Starting phenix.real_space_refine on Tue Jun 17 00:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gyt_34377/06_2025/8gyt_34377.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gyt_34377/06_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_34377/06_2025/8gyt_34377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gyt_34377/06_2025/8gyt_34377.map" model { file = "/net/cci-nas-00/data/ceres_data/8gyt_34377/06_2025/8gyt_34377.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gyt_34377/06_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.00, per 1000 atoms: 0.62 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: 6.09 Conformation dependent library (CDL) restraints added in 2.4 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: 2.23 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: 6.33 Time building geometry restraints manager: 7.04 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 46.710 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 55.130 ------------------------------------------------------------------------------- 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 : 2.069 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: 0.3364 time to fit residues: 143.8925 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 : 2.249 ------------------------------------------------------------------------------- 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 = 0.177797 restraints weight = 241832.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.179409 restraints weight = 131689.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.178404 restraints weight = 117037.809| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 6.58101 ( 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 : 2.098 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: 0.8826 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 101 MET cc_start: 0.4921 (tpp) cc_final: 0.4679 (tpp) REVERT: B 187 PHE cc_start: 0.4758 (OUTLIER) cc_final: 0.4537 (p90) REVERT: B 263 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7880 (pt) REVERT: C 187 PHE cc_start: 0.5173 (OUTLIER) cc_final: 0.4886 (p90) REVERT: C 192 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6519 (mp) REVERT: C 340 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.6111 (mt) REVERT: D 187 PHE cc_start: 0.4902 (OUTLIER) cc_final: 0.4587 (p90) REVERT: D 192 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6767 (mp) REVERT: E 129 GLN cc_start: 0.7833 (tm-30) cc_final: 0.7602 (tm-30) REVERT: E 187 PHE cc_start: 0.4617 (OUTLIER) cc_final: 0.4205 (p90) REVERT: E 217 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8396 (mp) REVERT: E 249 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8061 (pt) REVERT: F 329 ILE cc_start: 0.7839 (mt) cc_final: 0.7479 (mt) REVERT: G 217 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8563 (mp) outliers start: 87 outliers final: 39 residues processed: 356 average time/residue: 0.2980 time to fit residues: 165.6034 Evaluate side-chains 305 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 186 TYR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 186 TYR Chi-restraints excluded: chain B residue 187 PHE Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 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: 3.9990 chunk 69 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 222 optimal weight: 4.9990 chunk 240 optimal weight: 1.9990 chunk 198 optimal weight: 0.1980 chunk 221 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.211825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.170656 restraints weight = 241501.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.171947 restraints weight = 130207.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.171411 restraints weight = 116712.724| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19972 Z= 0.210 Angle : 0.809 12.991 27137 Z= 0.376 Chirality : 0.045 0.510 3205 Planarity : 0.004 0.040 3309 Dihedral : 6.047 57.340 2799 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.06 % Favored : 93.60 % Rotamer: Outliers : 6.08 % Allowed : 22.57 % Favored : 71.34 % 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: 1.27 (0.18), residues: 2408 helix: 1.80 (0.12), residues: 1722 sheet: -3.03 (0.52), residues: 70 loop : -1.45 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 85 HIS 0.004 0.001 HIS B 90 PHE 0.031 0.002 PHE E 343 TYR 0.021 0.002 TYR D 122 ARG 0.003 0.000 ARG D 262 Details of bonding type rmsd link_NAG-ASN : bond 0.01002 ( 7) link_NAG-ASN : angle 6.53804 ( 21) hydrogen bonds : bond 0.04444 ( 1251) hydrogen bonds : angle 3.84317 ( 3711) SS BOND : bond 0.00971 ( 14) SS BOND : angle 2.56746 ( 28) covalent geometry : bond 0.00499 (19951) covalent geometry : angle 0.78433 (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 427 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 296 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8003 (pt) REVERT: A 276 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8546 (t) REVERT: A 283 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7470 (mp) REVERT: A 329 ILE cc_start: 0.7705 (mt) cc_final: 0.7452 (mt) REVERT: A 341 ILE cc_start: 0.4428 (OUTLIER) cc_final: 0.4044 (pt) REVERT: B 122 TYR cc_start: 0.7659 (t80) cc_final: 0.7393 (t80) REVERT: B 187 PHE cc_start: 0.5242 (OUTLIER) cc_final: 0.4789 (p90) REVERT: B 263 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.7952 (pt) REVERT: B 283 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7719 (mp) REVERT: C 192 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6576 (mp) REVERT: C 263 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.7969 (pt) REVERT: C 283 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7750 (mp) REVERT: C 288 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8297 (mt) REVERT: C 325 ASP cc_start: 0.7887 (t0) cc_final: 0.7685 (t0) REVERT: D 192 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6506 (mp) REVERT: D 263 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8185 (pt) REVERT: D 283 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7852 (mp) REVERT: E 159 GLN cc_start: 0.3153 (OUTLIER) cc_final: 0.2846 (mt0) REVERT: E 187 PHE cc_start: 0.4912 (OUTLIER) cc_final: 0.4103 (p90) REVERT: E 217 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8519 (mp) REVERT: E 249 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8396 (pt) REVERT: E 263 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8390 (pt) REVERT: E 276 SER cc_start: 0.8913 (OUTLIER) cc_final: 0.8651 (t) REVERT: E 283 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7642 (mp) REVERT: F 189 PHE cc_start: 0.6298 (m-80) cc_final: 0.6068 (m-80) REVERT: F 263 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8040 (pt) REVERT: F 283 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7736 (mp) REVERT: F 288 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8317 (mt) REVERT: G 263 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.7934 (pt) REVERT: G 283 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7852 (mp) outliers start: 131 outliers final: 61 residues processed: 394 average time/residue: 0.2652 time to fit residues: 165.4683 Evaluate side-chains 349 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 292 THR 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 329 ILE Chi-restraints excluded: chain D residue 50 MET Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 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 283 LEU Chi-restraints excluded: chain D residue 292 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 232 LEU 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 263 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 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 F residue 292 THR 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 283 LEU Chi-restraints excluded: chain G residue 292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 223 optimal weight: 8.9990 chunk 236 optimal weight: 1.9990 chunk 116 optimal weight: 7.9990 chunk 212 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 213 ASN G 129 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.212211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.171146 restraints weight = 241900.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.172554 restraints weight = 131267.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.171659 restraints weight = 116808.185| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19972 Z= 0.190 Angle : 0.786 13.947 27137 Z= 0.363 Chirality : 0.043 0.452 3205 Planarity : 0.004 0.039 3309 Dihedral : 5.688 51.282 2799 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.86 % Favored : 93.81 % Rotamer: Outliers : 6.04 % Allowed : 23.36 % Favored : 70.60 % 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: 1.19 (0.18), residues: 2408 helix: 1.76 (0.12), residues: 1722 sheet: -2.92 (0.52), residues: 70 loop : -1.58 (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 D 254 PHE 0.027 0.002 PHE F 142 TYR 0.026 0.002 TYR F 122 ARG 0.003 0.000 ARG E 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00999 ( 7) link_NAG-ASN : angle 6.38995 ( 21) hydrogen bonds : bond 0.04207 ( 1251) hydrogen bonds : angle 3.78857 ( 3711) SS BOND : bond 0.00878 ( 14) SS BOND : angle 2.50458 ( 28) covalent geometry : bond 0.00448 (19951) covalent geometry : angle 0.76164 (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 430 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 300 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4468 (tmtt) cc_final: 0.4144 (tttm) REVERT: A 263 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.7994 (pt) REVERT: A 283 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7637 (mp) REVERT: A 340 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5810 (mt) REVERT: A 341 ILE cc_start: 0.4508 (OUTLIER) cc_final: 0.4152 (pt) REVERT: B 36 SER cc_start: 0.8559 (p) cc_final: 0.8244 (t) REVERT: B 149 LYS cc_start: 0.7453 (ptpp) cc_final: 0.7241 (pptt) REVERT: B 187 PHE cc_start: 0.5254 (OUTLIER) cc_final: 0.4518 (p90) REVERT: B 263 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.7794 (pt) REVERT: B 276 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8484 (t) REVERT: B 283 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7474 (mp) REVERT: C 192 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6286 (mp) REVERT: C 263 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.7917 (pt) REVERT: C 276 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8498 (t) REVERT: C 283 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7682 (mp) REVERT: C 288 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8239 (mt) REVERT: C 291 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7885 (tt) REVERT: C 325 ASP cc_start: 0.7652 (t0) cc_final: 0.7393 (t0) REVERT: D 25 LEU cc_start: 0.3155 (OUTLIER) cc_final: 0.2792 (pt) REVERT: D 192 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6435 (mp) REVERT: D 218 ILE cc_start: 0.8578 (mm) cc_final: 0.8370 (mt) REVERT: D 263 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8026 (pt) REVERT: D 276 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8671 (t) REVERT: D 283 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7824 (mp) REVERT: E 30 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7277 (mt) REVERT: E 101 MET cc_start: 0.4365 (tpp) cc_final: 0.4100 (tpp) REVERT: E 187 PHE cc_start: 0.5117 (OUTLIER) cc_final: 0.4612 (p90) REVERT: E 249 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8435 (pt) REVERT: E 263 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8295 (pt) REVERT: E 276 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8520 (t) REVERT: F 122 TYR cc_start: 0.7548 (t80) cc_final: 0.7310 (t80) REVERT: F 200 GLN cc_start: 0.7708 (mm110) cc_final: 0.7402 (mm110) REVERT: F 263 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.7860 (pt) REVERT: F 283 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7777 (mp) REVERT: F 288 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8331 (mt) REVERT: G 142 PHE cc_start: 0.7425 (t80) cc_final: 0.7173 (t80) REVERT: G 263 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.7899 (pt) REVERT: G 276 SER cc_start: 0.8918 (OUTLIER) cc_final: 0.8607 (t) REVERT: G 283 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7874 (mp) outliers start: 130 outliers final: 53 residues processed: 400 average time/residue: 0.3005 time to fit residues: 187.6472 Evaluate side-chains 352 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 269 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 161 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 340 LEU 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 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 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 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 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 125 VAL 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 249 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 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 176 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 202 optimal weight: 0.3980 chunk 163 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 120 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 ASN C 254 HIS D 254 HIS E 213 ASN G 254 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.208537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206231 restraints weight = 24164.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.206046 restraints weight = 48022.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.176679 restraints weight = 48907.185| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19972 Z= 0.147 Angle : 0.747 12.906 27137 Z= 0.344 Chirality : 0.041 0.424 3205 Planarity : 0.004 0.039 3309 Dihedral : 5.093 41.909 2799 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.40 % Favored : 94.27 % Rotamer: Outliers : 4.64 % Allowed : 25.36 % Favored : 70.00 % 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: 1.37 (0.18), residues: 2408 helix: 1.86 (0.12), residues: 1736 sheet: -2.87 (0.50), residues: 70 loop : -1.48 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 128 HIS 0.002 0.001 HIS F 254 PHE 0.026 0.002 PHE G 142 TYR 0.024 0.001 TYR F 122 ARG 0.003 0.000 ARG D 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 7) link_NAG-ASN : angle 5.95513 ( 21) hydrogen bonds : bond 0.03796 ( 1251) hydrogen bonds : angle 3.70115 ( 3711) SS BOND : bond 0.00784 ( 14) SS BOND : angle 1.82014 ( 28) covalent geometry : bond 0.00332 (19951) covalent geometry : angle 0.72709 (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 396 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 296 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4027 (tmtt) cc_final: 0.3663 (tttm) REVERT: A 101 MET cc_start: 0.4658 (ppp) cc_final: 0.4410 (ppp) REVERT: A 263 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.7818 (pt) REVERT: A 276 SER cc_start: 0.8788 (OUTLIER) cc_final: 0.8503 (t) REVERT: A 283 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7645 (mp) REVERT: B 36 SER cc_start: 0.8216 (p) cc_final: 0.7785 (t) REVERT: B 122 TYR cc_start: 0.7129 (t80) cc_final: 0.6916 (t80) REVERT: B 187 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4844 (p90) REVERT: B 283 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7803 (mp) REVERT: C 187 PHE cc_start: 0.5559 (p90) cc_final: 0.5216 (p90) REVERT: C 192 LEU cc_start: 0.6829 (OUTLIER) cc_final: 0.6561 (mp) REVERT: C 263 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7544 (pt) REVERT: C 283 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7929 (mp) REVERT: C 291 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8077 (tt) REVERT: C 325 ASP cc_start: 0.7849 (t0) cc_final: 0.7632 (t0) REVERT: D 25 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.2766 (pt) REVERT: D 263 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7936 (pt) REVERT: D 283 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7841 (mp) REVERT: E 30 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6928 (mt) REVERT: E 159 GLN cc_start: 0.4208 (OUTLIER) cc_final: 0.3701 (mt0) REVERT: E 187 PHE cc_start: 0.5682 (OUTLIER) cc_final: 0.4922 (p90) REVERT: E 263 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.7890 (pt) REVERT: E 283 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7633 (mp) REVERT: F 263 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7468 (pt) REVERT: F 283 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7815 (mp) REVERT: G 263 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7743 (pt) REVERT: G 283 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7868 (mp) outliers start: 100 outliers final: 51 residues processed: 368 average time/residue: 0.2883 time to fit residues: 168.4311 Evaluate side-chains 347 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 275 time to evaluate : 2.230 ------------------------------------------------------------------------------- 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 217 LEU 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 186 TYR 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 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 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 223 THR 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 D residue 294 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 159 GLN 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 263 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 253 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 232 LEU Chi-restraints excluded: chain G residue 253 THR Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain G residue 283 LEU Chi-restraints excluded: chain G residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 147 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 186 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.4306 r_free = 0.4306 target = 0.204575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.202798 restraints weight = 24099.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169994 restraints weight = 55564.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.165742 restraints weight = 62524.013| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 19972 Z= 0.227 Angle : 0.835 13.384 27137 Z= 0.387 Chirality : 0.045 0.619 3205 Planarity : 0.004 0.039 3309 Dihedral : 5.245 41.753 2799 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.19 % Favored : 93.48 % Rotamer: Outliers : 5.67 % Allowed : 24.71 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.18), residues: 2408 helix: 1.69 (0.12), residues: 1722 sheet: -2.53 (0.54), residues: 70 loop : -1.72 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 85 HIS 0.004 0.001 HIS E 254 PHE 0.024 0.002 PHE B 269 TYR 0.018 0.002 TYR B 122 ARG 0.003 0.000 ARG A 201 Details of bonding type rmsd link_NAG-ASN : bond 0.01195 ( 7) link_NAG-ASN : angle 6.37903 ( 21) hydrogen bonds : bond 0.04475 ( 1251) hydrogen bonds : angle 3.90652 ( 3711) SS BOND : bond 0.00994 ( 14) SS BOND : angle 2.96803 ( 28) covalent geometry : bond 0.00544 (19951) covalent geometry : angle 0.81119 (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 404 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 282 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4285 (tmtt) cc_final: 0.3930 (tttm) REVERT: A 101 MET cc_start: 0.4873 (ppp) cc_final: 0.4645 (ppp) REVERT: A 263 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8042 (pt) REVERT: A 276 SER cc_start: 0.8931 (OUTLIER) cc_final: 0.8620 (t) REVERT: A 283 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7498 (mp) REVERT: B 36 SER cc_start: 0.8518 (p) cc_final: 0.8230 (t) REVERT: B 122 TYR cc_start: 0.7212 (t80) cc_final: 0.6973 (t80) REVERT: B 187 PHE cc_start: 0.5493 (OUTLIER) cc_final: 0.5002 (p90) REVERT: B 263 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.7973 (pt) REVERT: B 276 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8462 (t) REVERT: B 283 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 301 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.3928 (mt) REVERT: C 187 PHE cc_start: 0.5702 (p90) cc_final: 0.5390 (p90) REVERT: C 263 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.7910 (pt) REVERT: C 276 SER cc_start: 0.8846 (OUTLIER) cc_final: 0.8529 (t) REVERT: C 283 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7644 (mp) REVERT: C 288 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8647 (mt) REVERT: C 291 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8059 (tt) REVERT: C 325 ASP cc_start: 0.8005 (t0) cc_final: 0.7783 (t0) REVERT: D 25 LEU cc_start: 0.3206 (OUTLIER) cc_final: 0.2852 (pt) REVERT: D 187 PHE cc_start: 0.6564 (p90) cc_final: 0.5815 (p90) REVERT: D 263 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8119 (pt) REVERT: D 276 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8635 (t) REVERT: D 283 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7504 (mp) REVERT: E 30 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.7015 (mt) REVERT: E 36 SER cc_start: 0.8370 (p) cc_final: 0.8157 (t) REVERT: E 100 LYS cc_start: 0.4293 (tmtt) cc_final: 0.3568 (tttm) REVERT: E 187 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.5200 (p90) REVERT: E 263 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8120 (pt) REVERT: E 276 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8528 (t) REVERT: E 283 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7656 (mp) REVERT: F 83 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.8179 (t) REVERT: F 263 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8039 (pt) REVERT: F 283 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7426 (mp) REVERT: F 288 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8812 (mt) REVERT: G 263 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.7950 (pt) REVERT: G 276 SER cc_start: 0.8923 (OUTLIER) cc_final: 0.8654 (t) REVERT: G 283 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7899 (mp) outliers start: 122 outliers final: 68 residues processed: 374 average time/residue: 0.2776 time to fit residues: 165.2779 Evaluate side-chains 359 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 262 time to evaluate : 2.122 ------------------------------------------------------------------------------- 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 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 255 VAL 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 186 TYR 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 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 B residue 301 LEU Chi-restraints excluded: chain C residue 83 SER Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 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 329 ILE 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 83 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 MET 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 161 MET Chi-restraints excluded: chain E residue 187 PHE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 268 ILE Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 83 SER Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 345 TRP Chi-restraints excluded: chain G residue 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 45 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 142 optimal weight: 0.7980 chunk 182 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 226 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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 = 0.4347 r_free = 0.4347 target = 0.208618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.206830 restraints weight = 24319.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.173585 restraints weight = 47555.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.172239 restraints weight = 57670.098| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3576 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 : 0.741 15.494 27137 Z= 0.340 Chirality : 0.041 0.457 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.740 33.469 2799 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.15 % Favored : 94.52 % Rotamer: Outliers : 4.46 % Allowed : 26.34 % Favored : 69.21 % 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: 1.38 (0.18), residues: 2408 helix: 1.87 (0.12), residues: 1736 sheet: -2.50 (0.52), residues: 70 loop : -1.52 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 128 HIS 0.003 0.001 HIS G 254 PHE 0.031 0.002 PHE G 142 TYR 0.020 0.001 TYR G 122 ARG 0.011 0.000 ARG B 334 Details of bonding type rmsd link_NAG-ASN : bond 0.00651 ( 7) link_NAG-ASN : angle 5.47001 ( 21) hydrogen bonds : bond 0.03698 ( 1251) hydrogen bonds : angle 3.69397 ( 3711) SS BOND : bond 0.00765 ( 14) SS BOND : angle 1.78599 ( 28) covalent geometry : bond 0.00310 (19951) covalent geometry : angle 0.72362 (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 397 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 301 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4284 (tmtt) cc_final: 0.3952 (tttm) REVERT: A 101 MET cc_start: 0.4756 (ppp) cc_final: 0.4517 (ppp) REVERT: A 263 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.7895 (pt) REVERT: A 276 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8493 (t) REVERT: A 283 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7554 (mp) REVERT: B 122 TYR cc_start: 0.7130 (t80) cc_final: 0.6925 (t80) REVERT: B 187 PHE cc_start: 0.5412 (OUTLIER) cc_final: 0.4817 (p90) REVERT: B 263 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7892 (pt) REVERT: B 276 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8359 (t) REVERT: B 283 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7587 (mp) REVERT: C 187 PHE cc_start: 0.5761 (p90) cc_final: 0.5417 (p90) REVERT: C 263 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7659 (pt) REVERT: C 276 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8428 (t) REVERT: C 283 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7565 (mp) REVERT: C 288 ILE cc_start: 0.8338 (mm) cc_final: 0.8028 (mt) REVERT: C 291 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8120 (tt) REVERT: D 187 PHE cc_start: 0.6497 (p90) cc_final: 0.5754 (p90) REVERT: D 263 LEU cc_start: 0.8675 (pt) cc_final: 0.7899 (pt) REVERT: D 283 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7752 (mp) REVERT: E 30 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7004 (mt) REVERT: E 100 LYS cc_start: 0.4011 (tmtt) cc_final: 0.3334 (tttm) REVERT: E 187 PHE cc_start: 0.5516 (OUTLIER) cc_final: 0.5125 (p90) REVERT: E 263 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.7974 (pt) REVERT: E 283 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7629 (mp) REVERT: F 263 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.7726 (pt) REVERT: F 283 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7646 (mp) REVERT: F 288 ILE cc_start: 0.8536 (mm) cc_final: 0.8283 (mt) REVERT: F 345 TRP cc_start: 0.6192 (OUTLIER) cc_final: 0.4861 (p90) REVERT: G 263 LEU cc_start: 0.8631 (pt) cc_final: 0.7780 (pt) REVERT: G 276 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8550 (t) REVERT: G 283 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7810 (mp) REVERT: G 329 ILE cc_start: 0.7776 (mm) cc_final: 0.7352 (mm) outliers start: 96 outliers final: 56 residues processed: 374 average time/residue: 0.2815 time to fit residues: 167.0813 Evaluate side-chains 362 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 285 time to evaluate : 2.133 ------------------------------------------------------------------------------- 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 255 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU 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 83 SER 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 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 276 SER 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 260 THR Chi-restraints excluded: chain C residue 263 LEU 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 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 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 MET Chi-restraints excluded: chain E residue 91 HIS 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 263 LEU Chi-restraints excluded: chain E residue 283 LEU Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 345 TRP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 241 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 155 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 223 optimal weight: 9.9990 chunk 242 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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** E 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.212421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.171677 restraints weight = 239235.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.173436 restraints weight = 129859.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.172321 restraints weight = 115759.564| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19972 Z= 0.160 Angle : 0.761 14.496 27137 Z= 0.352 Chirality : 0.042 0.424 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.521 26.393 2799 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.73 % Favored : 93.94 % Rotamer: Outliers : 4.78 % Allowed : 26.57 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.40 (0.18), residues: 2408 helix: 1.88 (0.12), residues: 1736 sheet: -2.35 (0.53), residues: 70 loop : -1.54 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 85 HIS 0.003 0.001 HIS A 231 PHE 0.032 0.002 PHE G 142 TYR 0.015 0.001 TYR E 186 ARG 0.001 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00748 ( 7) link_NAG-ASN : angle 5.28929 ( 21) hydrogen bonds : bond 0.03873 ( 1251) hydrogen bonds : angle 3.73534 ( 3711) SS BOND : bond 0.00861 ( 14) SS BOND : angle 2.11589 ( 28) covalent geometry : bond 0.00373 (19951) covalent geometry : angle 0.74409 (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 379 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 276 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4656 (tmtt) cc_final: 0.4400 (tttm) REVERT: A 263 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.7870 (pt) REVERT: A 276 SER cc_start: 0.8847 (OUTLIER) cc_final: 0.8525 (t) REVERT: A 283 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7489 (mp) REVERT: B 263 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7901 (pt) REVERT: B 276 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.8415 (t) REVERT: B 283 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7538 (mp) REVERT: C 187 PHE cc_start: 0.5992 (p90) cc_final: 0.5652 (p90) REVERT: C 263 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.7743 (pt) REVERT: C 276 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8499 (t) REVERT: C 283 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7738 (mp) REVERT: C 288 ILE cc_start: 0.8353 (mm) cc_final: 0.8101 (mt) REVERT: C 291 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (tt) REVERT: D 187 PHE cc_start: 0.6402 (p90) cc_final: 0.5784 (p90) REVERT: D 283 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7769 (mp) REVERT: E 30 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7345 (mt) REVERT: E 100 LYS cc_start: 0.4623 (tmtt) cc_final: 0.3953 (tttm) REVERT: E 187 PHE cc_start: 0.5537 (OUTLIER) cc_final: 0.5147 (p90) REVERT: E 263 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.7897 (pt) REVERT: E 276 SER cc_start: 0.8825 (OUTLIER) cc_final: 0.8484 (t) REVERT: E 283 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7472 (mp) REVERT: F 83 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8208 (t) REVERT: F 187 PHE cc_start: 0.6273 (p90) cc_final: 0.5955 (p90) REVERT: F 263 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7786 (pt) REVERT: F 276 SER cc_start: 0.8748 (OUTLIER) cc_final: 0.8433 (t) REVERT: F 283 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7784 (mp) REVERT: F 288 ILE cc_start: 0.8730 (mm) cc_final: 0.8514 (mt) REVERT: F 345 TRP cc_start: 0.7022 (OUTLIER) cc_final: 0.5213 (p-90) REVERT: G 187 PHE cc_start: 0.6593 (p90) cc_final: 0.6151 (p90) REVERT: G 263 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7815 (pt) REVERT: G 276 SER cc_start: 0.8841 (OUTLIER) cc_final: 0.8537 (t) REVERT: G 283 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7739 (mp) REVERT: G 329 ILE cc_start: 0.7819 (mm) cc_final: 0.7391 (mm) outliers start: 103 outliers final: 69 residues processed: 355 average time/residue: 0.2792 time to fit residues: 159.4557 Evaluate side-chains 363 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 270 time to evaluate : 2.270 ------------------------------------------------------------------------------- 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 255 VAL Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 68 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain B residue 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 149 LYS 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 37 ILE Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 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 50 MET 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 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 263 LEU 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 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 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 345 TRP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 91 HIS Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 241 SER 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 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 50 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 178 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.214087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.174077 restraints weight = 241150.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.175686 restraints weight = 128925.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.174901 restraints weight = 114470.671| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19972 Z= 0.140 Angle : 0.737 13.916 27137 Z= 0.340 Chirality : 0.041 0.421 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.331 26.348 2799 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.11 % Favored : 94.56 % Rotamer: Outliers : 4.51 % Allowed : 26.94 % Favored : 68.56 % 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: 1.54 (0.18), residues: 2408 helix: 1.98 (0.12), residues: 1736 sheet: -2.34 (0.52), residues: 70 loop : -1.46 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 128 HIS 0.003 0.001 HIS G 254 PHE 0.023 0.002 PHE D 142 TYR 0.019 0.001 TYR G 122 ARG 0.002 0.000 ARG E 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00547 ( 7) link_NAG-ASN : angle 4.69716 ( 21) hydrogen bonds : bond 0.03622 ( 1251) hydrogen bonds : angle 3.67414 ( 3711) SS BOND : bond 0.00769 ( 14) SS BOND : angle 1.77071 ( 28) covalent geometry : bond 0.00318 (19951) covalent geometry : angle 0.72413 (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 378 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 281 time to evaluate : 2.115 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4692 (tmtt) cc_final: 0.4364 (tttm) REVERT: A 263 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.7768 (pt) REVERT: A 276 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8540 (t) REVERT: A 283 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7486 (mp) REVERT: B 276 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8387 (t) REVERT: B 283 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7746 (mp) REVERT: C 187 PHE cc_start: 0.6051 (p90) cc_final: 0.5674 (p90) REVERT: C 263 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.7671 (pt) REVERT: C 276 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8481 (t) REVERT: C 283 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7698 (mp) REVERT: C 288 ILE cc_start: 0.8567 (mm) cc_final: 0.8287 (mt) REVERT: C 291 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8087 (tt) REVERT: D 187 PHE cc_start: 0.6546 (p90) cc_final: 0.5854 (p90) REVERT: D 263 LEU cc_start: 0.8633 (pt) cc_final: 0.7851 (pt) REVERT: D 276 SER cc_start: 0.8835 (OUTLIER) cc_final: 0.8511 (t) REVERT: D 283 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7762 (mp) REVERT: E 30 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7237 (mt) REVERT: E 100 LYS cc_start: 0.4593 (tmtt) cc_final: 0.3943 (tttm) REVERT: E 187 PHE cc_start: 0.5471 (OUTLIER) cc_final: 0.5139 (p90) REVERT: E 263 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.7905 (pt) REVERT: E 276 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8504 (t) REVERT: E 283 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7646 (mp) REVERT: F 187 PHE cc_start: 0.6292 (p90) cc_final: 0.5978 (p90) REVERT: F 263 LEU cc_start: 0.8624 (pt) cc_final: 0.7775 (pt) REVERT: F 283 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7761 (mp) REVERT: F 345 TRP cc_start: 0.7027 (OUTLIER) cc_final: 0.5307 (p-90) REVERT: G 121 MET cc_start: 0.7918 (mmp) cc_final: 0.7638 (mmp) REVERT: G 187 PHE cc_start: 0.6552 (p90) cc_final: 0.6073 (p90) REVERT: G 263 LEU cc_start: 0.8632 (pt) cc_final: 0.7806 (pt) REVERT: G 276 SER cc_start: 0.8911 (OUTLIER) cc_final: 0.8643 (t) REVERT: G 283 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7771 (mp) REVERT: G 329 ILE cc_start: 0.7675 (mm) cc_final: 0.7253 (mm) outliers start: 97 outliers final: 68 residues processed: 355 average time/residue: 0.2672 time to fit residues: 153.2874 Evaluate side-chains 360 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 272 time to evaluate : 2.166 ------------------------------------------------------------------------------- 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 255 VAL 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 83 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 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 329 ILE 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 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 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 50 MET 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 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 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 304 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 345 TRP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 241 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 6 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 35 optimal weight: 30.0000 chunk 230 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 207 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4387 r_free = 0.4387 target = 0.213581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.173527 restraints weight = 239114.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.174892 restraints weight = 128680.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.173908 restraints weight = 116043.705| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19972 Z= 0.143 Angle : 0.741 14.011 27137 Z= 0.341 Chirality : 0.041 0.432 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.189 26.440 2799 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.44 % Favored : 94.23 % Rotamer: Outliers : 4.23 % Allowed : 27.22 % Favored : 68.56 % 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: 2.04 (0.12), residues: 1715 sheet: -2.30 (0.52), residues: 70 loop : -1.27 (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 G 254 PHE 0.029 0.002 PHE D 142 TYR 0.015 0.001 TYR A 195 ARG 0.002 0.000 ARG D 194 Details of bonding type rmsd link_NAG-ASN : bond 0.00503 ( 7) link_NAG-ASN : angle 4.35797 ( 21) hydrogen bonds : bond 0.03613 ( 1251) hydrogen bonds : angle 3.65567 ( 3711) SS BOND : bond 0.00788 ( 14) SS BOND : angle 1.81719 ( 28) covalent geometry : bond 0.00326 (19951) covalent geometry : angle 0.72927 (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 374 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 283 time to evaluate : 2.407 Fit side-chains revert: symmetry clash REVERT: A 100 LYS cc_start: 0.4827 (tmtt) cc_final: 0.4525 (tttm) REVERT: A 263 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.7888 (pt) REVERT: A 276 SER cc_start: 0.8804 (OUTLIER) cc_final: 0.8462 (t) REVERT: A 283 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7425 (mp) REVERT: B 187 PHE cc_start: 0.5727 (p90) cc_final: 0.5109 (p90) REVERT: B 276 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8497 (t) REVERT: B 283 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7684 (mp) REVERT: C 187 PHE cc_start: 0.6294 (p90) cc_final: 0.5973 (p90) REVERT: C 263 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.7743 (pt) REVERT: C 276 SER cc_start: 0.8810 (OUTLIER) cc_final: 0.8440 (t) REVERT: C 283 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7660 (mp) REVERT: C 288 ILE cc_start: 0.8500 (mm) cc_final: 0.8258 (mt) REVERT: D 187 PHE cc_start: 0.6282 (p90) cc_final: 0.5715 (p90) REVERT: D 276 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8491 (t) REVERT: D 283 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7808 (mp) REVERT: E 30 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7489 (mt) REVERT: E 100 LYS cc_start: 0.4648 (tmtt) cc_final: 0.3944 (tttm) REVERT: E 187 PHE cc_start: 0.5248 (OUTLIER) cc_final: 0.4909 (p90) REVERT: E 263 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.7893 (pt) REVERT: E 276 SER cc_start: 0.8796 (OUTLIER) cc_final: 0.8412 (t) REVERT: F 187 PHE cc_start: 0.6227 (p90) cc_final: 0.5910 (p90) REVERT: F 263 LEU cc_start: 0.8671 (pt) cc_final: 0.7827 (pt) REVERT: F 283 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7728 (mp) REVERT: F 345 TRP cc_start: 0.6963 (OUTLIER) cc_final: 0.5327 (p-90) REVERT: G 187 PHE cc_start: 0.6420 (p90) cc_final: 0.5898 (p90) REVERT: G 263 LEU cc_start: 0.8610 (pt) cc_final: 0.7740 (pt) REVERT: G 276 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8635 (t) REVERT: G 283 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7786 (mp) REVERT: G 329 ILE cc_start: 0.7673 (mm) cc_final: 0.7245 (mm) outliers start: 91 outliers final: 68 residues processed: 353 average time/residue: 0.2780 time to fit residues: 158.9904 Evaluate side-chains 363 residues out of total 2247 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 277 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 255 VAL 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 83 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 319 LEU Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 50 MET 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 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 263 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 223 THR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 245 LYS Chi-restraints excluded: chain F residue 253 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain F residue 268 ILE Chi-restraints excluded: chain F residue 283 LEU Chi-restraints excluded: chain F residue 345 TRP Chi-restraints excluded: chain G residue 39 LYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 232 LEU Chi-restraints excluded: chain G residue 241 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 2.9990 chunk 221 optimal weight: 0.5980 chunk 191 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 224 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.212800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.172021 restraints weight = 239043.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.173839 restraints weight = 129085.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.172490 restraints weight = 114166.425| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19972 Z= 0.156 Angle : 0.756 13.576 27137 Z= 0.350 Chirality : 0.042 0.451 3205 Planarity : 0.004 0.039 3309 Dihedral : 4.239 26.791 2799 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.27 % Favored : 94.39 % Rotamer: Outliers : 4.41 % Allowed : 27.26 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.59 (0.18), residues: 2408 helix: 2.01 (0.12), residues: 1715 sheet: -2.19 (0.52), residues: 70 loop : -1.33 (0.26), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 85 HIS 0.003 0.001 HIS A 231 PHE 0.024 0.002 PHE D 142 TYR 0.014 0.001 TYR G 122 ARG 0.003 0.000 ARG G 153 Details of bonding type rmsd link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 4.22113 ( 21) hydrogen bonds : bond 0.03742 ( 1251) hydrogen bonds : angle 3.69391 ( 3711) SS BOND : bond 0.00848 ( 14) SS BOND : angle 2.07302 ( 28) covalent geometry : bond 0.00364 (19951) covalent geometry : angle 0.74427 (27088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5887.52 seconds wall clock time: 103 minutes 44.63 seconds (6224.63 seconds total)