Starting phenix.real_space_refine on Tue May 20 01:25:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyt_34377/05_2025/8gyt_34377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyt_34377/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gyt_34377/05_2025/8gyt_34377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyt_34377/05_2025/8gyt_34377.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyt_34377/05_2025/8gyt_34377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyt_34377/05_2025/8gyt_34377.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: {'PHE:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} 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: 11.16, per 1000 atoms: 0.57 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: 4.82 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.70 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: 5.24 Time building geometry restraints manager: 5.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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 374 or resid 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 374 or resi \ d 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 374 or resid 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 374 or resi \ d 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 374 or resi \ d 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 374 or resi \ d 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 374 or resi \ d 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.780 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 40.410 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.020 ------------------------------------------------------------------------------- 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 : 7.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (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 TRP 0.007 0.001 TRP C 105 HIS 0.003 0.001 HIS G 231 PHE 0.021 0.001 PHE B 343 TYR 0.008 0.001 TYR A 280 ARG 0.004 0.000 ARG D 165 Details of bonding type rmsd link_NAG-ASN : bond 0.06069 ( 7) link_NAG-ASN : angle 10.07499 ( 21) hydrogen bonds : bond 0.11138 ( 1251) hydrogen bonds : angle 4.38799 ( 3711) SS BOND : bond 0.00551 ( 14) SS BOND : angle 1.49234 ( 28) covalent geometry : bond 0.00291 (19951) covalent geometry : angle 0.60080 (27088) *********************** 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 : 2.026 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: 0.3300 time to fit residues: 140.6259 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 : 2.042 ------------------------------------------------------------------------------- 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 206 optimal weight: 4.9990 chunk 185 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 192 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 222 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** E 237 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 = 0.4406 r_free = 0.4406 target = 0.216379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.177798 restraints weight = 241832.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.179407 restraints weight = 131689.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.178421 restraints weight = 117105.847| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19972 Z= 0.156 Angle : 0.751 13.138 27137 Z= 0.343 Chirality : 0.039 0.130 3205 Planarity : 0.004 0.044 3309 Dihedral : 6.310 61.651 2800 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 4.04 % Allowed : 24.52 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.18), residues: 2408 helix: 2.21 (0.13), residues: 1701 sheet: -3.69 (0.48), residues: 70 loop : -1.07 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 128 HIS 0.002 0.001 HIS B 107 PHE 0.020 0.002 PHE C 269 TYR 0.011 0.001 TYR A 195 ARG 0.004 0.000 ARG E 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00925 ( 7) link_NAG-ASN : angle 6.58102 ( 21) hydrogen bonds : bond 0.04105 ( 1251) hydrogen bonds : angle 3.68901 ( 3711) SS BOND : bond 0.00755 ( 14) SS BOND : angle 1.64813 ( 28) covalent geometry : bond 0.00353 (19951) covalent geometry : angle 0.72701 (27088) *********************** 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 374 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 287 time to evaluate : 2.243 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: 0.8823 (OUTLIER) cc_final: 0.8541 (mp) REVERT: A 323 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8171 (mp) REVERT: B 101 MET cc_start: 0.4924 (tpp) cc_final: 0.4683 (tpp) REVERT: B 187 PHE cc_start: 0.4756 (OUTLIER) cc_final: 0.4536 (p90) REVERT: B 263 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7880 (pt) REVERT: C 187 PHE cc_start: 0.5168 (OUTLIER) cc_final: 0.4882 (p90) REVERT: C 192 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6515 (mp) REVERT: C 340 LEU cc_start: 0.6406 (OUTLIER) cc_final: 0.6113 (mt) REVERT: D 187 PHE cc_start: 0.4899 (OUTLIER) cc_final: 0.4584 (p90) REVERT: D 192 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6768 (mp) REVERT: E 129 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7605 (tm-30) REVERT: E 187 PHE cc_start: 0.4619 (OUTLIER) cc_final: 0.4205 (p90) REVERT: E 217 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8395 (mp) REVERT: E 249 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8061 (pt) REVERT: F 329 ILE cc_start: 0.7833 (mt) cc_final: 0.7473 (mt) REVERT: G 217 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8562 (mp) outliers start: 87 outliers final: 39 residues processed: 356 average time/residue: 0.2938 time to fit residues: 162.5166 Evaluate side-chains 306 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 254 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 A residue 323 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 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 277 VAL 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 192 LEU 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 340 LEU 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 192 LEU 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 E residue 68 SER 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 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 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain G residue 68 SER 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 123 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 240 optimal weight: 0.6980 chunk 198 optimal weight: 0.0970 chunk 221 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN B 237 GLN C 129 GLN E 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.212615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.171857 restraints weight = 241340.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.173037 restraints weight = 130201.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.172491 restraints weight = 117354.730| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 19972 Z= 0.191 Angle : 0.787 12.989 27137 Z= 0.365 Chirality : 0.044 0.509 3205 Planarity : 0.004 0.040 3309 Dihedral : 5.804 54.397 2799 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.90 % Favored : 93.77 % Rotamer: Outliers : 6.18 % Allowed : 22.53 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.18), residues: 2408 helix: 1.85 (0.12), residues: 1722 sheet: -3.04 (0.51), residues: 70 loop : -1.40 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 85 HIS 0.004 0.001 HIS B 90 PHE 0.033 0.002 PHE E 343 TYR 0.021 0.002 TYR D 122 ARG 0.003 0.000 ARG G 165 Details of bonding type rmsd link_NAG-ASN : bond 0.01002 ( 7) link_NAG-ASN : angle 6.52347 ( 21) hydrogen bonds : bond 0.04267 ( 1251) hydrogen bonds : angle 3.79271 ( 3711) SS BOND : bond 0.00936 ( 14) SS BOND : angle 2.36205 ( 28) covalent geometry : bond 0.00450 (19951) covalent geometry : angle 0.76321 (27088) *********************** 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 428 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 295 time to evaluate : 2.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.7980 (pt) REVERT: A 276 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8550 (t) REVERT: A 283 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (mp) REVERT: A 323 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8202 (mp) REVERT: A 341 ILE cc_start: 0.4538 (OUTLIER) cc_final: 0.4172 (pt) REVERT: B 122 TYR cc_start: 0.7637 (t80) cc_final: 0.7431 (t80) REVERT: B 187 PHE cc_start: 0.5220 (OUTLIER) cc_final: 0.4775 (p90) REVERT: B 263 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.7903 (pt) REVERT: B 283 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7694 (mp) REVERT: C 192 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6519 (mp) REVERT: C 263 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.7952 (pt) REVERT: C 283 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7770 (mp) REVERT: C 288 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8128 (mt) REVERT: C 291 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8233 (tt) REVERT: C 325 ASP cc_start: 0.7800 (t0) cc_final: 0.7573 (t0) REVERT: D 192 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6382 (mp) REVERT: D 263 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8145 (pt) REVERT: D 283 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7818 (mp) REVERT: E 159 GLN cc_start: 0.3154 (OUTLIER) cc_final: 0.2838 (mt0) REVERT: E 217 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8474 (mp) REVERT: E 263 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8333 (pt) REVERT: E 276 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8614 (t) REVERT: E 283 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7711 (mp) REVERT: F 263 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8030 (pt) REVERT: F 283 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7644 (mp) REVERT: F 288 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8326 (mt) REVERT: G 263 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.7901 (pt) REVERT: G 283 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7806 (mp) outliers start: 133 outliers final: 57 residues processed: 395 average time/residue: 0.2669 time to fit residues: 167.6301 Evaluate side-chains 343 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 260 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE 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 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 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 341 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 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 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 192 LEU 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 291 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 43 VAL 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 192 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 232 LEU 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 283 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 LEU 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 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 223 optimal weight: 8.9990 chunk 236 optimal weight: 0.4980 chunk 116 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 254 HIS E 129 GLN G 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.210447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.208747 restraints weight = 24199.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.173197 restraints weight = 46372.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.171355 restraints weight = 56985.741| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19972 Z= 0.142 Angle : 0.729 13.706 27137 Z= 0.335 Chirality : 0.041 0.443 3205 Planarity : 0.004 0.039 3309 Dihedral : 5.174 42.919 2799 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.36 % Favored : 94.31 % Rotamer: Outliers : 4.23 % Allowed : 25.59 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2408 helix: 1.98 (0.12), residues: 1722 sheet: -2.94 (0.50), residues: 70 loop : -1.33 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 128 HIS 0.002 0.001 HIS F 254 PHE 0.028 0.002 PHE F 142 TYR 0.023 0.001 TYR G 122 ARG 0.008 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 7) link_NAG-ASN : angle 6.02548 ( 21) hydrogen bonds : bond 0.03757 ( 1251) hydrogen bonds : angle 3.63766 ( 3711) SS BOND : bond 0.00768 ( 14) SS BOND : angle 1.75692 ( 28) covalent geometry : bond 0.00318 (19951) covalent geometry : angle 0.70815 (27088) *********************** 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 393 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 302 time to evaluate : 2.080 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4010 (tmtt) cc_final: 0.3640 (tttm) REVERT: A 217 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8538 (mp) REVERT: A 263 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7886 (pt) REVERT: A 283 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7649 (mp) REVERT: B 122 TYR cc_start: 0.7350 (t80) cc_final: 0.7052 (t80) REVERT: B 187 PHE cc_start: 0.4966 (OUTLIER) cc_final: 0.4466 (p90) REVERT: B 217 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8671 (mp) REVERT: B 283 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7770 (mp) REVERT: C 122 TYR cc_start: 0.7240 (t80) cc_final: 0.6985 (t80) REVERT: C 192 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6357 (mp) REVERT: C 263 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7816 (pt) REVERT: C 283 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7776 (mp) REVERT: C 291 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7827 (tt) REVERT: C 325 ASP cc_start: 0.7849 (t0) cc_final: 0.7612 (t0) REVERT: D 25 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2730 (pt) REVERT: D 192 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6653 (mp) REVERT: D 263 LEU cc_start: 0.8658 (pt) cc_final: 0.7867 (pt) REVERT: D 283 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7866 (mp) REVERT: E 30 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6983 (mt) REVERT: E 187 PHE cc_start: 0.5016 (OUTLIER) cc_final: 0.4495 (p90) REVERT: E 263 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7838 (pt) REVERT: F 122 TYR cc_start: 0.7181 (t80) cc_final: 0.6920 (t80) REVERT: F 189 PHE cc_start: 0.6597 (m-10) cc_final: 0.6293 (m-80) REVERT: F 263 LEU cc_start: 0.8630 (pt) cc_final: 0.7782 (pt) REVERT: F 283 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7777 (mp) REVERT: F 294 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8061 (mp) REVERT: G 122 TYR cc_start: 0.7133 (t80) cc_final: 0.6804 (t80) REVERT: G 263 LEU cc_start: 0.8618 (pt) cc_final: 0.7757 (pt) REVERT: G 283 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7787 (mp) outliers start: 91 outliers final: 39 residues processed: 369 average time/residue: 0.2772 time to fit residues: 159.4515 Evaluate side-chains 336 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 278 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 187 PHE 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 268 ILE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 192 LEU 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 291 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 192 LEU 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 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 187 PHE Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU 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 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 253 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 295 CYS Chi-restraints excluded: chain G residue 319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 208 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 197 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.206708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.204200 restraints weight = 24071.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.166795 restraints weight = 59836.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.163849 restraints weight = 68085.302| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19972 Z= 0.190 Angle : 0.787 12.880 27137 Z= 0.365 Chirality : 0.044 0.576 3205 Planarity : 0.004 0.039 3309 Dihedral : 5.041 37.768 2799 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.98 % Favored : 93.69 % Rotamer: Outliers : 5.95 % Allowed : 24.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.18), residues: 2408 helix: 1.84 (0.12), residues: 1722 sheet: -2.73 (0.53), residues: 70 loop : -1.51 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 85 HIS 0.003 0.001 HIS E 254 PHE 0.023 0.002 PHE B 269 TYR 0.020 0.002 TYR G 122 ARG 0.004 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00985 ( 7) link_NAG-ASN : angle 6.17301 ( 21) hydrogen bonds : bond 0.04148 ( 1251) hydrogen bonds : angle 3.76139 ( 3711) SS BOND : bond 0.00908 ( 14) SS BOND : angle 2.45453 ( 28) covalent geometry : bond 0.00451 (19951) covalent geometry : angle 0.76515 (27088) *********************** 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 420 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 292 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 SER cc_start: 0.8202 (t) cc_final: 0.7952 (p) REVERT: A 100 LYS cc_start: 0.4293 (tmtt) cc_final: 0.3927 (tttm) REVERT: A 217 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 263 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8075 (pt) REVERT: A 276 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8501 (t) REVERT: A 283 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7618 (mp) REVERT: B 263 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.7958 (pt) REVERT: B 276 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8512 (t) REVERT: B 283 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7647 (mp) REVERT: C 187 PHE cc_start: 0.5635 (p90) cc_final: 0.5165 (p90) REVERT: C 192 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6505 (mp) REVERT: C 263 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.7935 (pt) REVERT: C 276 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8521 (t) REVERT: C 283 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7703 (mp) REVERT: C 288 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8145 (mt) REVERT: C 291 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7756 (tt) REVERT: C 325 ASP cc_start: 0.7945 (t0) cc_final: 0.7648 (t0) REVERT: D 25 LEU cc_start: 0.3225 (OUTLIER) cc_final: 0.2836 (pt) REVERT: D 122 TYR cc_start: 0.7266 (t80) cc_final: 0.6962 (t80) REVERT: D 192 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.6308 (mp) REVERT: D 263 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8049 (pt) REVERT: D 276 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8657 (t) REVERT: D 283 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7866 (mp) REVERT: E 30 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7010 (mt) REVERT: E 100 LYS cc_start: 0.4478 (tmtt) cc_final: 0.3788 (tttm) REVERT: E 159 GLN cc_start: 0.3413 (OUTLIER) cc_final: 0.2986 (mt0) REVERT: E 187 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.4748 (p90) REVERT: E 263 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.7976 (pt) REVERT: E 276 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8496 (t) REVERT: E 283 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7603 (mp) REVERT: F 101 MET cc_start: 0.4477 (ppp) cc_final: 0.4260 (ppp) REVERT: F 200 GLN cc_start: 0.7545 (mm110) cc_final: 0.7309 (mm110) REVERT: F 263 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.7981 (pt) REVERT: F 283 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7761 (mp) REVERT: F 288 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8246 (mt) REVERT: F 294 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7837 (mp) REVERT: F 329 ILE cc_start: 0.7975 (mm) cc_final: 0.7508 (mm) REVERT: G 122 TYR cc_start: 0.7158 (t80) cc_final: 0.6878 (t80) REVERT: G 263 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.7915 (pt) REVERT: G 276 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8519 (t) REVERT: G 283 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7759 (mp) outliers start: 128 outliers final: 59 residues processed: 386 average time/residue: 0.2618 time to fit residues: 161.0090 Evaluate side-chains 358 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 268 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 HIS 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 133 VAL 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 192 LEU 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 276 SER 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 291 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 25 LEU 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 192 LEU 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 263 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 292 THR Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 91 HIS Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 159 GLN Chi-restraints excluded: chain E residue 161 MET 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 271 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 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 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 292 THR 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 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 295 CYS 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 193 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 90 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 183 optimal weight: 0.8980 chunk 242 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS B 336 ASN C 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.209631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.207919 restraints weight = 24469.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.176614 restraints weight = 55874.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.172421 restraints weight = 62650.424| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19972 Z= 0.139 Angle : 0.729 13.707 27137 Z= 0.336 Chirality : 0.041 0.460 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.621 28.563 2799 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.02 % Favored : 94.64 % Rotamer: Outliers : 3.95 % Allowed : 25.92 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.18), residues: 2408 helix: 1.91 (0.12), residues: 1736 sheet: -2.63 (0.52), residues: 70 loop : -1.41 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 345 HIS 0.003 0.001 HIS G 254 PHE 0.039 0.002 PHE G 142 TYR 0.026 0.001 TYR G 122 ARG 0.003 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 7) link_NAG-ASN : angle 5.37145 ( 21) hydrogen bonds : bond 0.03685 ( 1251) hydrogen bonds : angle 3.65911 ( 3711) SS BOND : bond 0.00739 ( 14) SS BOND : angle 1.74606 ( 28) covalent geometry : bond 0.00312 (19951) covalent geometry : angle 0.71234 (27088) *********************** 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 393 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 308 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4093 (tmtt) cc_final: 0.3758 (tttm) REVERT: A 263 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.7849 (pt) REVERT: A 283 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7377 (mp) REVERT: B 263 LEU cc_start: 0.8633 (pt) cc_final: 0.7843 (pt) REVERT: B 276 SER cc_start: 0.8728 (OUTLIER) cc_final: 0.8353 (t) REVERT: B 283 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7690 (mp) REVERT: B 301 LEU cc_start: 0.4825 (OUTLIER) cc_final: 0.3742 (mt) REVERT: C 187 PHE cc_start: 0.5713 (p90) cc_final: 0.5405 (p90) REVERT: C 192 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7006 (mp) REVERT: C 263 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7759 (pt) REVERT: C 283 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7835 (mp) REVERT: C 288 ILE cc_start: 0.8593 (mm) cc_final: 0.8292 (mt) REVERT: C 291 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8196 (tt) REVERT: C 314 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7911 (tt) REVERT: C 325 ASP cc_start: 0.7831 (t0) cc_final: 0.7577 (t0) REVERT: D 25 LEU cc_start: 0.3203 (OUTLIER) cc_final: 0.2853 (pt) REVERT: D 121 MET cc_start: 0.8109 (mmp) cc_final: 0.7886 (mmp) REVERT: D 122 TYR cc_start: 0.7169 (t80) cc_final: 0.6876 (t80) REVERT: D 187 PHE cc_start: 0.6193 (p90) cc_final: 0.5441 (p90) REVERT: D 263 LEU cc_start: 0.8697 (pt) cc_final: 0.7840 (pt) REVERT: D 283 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7524 (mp) REVERT: E 30 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6847 (mt) REVERT: E 100 LYS cc_start: 0.4202 (tmtt) cc_final: 0.3603 (tttm) REVERT: E 130 TYR cc_start: 0.6840 (m-10) cc_final: 0.6530 (m-80) REVERT: E 187 PHE cc_start: 0.5632 (OUTLIER) cc_final: 0.4946 (p90) REVERT: E 217 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8555 (mp) REVERT: E 263 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.7808 (pt) REVERT: F 101 MET cc_start: 0.4670 (ppp) cc_final: 0.4278 (ppp) REVERT: F 263 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.7713 (pt) REVERT: F 283 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7752 (mp) REVERT: G 122 TYR cc_start: 0.7135 (t80) cc_final: 0.6933 (t80) REVERT: G 263 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7634 (pt) REVERT: G 276 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8479 (t) REVERT: G 283 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7717 (mp) outliers start: 85 outliers final: 50 residues processed: 372 average time/residue: 0.2728 time to fit residues: 160.6750 Evaluate side-chains 362 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 291 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET 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 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 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 B residue 301 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 192 LEU 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 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 337 ILE 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 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR 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 91 HIS 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 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 245 LYS 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 133 VAL Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 295 CYS Chi-restraints excluded: chain G residue 319 LEU Chi-restraints excluded: chain G residue 340 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 213 optimal weight: 0.8980 chunk 217 optimal weight: 0.0000 chunk 75 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 0.0050 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 147 optimal weight: 7.9990 chunk 210 optimal weight: 30.0000 chunk 13 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.210715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.209152 restraints weight = 24534.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.178153 restraints weight = 55787.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.173606 restraints weight = 61637.260| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3458 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= 0.128 Angle : 0.705 13.456 27137 Z= 0.326 Chirality : 0.041 0.422 3205 Planarity : 0.003 0.039 3309 Dihedral : 4.235 26.212 2799 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.19 % Favored : 94.48 % Rotamer: Outliers : 3.44 % Allowed : 27.12 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2408 helix: 2.05 (0.12), residues: 1722 sheet: -2.49 (0.52), residues: 70 loop : -1.30 (0.27), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 85 HIS 0.004 0.000 HIS B 254 PHE 0.017 0.001 PHE B 269 TYR 0.019 0.001 TYR G 122 ARG 0.004 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 7) link_NAG-ASN : angle 4.57330 ( 21) hydrogen bonds : bond 0.03457 ( 1251) hydrogen bonds : angle 3.57544 ( 3711) SS BOND : bond 0.00707 ( 14) SS BOND : angle 1.44196 ( 28) covalent geometry : bond 0.00279 (19951) covalent geometry : angle 0.69268 (27088) *********************** 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 390 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 316 time to evaluate : 2.473 Fit side-chains REVERT: A 36 SER cc_start: 0.8323 (p) cc_final: 0.7947 (t) REVERT: A 100 LYS cc_start: 0.4127 (tmtt) cc_final: 0.3758 (tttm) REVERT: A 263 LEU cc_start: 0.8589 (pt) cc_final: 0.7746 (pt) REVERT: B 187 PHE cc_start: 0.5690 (p90) cc_final: 0.4989 (p90) REVERT: B 263 LEU cc_start: 0.8581 (pt) cc_final: 0.7728 (pt) REVERT: B 283 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7776 (mp) REVERT: C 187 PHE cc_start: 0.5644 (p90) cc_final: 0.5327 (p90) REVERT: C 192 LEU cc_start: 0.7044 (OUTLIER) cc_final: 0.6750 (mp) REVERT: C 263 LEU cc_start: 0.8590 (pt) cc_final: 0.7695 (pt) REVERT: C 276 SER cc_start: 0.8732 (OUTLIER) cc_final: 0.8309 (t) REVERT: C 283 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7614 (mp) REVERT: C 288 ILE cc_start: 0.8701 (mm) cc_final: 0.8399 (mt) REVERT: C 291 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8101 (tt) REVERT: C 325 ASP cc_start: 0.7852 (t0) cc_final: 0.7636 (t0) REVERT: D 25 LEU cc_start: 0.3212 (OUTLIER) cc_final: 0.2860 (pt) REVERT: D 122 TYR cc_start: 0.7220 (t80) cc_final: 0.6934 (t80) REVERT: D 187 PHE cc_start: 0.6319 (p90) cc_final: 0.5599 (p90) REVERT: D 263 LEU cc_start: 0.8605 (pt) cc_final: 0.7687 (pt) REVERT: E 30 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6822 (mt) REVERT: E 100 LYS cc_start: 0.4443 (tmtt) cc_final: 0.3881 (tttm) REVERT: E 187 PHE cc_start: 0.5518 (OUTLIER) cc_final: 0.5096 (p90) REVERT: E 217 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8582 (mp) REVERT: E 263 LEU cc_start: 0.8660 (pt) cc_final: 0.7885 (pt) REVERT: E 276 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (t) REVERT: E 283 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7522 (mp) REVERT: F 263 LEU cc_start: 0.8474 (pt) cc_final: 0.7580 (pt) REVERT: F 288 ILE cc_start: 0.8764 (mm) cc_final: 0.8553 (mt) REVERT: F 294 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7786 (mp) REVERT: F 329 ILE cc_start: 0.7717 (mm) cc_final: 0.7034 (mm) REVERT: G 122 TYR cc_start: 0.7309 (t80) cc_final: 0.7049 (t80) REVERT: G 263 LEU cc_start: 0.8554 (pt) cc_final: 0.7674 (pt) REVERT: G 276 SER cc_start: 0.8842 (OUTLIER) cc_final: 0.8426 (t) REVERT: G 283 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7732 (mp) outliers start: 74 outliers final: 44 residues processed: 372 average time/residue: 0.2812 time to fit residues: 164.5380 Evaluate side-chains 349 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 2.189 ------------------------------------------------------------------------------- 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 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 268 ILE Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 291 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 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 260 THR Chi-restraints excluded: chain D residue 268 ILE 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 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 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 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 268 ILE 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 276 SER 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 50 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 225 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 233 optimal weight: 0.2980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 144 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4358 r_free = 0.4358 target = 0.209660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.208042 restraints weight = 24340.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.175799 restraints weight = 57370.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.172343 restraints weight = 61876.433| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3611 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= 0.133 Angle : 0.722 13.273 27137 Z= 0.331 Chirality : 0.041 0.428 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.088 25.678 2799 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 3.76 % Allowed : 26.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.18), residues: 2408 helix: 2.05 (0.12), residues: 1715 sheet: -2.43 (0.51), residues: 70 loop : -1.09 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.003 0.001 HIS B 254 PHE 0.031 0.002 PHE G 142 TYR 0.019 0.001 TYR G 122 ARG 0.004 0.000 ARG G 316 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 7) link_NAG-ASN : angle 4.24840 ( 21) hydrogen bonds : bond 0.03503 ( 1251) hydrogen bonds : angle 3.59179 ( 3711) SS BOND : bond 0.00751 ( 14) SS BOND : angle 1.60427 ( 28) covalent geometry : bond 0.00296 (19951) covalent geometry : angle 0.71064 (27088) *********************** 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 374 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 293 time to evaluate : 2.311 Fit side-chains REVERT: A 100 LYS cc_start: 0.4135 (tmtt) cc_final: 0.3821 (tttm) REVERT: A 263 LEU cc_start: 0.8557 (pt) cc_final: 0.7700 (pt) REVERT: A 276 SER cc_start: 0.8792 (OUTLIER) cc_final: 0.8434 (t) REVERT: A 283 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7439 (mp) REVERT: B 187 PHE cc_start: 0.5871 (p90) cc_final: 0.5404 (p90) REVERT: B 276 SER cc_start: 0.8690 (OUTLIER) cc_final: 0.8334 (t) REVERT: B 283 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7767 (mp) REVERT: C 187 PHE cc_start: 0.5570 (p90) cc_final: 0.5261 (p90) REVERT: C 283 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7626 (mp) REVERT: C 288 ILE cc_start: 0.8691 (mm) cc_final: 0.8357 (mt) REVERT: C 291 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8167 (tt) REVERT: D 25 LEU cc_start: 0.2967 (OUTLIER) cc_final: 0.2692 (pt) REVERT: D 122 TYR cc_start: 0.7236 (t80) cc_final: 0.6945 (t80) REVERT: D 187 PHE cc_start: 0.6232 (p90) cc_final: 0.5496 (p90) REVERT: D 263 LEU cc_start: 0.8602 (pt) cc_final: 0.7710 (pt) REVERT: D 283 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7619 (mp) REVERT: E 30 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6808 (mt) REVERT: E 36 SER cc_start: 0.8285 (p) cc_final: 0.7965 (t) REVERT: E 100 LYS cc_start: 0.4296 (tmtt) cc_final: 0.3822 (tttm) REVERT: E 187 PHE cc_start: 0.5539 (OUTLIER) cc_final: 0.5118 (p90) REVERT: E 217 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8545 (mp) REVERT: E 263 LEU cc_start: 0.8700 (pt) cc_final: 0.7957 (pt) REVERT: E 276 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8429 (t) REVERT: E 283 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7537 (mp) REVERT: F 263 LEU cc_start: 0.8467 (pt) cc_final: 0.7532 (pt) REVERT: F 288 ILE cc_start: 0.8633 (mm) cc_final: 0.8417 (mt) REVERT: F 294 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7860 (mp) REVERT: F 345 TRP cc_start: 0.6190 (OUTLIER) cc_final: 0.4839 (p90) REVERT: G 122 TYR cc_start: 0.7154 (t80) cc_final: 0.6832 (t80) REVERT: G 263 LEU cc_start: 0.8470 (pt) cc_final: 0.7575 (pt) REVERT: G 276 SER cc_start: 0.8834 (OUTLIER) cc_final: 0.8473 (t) REVERT: G 283 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7737 (mp) outliers start: 81 outliers final: 53 residues processed: 356 average time/residue: 0.2698 time to fit residues: 153.9511 Evaluate side-chains 356 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 286 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 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 276 SER 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 253 THR Chi-restraints excluded: chain B residue 260 THR 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 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 268 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 291 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 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 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 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 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 F residue 345 TRP 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 260 THR Chi-restraints excluded: chain G residue 276 SER 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 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.0170 chunk 209 optimal weight: 40.0000 chunk 74 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 163 optimal weight: 0.7980 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.208144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.170597 restraints weight = 24218.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.169772 restraints weight = 47528.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.169924 restraints weight = 45028.184| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19972 Z= 0.147 Angle : 0.737 14.419 27137 Z= 0.340 Chirality : 0.041 0.424 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.074 26.148 2799 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.36 % Favored : 94.31 % Rotamer: Outliers : 4.23 % Allowed : 26.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.18), residues: 2408 helix: 2.01 (0.12), residues: 1715 sheet: -2.39 (0.51), residues: 70 loop : -1.15 (0.27), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 85 HIS 0.003 0.001 HIS B 254 PHE 0.032 0.002 PHE G 142 TYR 0.019 0.001 TYR G 122 ARG 0.003 0.000 ARG F 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 7) link_NAG-ASN : angle 4.09698 ( 21) hydrogen bonds : bond 0.03659 ( 1251) hydrogen bonds : angle 3.63796 ( 3711) SS BOND : bond 0.00804 ( 14) SS BOND : angle 1.87638 ( 28) covalent geometry : bond 0.00338 (19951) covalent geometry : angle 0.72586 (27088) *********************** 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 384 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 293 time to evaluate : 2.033 Fit side-chains REVERT: A 100 LYS cc_start: 0.4136 (tmtt) cc_final: 0.3781 (tttm) REVERT: A 263 LEU cc_start: 0.8615 (pt) cc_final: 0.7787 (pt) REVERT: A 276 SER cc_start: 0.8816 (OUTLIER) cc_final: 0.8460 (t) REVERT: A 283 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7516 (mp) REVERT: B 187 PHE cc_start: 0.6040 (p90) cc_final: 0.5491 (p90) REVERT: B 276 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8397 (t) REVERT: B 283 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7750 (mp) REVERT: C 187 PHE cc_start: 0.5728 (p90) cc_final: 0.5443 (p90) REVERT: C 263 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.7859 (pt) REVERT: C 276 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8461 (t) REVERT: C 283 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7764 (mp) REVERT: C 288 ILE cc_start: 0.8506 (mm) cc_final: 0.8259 (mt) REVERT: C 291 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8074 (tt) REVERT: C 325 ASP cc_start: 0.7893 (t0) cc_final: 0.7649 (t0) REVERT: D 25 LEU cc_start: 0.3004 (OUTLIER) cc_final: 0.2623 (pt) REVERT: D 187 PHE cc_start: 0.6055 (p90) cc_final: 0.5445 (p90) REVERT: D 263 LEU cc_start: 0.8641 (pt) cc_final: 0.7774 (pt) REVERT: D 276 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8577 (t) REVERT: D 283 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7781 (mp) REVERT: E 30 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6780 (mt) REVERT: E 36 SER cc_start: 0.8227 (p) cc_final: 0.7828 (t) REVERT: E 100 LYS cc_start: 0.4534 (tmtt) cc_final: 0.4123 (tttm) REVERT: E 187 PHE cc_start: 0.5433 (OUTLIER) cc_final: 0.5107 (p90) REVERT: E 217 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8506 (mp) REVERT: E 276 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8446 (t) REVERT: E 283 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7790 (mp) REVERT: F 83 SER cc_start: 0.8486 (OUTLIER) cc_final: 0.8244 (t) REVERT: F 263 LEU cc_start: 0.8547 (pt) cc_final: 0.7632 (pt) REVERT: F 283 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7752 (mp) REVERT: F 288 ILE cc_start: 0.8749 (mm) cc_final: 0.8533 (mt) REVERT: F 294 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7818 (mp) REVERT: F 329 ILE cc_start: 0.7750 (mm) cc_final: 0.6939 (mm) REVERT: F 345 TRP cc_start: 0.6268 (OUTLIER) cc_final: 0.5166 (p-90) REVERT: G 36 SER cc_start: 0.8456 (p) cc_final: 0.8119 (t) REVERT: G 122 TYR cc_start: 0.7220 (t80) cc_final: 0.6938 (t80) REVERT: G 187 PHE cc_start: 0.6286 (p90) cc_final: 0.5850 (p90) REVERT: G 263 LEU cc_start: 0.8506 (pt) cc_final: 0.7615 (pt) REVERT: G 276 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8516 (t) REVERT: G 283 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7797 (mp) outliers start: 91 outliers final: 61 residues processed: 365 average time/residue: 0.2517 time to fit residues: 147.7216 Evaluate side-chains 365 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 282 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 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 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 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 276 SER Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 283 LEU Chi-restraints excluded: chain C residue 291 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 37 ILE 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 276 SER 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 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 83 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 F residue 294 LEU Chi-restraints excluded: chain F residue 345 TRP 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 260 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 276 SER 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 36 optimal weight: 0.2980 chunk 194 optimal weight: 1.9990 chunk 210 optimal weight: 40.0000 chunk 42 optimal weight: 0.3980 chunk 208 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 15 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 211 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN ** B 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.209057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.207204 restraints weight = 24430.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178455 restraints weight = 50053.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.176731 restraints weight = 60908.855| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3891 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= 0.139 Angle : 0.738 13.885 27137 Z= 0.339 Chirality : 0.041 0.428 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.045 26.200 2799 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 3.90 % Allowed : 26.94 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.18), residues: 2408 helix: 2.11 (0.12), residues: 1701 sheet: -2.37 (0.51), residues: 70 loop : -1.12 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 128 HIS 0.003 0.001 HIS B 254 PHE 0.019 0.002 PHE B 269 TYR 0.018 0.001 TYR G 122 ARG 0.003 0.000 ARG F 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 7) link_NAG-ASN : angle 3.72217 ( 21) hydrogen bonds : bond 0.03555 ( 1251) hydrogen bonds : angle 3.60693 ( 3711) SS BOND : bond 0.00744 ( 14) SS BOND : angle 1.73960 ( 28) covalent geometry : bond 0.00316 (19951) covalent geometry : angle 0.72876 (27088) ********************** 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 369 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 285 time to evaluate : 2.338 Fit side-chains REVERT: A 100 LYS cc_start: 0.4272 (tmtt) cc_final: 0.3870 (tttm) REVERT: A 263 LEU cc_start: 0.8556 (pt) cc_final: 0.7649 (pt) REVERT: A 283 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7484 (mp) REVERT: B 100 LYS cc_start: 0.4276 (tmtt) cc_final: 0.3445 (tttm) REVERT: B 187 PHE cc_start: 0.5994 (p90) cc_final: 0.5461 (p90) REVERT: B 276 SER cc_start: 0.8687 (OUTLIER) cc_final: 0.8342 (t) REVERT: B 283 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7686 (mp) REVERT: C 187 PHE cc_start: 0.5765 (p90) cc_final: 0.5548 (p90) REVERT: C 263 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.7783 (pt) REVERT: C 283 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7740 (mp) REVERT: C 288 ILE cc_start: 0.8645 (mm) cc_final: 0.8398 (mt) REVERT: C 291 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7960 (tt) REVERT: D 121 MET cc_start: 0.8199 (mmp) cc_final: 0.7839 (mmt) REVERT: D 187 PHE cc_start: 0.5951 (p90) cc_final: 0.5340 (p90) REVERT: D 263 LEU cc_start: 0.8648 (pt) cc_final: 0.7735 (pt) REVERT: D 283 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7906 (mp) REVERT: E 30 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6770 (mt) REVERT: E 100 LYS cc_start: 0.4505 (tmtt) cc_final: 0.4217 (tttm) REVERT: E 187 PHE cc_start: 0.5358 (OUTLIER) cc_final: 0.4721 (p90) REVERT: E 217 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8527 (mp) REVERT: E 263 LEU cc_start: 0.8614 (pt) cc_final: 0.7811 (pt) REVERT: E 276 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8467 (t) REVERT: E 283 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7727 (mp) REVERT: F 83 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8238 (t) REVERT: F 263 LEU cc_start: 0.8503 (pt) cc_final: 0.7572 (pt) REVERT: F 329 ILE cc_start: 0.7774 (mm) cc_final: 0.7014 (mm) REVERT: F 345 TRP cc_start: 0.5746 (OUTLIER) cc_final: 0.5150 (p-90) REVERT: G 36 SER cc_start: 0.8339 (p) cc_final: 0.8040 (t) REVERT: G 122 TYR cc_start: 0.7148 (t80) cc_final: 0.6850 (t80) REVERT: G 187 PHE cc_start: 0.6203 (p90) cc_final: 0.5803 (p90) REVERT: G 263 LEU cc_start: 0.8462 (pt) cc_final: 0.7550 (pt) REVERT: G 276 SER cc_start: 0.8874 (OUTLIER) cc_final: 0.8502 (t) REVERT: G 283 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7646 (mp) outliers start: 84 outliers final: 61 residues processed: 355 average time/residue: 0.2917 time to fit residues: 169.5723 Evaluate side-chains 360 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 283 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 260 THR 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 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 291 LEU Chi-restraints excluded: chain C residue 319 LEU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 37 ILE 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 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 242 CYS 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 83 SER Chi-restraints excluded: chain F residue 133 VAL 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 345 TRP 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 260 THR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 276 SER 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 82 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 chunk 114 optimal weight: 0.7980 chunk 210 optimal weight: 30.0000 chunk 172 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 224 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 120 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 213 ASN 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 = 0.209487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.207674 restraints weight = 24474.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.170899 restraints weight = 44895.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.170443 restraints weight = 60182.935| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4001 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 : 0.734 13.776 27137 Z= 0.337 Chirality : 0.041 0.433 3205 Planarity : 0.004 0.039 3309 Dihedral : 3.947 25.907 2799 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.27 % Favored : 94.39 % Rotamer: Outliers : 3.99 % Allowed : 26.85 % Favored : 69.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.18), residues: 2408 helix: 2.17 (0.12), residues: 1701 sheet: -2.35 (0.51), residues: 70 loop : -1.10 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 85 HIS 0.003 0.001 HIS B 254 PHE 0.020 0.001 PHE G 142 TYR 0.019 0.001 TYR A 195 ARG 0.003 0.000 ARG F 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 7) link_NAG-ASN : angle 3.34678 ( 21) hydrogen bonds : bond 0.03470 ( 1251) hydrogen bonds : angle 3.57893 ( 3711) SS BOND : bond 0.00743 ( 14) SS BOND : angle 1.65722 ( 28) covalent geometry : bond 0.00302 (19951) covalent geometry : angle 0.72687 (27088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5490.01 seconds wall clock time: 97 minutes 35.85 seconds (5855.85 seconds total)