 " model vdw 2.017 3.040 nonbonded pdb=" OH TYR G 224 " pdb=" OG1 THR G 281 " model vdw 2.040 3.040 nonbonded pdb=" OH TYR D 224 " pdb=" OG1 THR D 281 " model vdw 2.079 3.040 nonbonded pdb=" OD2 ASP E 35 " pdb=" ND2 ASN E 290 " model vdw 2.117 3.120 ... (remaining 151604 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 20 through 152 or (resid 153 and (name N or name CA or nam \ e C or name O or name CB )) or resid 154 or (resid 155 and (name N or name CA or \ name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'B' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'C' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 401)) selection = (chain 'D' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'E' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'F' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) selection = (chain 'G' and (resid 20 through 145 or (resid 146 and (name N or name CA or nam \ e C or name O or name CB )) or resid 147 through 152 or (resid 153 and (name N o \ r name CA or name C or name O or name CB )) or resid 154 or (resid 155 and (name \ N or name CA or name C or name O or name CB )) or resid 156 through 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.800 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 19972 Z= 0.148 Angle : 0.664 24.875 27137 Z= 0.323 Chirality : 0.034 0.139 3205 Planarity : 0.004 0.049 3309 Dihedral : 16.927 83.250 7347 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.10 % Favored : 93.56 % Rotamer: Outliers : 0.09 % Allowed : 26.80 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.18), residues: 2408 helix: 2.32 (0.13), residues: 1701 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 165 TYR 0.008 0.001 TYR A 280 PHE 0.021 0.001 PHE B 343 TRP 0.007 0.001 TRP C 105 HIS 0.003 0.001 HIS G 231 Details of bonding type rmsd covalent geometry : bond 0.00291 (19951) covalent geometry : angle 0.60080 (27088) SS BOND : bond 0.00551 ( 14) SS BOND : angle 1.49234 ( 28) hydrogen bonds : bond 0.11138 ( 1251) hydrogen bonds : angle 4.38799 ( 3711) link_NAG-ASN : bond 0.06069 ( 7) link_NAG-ASN : angle 10.07499 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 285 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 MET cc_start: 0.8340 (mmt) cc_final: 0.7762 (mmt) REVERT: F 329 ILE cc_start: 0.7997 (mt) cc_final: 0.7772 (mt) outliers start: 2 outliers final: 1 residues processed: 286 average time/residue: 0.1561 time to fit residues: 67.0619 Evaluate side-chains 238 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 292 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.0470 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 324 ASN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 90 HIS F 129 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.217615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.179980 restraints weight = 241873.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.181454 restraints weight = 131395.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.180301 restraints weight = 117850.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.180154 restraints weight = 116765.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.179923 restraints weight = 111262.915| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19972 Z= 0.146 Angle : 0.739 13.127 27137 Z= 0.337 Chirality : 0.038 0.131 3205 Planarity : 0.004 0.044 3309 Dihedral : 6.212 60.970 2800 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.11 % Favored : 94.56 % Rotamer: Outliers : 3.67 % Allowed : 24.80 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2408 helix: 2.23 (0.13), residues: 1701 sheet: -3.82 (0.47), residues: 70 loop : -1.04 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 156 TYR 0.011 0.001 TYR A 195 PHE 0.018 0.001 PHE B 269 TRP 0.007 0.001 TRP D 128 HIS 0.003 0.000 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00323 (19951) covalent geometry : angle 0.71613 (27088) SS BOND : bond 0.00712 ( 14) SS BOND : angle 1.46723 ( 28) hydrogen bonds : bond 0.03940 ( 1251) hydrogen bonds : angle 3.65293 ( 3711) link_NAG-ASN : bond 0.00852 ( 7) link_NAG-ASN : angle 6.35551 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8437 (mp) REVERT: B 101 MET cc_start: 0.4842 (tpp) cc_final: 0.4629 (tpp) REVERT: B 187 PHE cc_start: 0.4722 (OUTLIER) cc_final: 0.4519 (p90) REVERT: C 187 PHE cc_start: 0.5082 (OUTLIER) cc_final: 0.4771 (p90) REVERT: C 301 LEU cc_start: 0.5061 (tt) cc_final: 0.3039 (mt) REVERT: D 187 PHE cc_start: 0.4874 (OUTLIER) cc_final: 0.4584 (p90) REVERT: E 187 PHE cc_start: 0.4534 (OUTLIER) cc_final: 0.4127 (p90) REVERT: E 217 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8416 (mp) REVERT: E 249 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8063 (pt) REVERT: F 329 ILE cc_start: 0.7837 (mt) cc_final: 0.7537 (mt) REVERT: G 217 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8533 (mp) outliers start: 79 outliers final: 32 residues processed: 355 average time/residue: 0.1369 time to fit residues: 75.7351 Evaluate side-chains 295 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 187 PHE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 187 PHE Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 161 MET Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 228 optimal weight: 5.9990 chunk 232 optimal weight: 0.0270 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 35 optimal weight: 30.0000 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 129 GLN D 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.217453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.179496 restraints weight = 242897.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.181021 restraints weight = 132295.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.179910 restraints weight = 116481.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.179650 restraints weight = 115934.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.179359 restraints weight = 112616.974| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19972 Z= 0.141 Angle : 0.723 12.692 27137 Z= 0.332 Chirality : 0.042 0.526 3205 Planarity : 0.004 0.040 3309 Dihedral : 5.353 48.917 2799 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.64 % Rotamer: Outliers : 4.04 % Allowed : 23.73 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2408 helix: 2.13 (0.12), residues: 1722 sheet: -3.61 (0.43), residues: 70 loop : -1.21 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 165 TYR 0.020 0.001 TYR D 186 PHE 0.030 0.002 PHE E 343 TRP 0.007 0.001 TRP G 128 HIS 0.002 0.000 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00314 (19951) covalent geometry : angle 0.70163 (27088) SS BOND : bond 0.00742 ( 14) SS BOND : angle 1.54689 ( 28) hydrogen bonds : bond 0.03693 ( 1251) hydrogen bonds : angle 3.59414 ( 3711) link_NAG-ASN : bond 0.00699 ( 7) link_NAG-ASN : angle 6.14852 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 293 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8631 (pt) cc_final: 0.7831 (pt) REVERT: A 283 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7429 (mp) REVERT: A 341 ILE cc_start: 0.3988 (OUTLIER) cc_final: 0.3725 (pt) REVERT: B 187 PHE cc_start: 0.4934 (OUTLIER) cc_final: 0.4499 (p90) REVERT: B 263 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7722 (pt) REVERT: B 283 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7684 (mp) REVERT: C 263 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.7799 (pt) REVERT: C 283 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7651 (mp) REVERT: D 283 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7733 (mp) REVERT: E 217 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8459 (mp) REVERT: E 249 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8035 (pt) REVERT: F 122 TYR cc_start: 0.7349 (t80) cc_final: 0.6995 (t80) REVERT: F 263 LEU cc_start: 0.8624 (pt) cc_final: 0.7871 (pt) REVERT: F 283 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7620 (mp) REVERT: G 122 TYR cc_start: 0.7409 (t80) cc_final: 0.6964 (t80) REVERT: G 283 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7606 (mp) outliers start: 87 outliers final: 45 residues processed: 355 average time/residue: 0.1306 time to fit residues: 74.1110 Evaluate side-chains 321 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 341 ILE Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 283 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 72 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 193 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 GLN ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.210538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.171875 restraints weight = 24370.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171264 restraints weight = 45345.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171253 restraints weight = 41087.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171284 restraints weight = 37531.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171367 restraints weight = 36573.624| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19972 Z= 0.151 Angle : 0.729 14.206 27137 Z= 0.337 Chirality : 0.041 0.450 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.847 34.989 2799 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.69 % Favored : 93.98 % Rotamer: Outliers : 5.06 % Allowed : 24.25 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.18), residues: 2408 helix: 2.08 (0.12), residues: 1701 sheet: -3.06 (0.48), residues: 70 loop : -1.07 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 316 TYR 0.013 0.001 TYR D 186 PHE 0.021 0.002 PHE E 343 TRP 0.008 0.001 TRP G 85 HIS 0.002 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00347 (19951) covalent geometry : angle 0.70904 (27088) SS BOND : bond 0.00787 ( 14) SS BOND : angle 1.81356 ( 28) hydrogen bonds : bond 0.03762 ( 1251) hydrogen bonds : angle 3.59701 ( 3711) link_NAG-ASN : bond 0.00724 ( 7) link_NAG-ASN : angle 5.87407 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 287 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8166 (p) cc_final: 0.7925 (t) REVERT: A 217 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 263 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7848 (pt) REVERT: A 283 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 263 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.7680 (pt) REVERT: B 283 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7699 (mp) REVERT: C 263 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7760 (pt) REVERT: C 283 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7730 (mp) REVERT: C 325 ASP cc_start: 0.7821 (t0) cc_final: 0.7552 (t0) REVERT: D 25 LEU cc_start: 0.2956 (OUTLIER) cc_final: 0.2623 (pt) REVERT: D 283 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7778 (mp) REVERT: E 187 PHE cc_start: 0.4950 (OUTLIER) cc_final: 0.4376 (p90) REVERT: E 263 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.7794 (pt) REVERT: E 283 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7663 (mp) REVERT: F 101 MET cc_start: 0.4367 (ppp) cc_final: 0.3946 (ppp) REVERT: F 122 TYR cc_start: 0.7109 (t80) cc_final: 0.6727 (t80) REVERT: F 150 SER cc_start: 0.7660 (m) cc_final: 0.7442 (t) REVERT: F 263 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.7879 (pt) REVERT: F 283 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7753 (mp) REVERT: F 294 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7817 (mp) REVERT: G 122 TYR cc_start: 0.7108 (t80) cc_final: 0.6644 (t80) REVERT: G 263 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7831 (pt) REVERT: G 283 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7801 (mp) outliers start: 109 outliers final: 52 residues processed: 366 average time/residue: 0.1330 time to fit residues: 76.9082 Evaluate side-chains 335 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 266 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 283 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 106 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 92 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 206 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS B 254 HIS C 254 HIS E 254 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.210843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.172595 restraints weight = 24544.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.171755 restraints weight = 48118.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171812 restraints weight = 42521.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.171708 restraints weight = 38852.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.171791 restraints weight = 37201.106| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19972 Z= 0.142 Angle : 0.717 13.424 27137 Z= 0.330 Chirality : 0.042 0.559 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.517 25.803 2799 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.68 % Rotamer: Outliers : 4.78 % Allowed : 24.57 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.18), residues: 2408 helix: 2.09 (0.13), residues: 1701 sheet: -2.84 (0.50), residues: 70 loop : -1.07 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 185 TYR 0.011 0.001 TYR C 130 PHE 0.020 0.002 PHE A 189 TRP 0.007 0.001 TRP B 128 HIS 0.002 0.001 HIS G 254 Details of bonding type rmsd covalent geometry : bond 0.00321 (19951) covalent geometry : angle 0.69983 (27088) SS BOND : bond 0.00744 ( 14) SS BOND : angle 1.74141 ( 28) hydrogen bonds : bond 0.03627 ( 1251) hydrogen bonds : angle 3.58072 ( 3711) link_NAG-ASN : bond 0.00642 ( 7) link_NAG-ASN : angle 5.35324 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 299 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 263 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7791 (pt) REVERT: A 276 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 283 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7591 (mp) REVERT: B 263 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7734 (pt) REVERT: B 283 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7739 (mp) REVERT: C 36 SER cc_start: 0.8086 (t) cc_final: 0.7784 (p) REVERT: C 263 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.7745 (pt) REVERT: C 283 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7718 (mp) REVERT: C 288 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8249 (mt) REVERT: C 325 ASP cc_start: 0.7882 (t0) cc_final: 0.7622 (t0) REVERT: D 25 LEU cc_start: 0.3055 (OUTLIER) cc_final: 0.2726 (pt) REVERT: D 263 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.7736 (pt) REVERT: D 283 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7794 (mp) REVERT: E 30 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6849 (mt) REVERT: E 100 LYS cc_start: 0.4165 (tmtt) cc_final: 0.3534 (tttm) REVERT: E 187 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4560 (p90) REVERT: E 263 LEU cc_start: 0.8599 (pt) cc_final: 0.7730 (pt) REVERT: E 276 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8430 (t) REVERT: E 283 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7727 (mp) REVERT: F 263 LEU cc_start: 0.8584 (pt) cc_final: 0.7703 (pt) REVERT: F 294 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7804 (mp) REVERT: G 122 TYR cc_start: 0.7049 (t80) cc_final: 0.6614 (t80) REVERT: G 283 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7776 (mp) outliers start: 103 outliers final: 59 residues processed: 370 average time/residue: 0.1306 time to fit residues: 76.3723 Evaluate side-chains 358 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 281 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 219 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.209862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.208388 restraints weight = 24429.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.177488 restraints weight = 58973.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172814 restraints weight = 66163.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.171803 restraints weight = 61061.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.171448 restraints weight = 52940.271| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19972 Z= 0.150 Angle : 0.734 13.965 27137 Z= 0.337 Chirality : 0.042 0.446 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.348 25.033 2799 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.48 % Favored : 94.19 % Rotamer: Outliers : 4.74 % Allowed : 24.94 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2408 helix: 2.03 (0.13), residues: 1715 sheet: -2.65 (0.52), residues: 70 loop : -1.11 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 185 TYR 0.020 0.001 TYR B 122 PHE 0.020 0.002 PHE B 269 TRP 0.009 0.001 TRP E 345 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00345 (19951) covalent geometry : angle 0.71912 (27088) SS BOND : bond 0.00773 ( 14) SS BOND : angle 1.88555 ( 28) hydrogen bonds : bond 0.03695 ( 1251) hydrogen bonds : angle 3.61978 ( 3711) link_NAG-ASN : bond 0.00663 ( 7) link_NAG-ASN : angle 4.98493 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 288 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.7837 (pt) REVERT: A 276 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8455 (t) REVERT: A 283 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7483 (mp) REVERT: B 263 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7671 (pt) REVERT: B 283 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7742 (mp) REVERT: B 307 MET cc_start: 0.5275 (mmm) cc_final: 0.4698 (mmm) REVERT: C 187 PHE cc_start: 0.5534 (p90) cc_final: 0.5191 (p90) REVERT: C 263 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.7846 (pt) REVERT: C 283 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 288 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8376 (mt) REVERT: C 325 ASP cc_start: 0.7881 (t0) cc_final: 0.7618 (t0) REVERT: D 25 LEU cc_start: 0.3151 (OUTLIER) cc_final: 0.2805 (pt) REVERT: D 263 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.7778 (pt) REVERT: D 283 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7746 (mp) REVERT: E 30 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6907 (mt) REVERT: E 100 LYS cc_start: 0.4192 (tmtt) cc_final: 0.3627 (tttm) REVERT: E 187 PHE cc_start: 0.5532 (OUTLIER) cc_final: 0.4725 (p90) REVERT: E 263 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.7747 (pt) REVERT: E 276 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8471 (t) REVERT: E 283 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (mp) REVERT: E 308 LEU cc_start: 0.4038 (OUTLIER) cc_final: 0.3104 (tp) REVERT: F 189 PHE cc_start: 0.6104 (m-10) cc_final: 0.5846 (m-80) REVERT: F 263 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.7747 (pt) REVERT: F 283 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7760 (mp) REVERT: F 288 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8440 (mt) REVERT: F 294 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7881 (mp) REVERT: G 122 TYR cc_start: 0.7112 (t80) cc_final: 0.6638 (t80) REVERT: G 263 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.7811 (pt) REVERT: G 283 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7705 (mp) outliers start: 102 outliers final: 63 residues processed: 359 average time/residue: 0.1280 time to fit residues: 73.6414 Evaluate side-chains 363 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 277 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 29 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 148 optimal weight: 0.6980 chunk 184 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 202 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.210169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.205368 restraints weight = 24225.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.179450 restraints weight = 64841.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.173303 restraints weight = 62902.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.172945 restraints weight = 50634.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.172239 restraints weight = 42454.854| |-----------------------------------------------------------------------------| r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19972 Z= 0.134 Angle : 0.712 13.900 27137 Z= 0.327 Chirality : 0.041 0.422 3205 Planarity : 0.003 0.039 3309 Dihedral : 4.123 26.408 2799 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.94 % Favored : 94.73 % Rotamer: Outliers : 3.81 % Allowed : 26.34 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.70 (0.18), residues: 2408 helix: 2.06 (0.12), residues: 1715 sheet: -2.54 (0.52), residues: 70 loop : -1.10 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 300 TYR 0.012 0.001 TYR G 195 PHE 0.035 0.001 PHE G 142 TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00300 (19951) covalent geometry : angle 0.70018 (27088) SS BOND : bond 0.00711 ( 14) SS BOND : angle 1.62561 ( 28) hydrogen bonds : bond 0.03508 ( 1251) hydrogen bonds : angle 3.54903 ( 3711) link_NAG-ASN : bond 0.00461 ( 7) link_NAG-ASN : angle 4.29191 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 312 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8627 (pt) cc_final: 0.7819 (pt) REVERT: A 276 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8377 (t) REVERT: B 187 PHE cc_start: 0.5884 (p90) cc_final: 0.5193 (p90) REVERT: B 263 LEU cc_start: 0.8575 (pt) cc_final: 0.7758 (pt) REVERT: B 283 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7607 (mp) REVERT: C 187 PHE cc_start: 0.5744 (p90) cc_final: 0.5351 (p90) REVERT: C 263 LEU cc_start: 0.8644 (pt) cc_final: 0.7773 (pt) REVERT: C 283 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 288 ILE cc_start: 0.8543 (mm) cc_final: 0.8212 (mt) REVERT: C 325 ASP cc_start: 0.7810 (t0) cc_final: 0.7567 (t0) REVERT: D 25 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2788 (pt) REVERT: D 187 PHE cc_start: 0.6103 (p90) cc_final: 0.5247 (p90) REVERT: D 263 LEU cc_start: 0.8610 (pt) cc_final: 0.7638 (pt) REVERT: D 283 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7815 (mp) REVERT: E 30 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6850 (mt) REVERT: E 100 LYS cc_start: 0.4139 (tmtt) cc_final: 0.3675 (tttm) REVERT: E 187 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.5056 (p90) REVERT: E 263 LEU cc_start: 0.8528 (pt) cc_final: 0.7618 (pt) REVERT: E 276 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8462 (t) REVERT: E 283 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7630 (mp) REVERT: E 308 LEU cc_start: 0.3849 (OUTLIER) cc_final: 0.3163 (tp) REVERT: F 122 TYR cc_start: 0.7249 (t80) cc_final: 0.6864 (t80) REVERT: F 263 LEU cc_start: 0.8460 (pt) cc_final: 0.7479 (pt) REVERT: F 283 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7713 (mp) REVERT: G 121 MET cc_start: 0.7680 (mmt) cc_final: 0.7107 (mmt) REVERT: G 122 TYR cc_start: 0.7153 (t80) cc_final: 0.6692 (t80) REVERT: G 263 LEU cc_start: 0.8608 (pt) cc_final: 0.7695 (pt) REVERT: G 283 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7757 (mp) outliers start: 82 outliers final: 63 residues processed: 371 average time/residue: 0.1305 time to fit residues: 77.7155 Evaluate side-chains 371 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 127 LEU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 340 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 226 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 190 optimal weight: 30.0000 chunk 215 optimal weight: 0.6980 chunk 139 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.210079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.208115 restraints weight = 24275.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.174417 restraints weight = 57045.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.170907 restraints weight = 58588.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.170807 restraints weight = 51644.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.170271 restraints weight = 44652.184| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19972 Z= 0.136 Angle : 0.719 13.538 27137 Z= 0.331 Chirality : 0.041 0.427 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.023 25.801 2799 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.36 % Favored : 94.31 % Rotamer: Outliers : 4.09 % Allowed : 26.57 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.18), residues: 2408 helix: 2.08 (0.12), residues: 1715 sheet: -2.40 (0.52), residues: 70 loop : -1.12 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 185 TYR 0.020 0.001 TYR D 122 PHE 0.037 0.002 PHE G 142 TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS B 254 Details of bonding type rmsd covalent geometry : bond 0.00308 (19951) covalent geometry : angle 0.70883 (27088) SS BOND : bond 0.00733 ( 14) SS BOND : angle 1.68911 ( 28) hydrogen bonds : bond 0.03567 ( 1251) hydrogen bonds : angle 3.58011 ( 3711) link_NAG-ASN : bond 0.00467 ( 7) link_NAG-ASN : angle 4.00430 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 298 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8555 (pt) cc_final: 0.7667 (pt) REVERT: A 276 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8447 (t) REVERT: A 283 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7449 (mp) REVERT: B 187 PHE cc_start: 0.5966 (p90) cc_final: 0.5487 (p90) REVERT: B 263 LEU cc_start: 0.8550 (pt) cc_final: 0.7677 (pt) REVERT: B 283 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7709 (mp) REVERT: C 187 PHE cc_start: 0.5735 (p90) cc_final: 0.5321 (p90) REVERT: C 263 LEU cc_start: 0.8618 (pt) cc_final: 0.7751 (pt) REVERT: C 283 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7634 (mp) REVERT: C 288 ILE cc_start: 0.8652 (mm) cc_final: 0.8348 (mt) REVERT: C 325 ASP cc_start: 0.7787 (t0) cc_final: 0.7525 (t0) REVERT: D 25 LEU cc_start: 0.3114 (OUTLIER) cc_final: 0.2668 (pt) REVERT: D 122 TYR cc_start: 0.7234 (t80) cc_final: 0.6928 (t80) REVERT: D 187 PHE cc_start: 0.6207 (p90) cc_final: 0.5386 (p90) REVERT: D 263 LEU cc_start: 0.8654 (pt) cc_final: 0.7692 (pt) REVERT: D 283 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7680 (mp) REVERT: E 30 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6897 (mt) REVERT: E 83 SER cc_start: 0.8418 (OUTLIER) cc_final: 0.8214 (t) REVERT: E 100 LYS cc_start: 0.4362 (tmtt) cc_final: 0.3891 (tttm) REVERT: E 187 PHE cc_start: 0.5540 (OUTLIER) cc_final: 0.5119 (p90) REVERT: E 276 SER cc_start: 0.8801 (OUTLIER) cc_final: 0.8459 (t) REVERT: E 283 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7560 (mp) REVERT: F 263 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7492 (pt) REVERT: F 283 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7790 (mp) REVERT: G 121 MET cc_start: 0.7806 (mmt) cc_final: 0.7267 (mmt) REVERT: G 122 TYR cc_start: 0.7078 (t80) cc_final: 0.6675 (t80) REVERT: G 263 LEU cc_start: 0.8608 (pt) cc_final: 0.7697 (pt) REVERT: G 283 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7719 (mp) outliers start: 88 outliers final: 63 residues processed: 366 average time/residue: 0.1287 time to fit residues: 74.9827 Evaluate side-chains 362 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 285 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 294 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 340 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 242 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 174 optimal weight: 40.0000 chunk 71 optimal weight: 0.0980 chunk 75 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN E 237 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.204398 restraints weight = 24307.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.171586 restraints weight = 51513.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.168030 restraints weight = 59156.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.166071 restraints weight = 55782.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.165271 restraints weight = 49761.086| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19972 Z= 0.204 Angle : 0.797 15.970 27137 Z= 0.370 Chirality : 0.044 0.441 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.349 26.251 2799 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 4.74 % Allowed : 25.64 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.18), residues: 2408 helix: 1.93 (0.12), residues: 1715 sheet: -2.28 (0.53), residues: 70 loop : -1.34 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 165 TYR 0.019 0.002 TYR D 122 PHE 0.031 0.002 PHE G 142 TRP 0.012 0.002 TRP G 85 HIS 0.004 0.001 HIS B 107 Details of bonding type rmsd covalent geometry : bond 0.00486 (19951) covalent geometry : angle 0.78401 (27088) SS BOND : bond 0.00953 ( 14) SS BOND : angle 2.66423 ( 28) hydrogen bonds : bond 0.04182 ( 1251) hydrogen bonds : angle 3.76828 ( 3711) link_NAG-ASN : bond 0.00810 ( 7) link_NAG-ASN : angle 4.40509 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 290 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4192 (tmtt) cc_final: 0.3683 (tttm) REVERT: A 263 LEU cc_start: 0.8707 (pt) cc_final: 0.7912 (pt) REVERT: A 276 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8558 (t) REVERT: A 283 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7606 (mp) REVERT: B 187 PHE cc_start: 0.6139 (p90) cc_final: 0.5637 (p90) REVERT: B 263 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.7882 (pt) REVERT: B 276 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8498 (t) REVERT: B 283 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7699 (mp) REVERT: C 187 PHE cc_start: 0.5737 (p90) cc_final: 0.5364 (p90) REVERT: C 263 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.7898 (pt) REVERT: C 283 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7637 (mp) REVERT: C 288 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8403 (mt) REVERT: C 325 ASP cc_start: 0.7972 (t0) cc_final: 0.7737 (t0) REVERT: D 122 TYR cc_start: 0.7442 (t80) cc_final: 0.7133 (t80) REVERT: D 187 PHE cc_start: 0.6249 (p90) cc_final: 0.5481 (p90) REVERT: D 263 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.7987 (pt) REVERT: D 283 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7605 (mp) REVERT: E 30 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6988 (mt) REVERT: E 100 LYS cc_start: 0.4387 (tmtt) cc_final: 0.3975 (tttm) REVERT: E 187 PHE cc_start: 0.5573 (OUTLIER) cc_final: 0.5088 (p90) REVERT: E 263 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.7863 (pt) REVERT: E 276 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8536 (t) REVERT: E 283 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7568 (mp) REVERT: F 122 TYR cc_start: 0.7249 (t80) cc_final: 0.6983 (t80) REVERT: F 263 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.7868 (pt) REVERT: F 283 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7772 (mp) REVERT: F 288 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8536 (mt) REVERT: F 345 TRP cc_start: 0.6339 (OUTLIER) cc_final: 0.5127 (p-90) REVERT: G 187 PHE cc_start: 0.6448 (p90) cc_final: 0.5712 (p90) REVERT: G 200 GLN cc_start: 0.7483 (mm110) cc_final: 0.7154 (mm110) REVERT: G 263 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.7857 (pt) REVERT: G 283 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7622 (mp) outliers start: 102 outliers final: 66 residues processed: 370 average time/residue: 0.1243 time to fit residues: 73.7557 Evaluate side-chains 361 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 274 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 288 ILE Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 345 TRP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 218 ILE Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 35 optimal weight: 30.0000 chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 132 optimal weight: 4.9990 chunk 236 optimal weight: 0.5980 chunk 40 optimal weight: 0.0770 chunk 61 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN D 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.206184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.172383 restraints weight = 243675.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.173317 restraints weight = 130887.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.172335 restraints weight = 120937.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.172195 restraints weight = 118020.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.171610 restraints weight = 112777.855| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19972 Z= 0.131 Angle : 0.729 14.227 27137 Z= 0.338 Chirality : 0.041 0.460 3205 Planarity : 0.003 0.039 3309 Dihedral : 4.086 26.050 2799 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.11 % Favored : 94.56 % Rotamer: Outliers : 2.46 % Allowed : 28.01 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.18), residues: 2408 helix: 2.10 (0.12), residues: 1715 sheet: -2.22 (0.52), residues: 70 loop : -1.21 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 194 TYR 0.026 0.001 TYR G 122 PHE 0.026 0.001 PHE G 142 TRP 0.006 0.001 TRP D 128 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00288 (19951) covalent geometry : angle 0.72095 (27088) SS BOND : bond 0.00703 ( 14) SS BOND : angle 1.54986 ( 28) hydrogen bonds : bond 0.03558 ( 1251) hydrogen bonds : angle 3.61289 ( 3711) link_NAG-ASN : bond 0.00335 ( 7) link_NAG-ASN : angle 3.49875 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.760 Fit side-chains REVERT: A 36 SER cc_start: 0.8461 (p) cc_final: 0.8214 (t) REVERT: A 263 LEU cc_start: 0.8465 (pt) cc_final: 0.7448 (pt) REVERT: A 276 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8447 (t) REVERT: A 283 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7415 (mp) REVERT: B 187 PHE cc_start: 0.6162 (p90) cc_final: 0.5650 (p90) REVERT: B 263 LEU cc_start: 0.8479 (pt) cc_final: 0.7652 (pt) REVERT: B 283 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7558 (mp) REVERT: C 187 PHE cc_start: 0.5829 (p90) cc_final: 0.5348 (p90) REVERT: C 263 LEU cc_start: 0.8565 (pt) cc_final: 0.7685 (pt) REVERT: C 283 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7718 (mp) REVERT: C 288 ILE cc_start: 0.8579 (mm) cc_final: 0.8354 (mt) REVERT: C 325 ASP cc_start: 0.7772 (t0) cc_final: 0.7550 (t0) REVERT: D 122 TYR cc_start: 0.7264 (t80) cc_final: 0.6987 (t80) REVERT: D 187 PHE cc_start: 0.6266 (p90) cc_final: 0.5497 (p90) REVERT: D 263 LEU cc_start: 0.8625 (pt) cc_final: 0.7642 (pt) REVERT: D 283 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7759 (mp) REVERT: E 30 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7242 (mt) REVERT: E 100 LYS cc_start: 0.4971 (tmtt) cc_final: 0.4560 (tttm) REVERT: E 263 LEU cc_start: 0.8503 (pt) cc_final: 0.7585 (pt) REVERT: E 276 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8473 (t) REVERT: E 283 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7555 (mp) REVERT: F 263 LEU cc_start: 0.8411 (pt) cc_final: 0.7411 (pt) REVERT: F 283 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7734 (mp) REVERT: F 288 ILE cc_start: 0.8627 (mm) cc_final: 0.8387 (mt) REVERT: G 36 SER cc_start: 0.8511 (p) cc_final: 0.8143 (t) REVERT: G 121 MET cc_start: 0.7890 (mmt) cc_final: 0.7491 (mmt) REVERT: G 187 PHE cc_start: 0.6494 (p90) cc_final: 0.5637 (p90) REVERT: G 263 LEU cc_start: 0.8554 (pt) cc_final: 0.7584 (pt) REVERT: G 283 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7663 (mp) outliers start: 53 outliers final: 35 residues processed: 343 average time/residue: 0.1223 time to fit residues: 67.7916 Evaluate side-chains 326 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain G residue 50 MET Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 127 LEU Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 48 optimal weight: 8.9990 chunk 223 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 212 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN E 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.205240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.169667 restraints weight = 242791.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.170635 restraints weight = 128982.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.169782 restraints weight = 118076.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.169546 restraints weight = 116667.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.169355 restraints weight = 111535.144| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19972 Z= 0.143 Angle : 0.736 14.191 27137 Z= 0.340 Chirality : 0.041 0.478 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.006 26.282 2799 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.36 % Favored : 94.31 % Rotamer: Outliers : 2.51 % Allowed : 27.64 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.18), residues: 2408 helix: 2.17 (0.12), residues: 1701 sheet: -2.24 (0.52), residues: 70 loop : -1.23 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 334 TYR 0.025 0.001 TYR D 122 PHE 0.040 0.002 PHE D 142 TRP 0.007 0.001 TRP G 85 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00326 (19951) covalent geometry : angle 0.72850 (27088) SS BOND : bond 0.00793 ( 14) SS BOND : angle 1.79283 ( 28) hydrogen bonds : bond 0.03638 ( 1251) hydrogen bonds : angle 3.63077 ( 3711) link_NAG-ASN : bond 0.00416 ( 7) link_NAG-ASN : angle 3.38827 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2974.38 seconds wall clock time: 52 minutes 50.22 seconds (3170.22 seconds total)