Starting phenix.real_space_refine on Thu Feb 5 09:43:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lh8_63089/02_2026/9lh8_63089.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lh8_63089/02_2026/9lh8_63089.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lh8_63089/02_2026/9lh8_63089.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lh8_63089/02_2026/9lh8_63089.map" model { file = "/net/cci-nas-00/data/ceres_data/9lh8_63089/02_2026/9lh8_63089.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lh8_63089/02_2026/9lh8_63089.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.067 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 115 5.16 5 C 10539 2.51 5 N 2604 2.21 5 O 2949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16207 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "B" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "C" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "D" Number of atoms: 3192 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 400, 3185 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 1, 'TRP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3263 Chain: "E" Number of atoms: 3177 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3170 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TRP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 400, 3170 Classifications: {'peptide': 400} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 377} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'TRP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 3246 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 26 Unusual residues: {'NAG': 1, 'NCT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.32, per 1000 atoms: 0.39 Number of scatterers: 16207 At special positions: 0 Unit cell: (89.89, 91.91, 170.69, 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 115 16.00 O 2949 8.00 N 2604 7.00 C 10539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 213 " distance=2.06 Simple disulfide: pdb=" SG CYS B 150 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 213 " distance=2.04 Simple disulfide: pdb=" SG CYS C 150 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 213 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 164 " distance=2.03 Simple disulfide: pdb=" SG CYS D 212 " - pdb=" SG CYS D 213 " distance=2.04 Simple disulfide: pdb=" SG CYS E 150 " - pdb=" SG CYS E 164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 212 " - pdb=" SG CYS E 213 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 602 " - " ASN A 46 " " NAG B 602 " - " ASN B 46 " " NAG C 602 " - " ASN C 46 " " NAG D 602 " - " ASN D 46 " " NAG E 601 " - " ASN E 46 " " NAG F 1 " - " ASN A 133 " " NAG G 1 " - " ASN B 133 " " NAG H 1 " - " ASN C 133 " " NAG I 1 " - " ASN D 133 " " NAG J 1 " - " ASN E 133 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 20 sheets defined 43.5% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.691A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.781A pdb=" N CYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 249 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 261 through 283 Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 336 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 431 through 489 Processing helix chain 'A' and resid 492 through 502 Processing helix chain 'B' and resid 24 through 35 removed outlier: 3.778A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 249 removed outlier: 4.771A pdb=" N ILE B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 260 through 281 Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.572A pdb=" N LEU B 343 " --> pdb=" O CYS B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 490 removed outlier: 4.244A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.686A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 248 removed outlier: 4.336A pdb=" N ILE C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 249 through 253 Processing helix chain 'C' and resid 261 through 281 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 338 through 344 Processing helix chain 'C' and resid 431 through 489 Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'D' and resid 24 through 35 removed outlier: 3.574A pdb=" N LYS D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 237 Processing helix chain 'D' and resid 237 through 250 Processing helix chain 'D' and resid 251 through 254 removed outlier: 3.550A pdb=" N LEU D 254 " --> pdb=" O VAL D 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 251 through 254' Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.831A pdb=" N LEU D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 336 Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 431 through 489 Processing helix chain 'D' and resid 492 through 502 Processing helix chain 'E' and resid 24 through 34 removed outlier: 3.632A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 248 removed outlier: 4.547A pdb=" N ILE E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 249 through 253 Processing helix chain 'E' and resid 260 through 281 Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 336 Processing helix chain 'E' and resid 337 through 344 Processing helix chain 'E' and resid 431 through 489 removed outlier: 4.091A pdb=" N LYS E 435 " --> pdb=" O PRO E 431 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 480 " --> pdb=" O SER E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.859A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.936A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.624A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU A 51 " --> pdb=" O ASP A 179 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLN A 181 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 53 " --> pdb=" O GLN A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.547A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR A 225 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.547A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLU A 215 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR A 210 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASP B 64 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 73 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ILE B 62 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN B 75 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 83 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR B 52 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.541A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR B 225 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.541A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG B 208 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 7.035A pdb=" N VAL C 71 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 64 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN C 75 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N THR C 83 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N THR C 52 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL C 53 " --> pdb=" O GLN C 181 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.522A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR C 225 " --> pdb=" O VAL C 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.522A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLU C 215 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N TYR C 210 " --> pdb=" O GLU C 215 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.766A pdb=" N VAL D 71 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASP D 64 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR D 73 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE D 62 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN D 75 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR D 83 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR D 52 " --> pdb=" O THR D 83 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU D 51 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N GLN D 181 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 53 " --> pdb=" O GLN D 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.682A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.682A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 6.749A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 5.169A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 5.169A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) 967 hydrogen bonds defined for protein. 2808 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: 2.24 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 2569 1.32 - 1.45: 4668 1.45 - 1.58: 9235 1.58 - 1.71: 8 1.71 - 1.85: 170 Bond restraints: 16650 Sorted by residual: bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.44e+01 bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.40e+01 bond pdb=" C6 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.623 -0.171 2.00e-02 2.50e+03 7.34e+01 bond pdb=" C6 NCT D 601 " pdb=" C7 NCT D 601 " ideal model delta sigma weight residual 1.536 1.368 0.168 2.00e-02 2.50e+03 7.07e+01 ... (remaining 16645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 22181 2.15 - 4.31: 405 4.31 - 6.46: 105 6.46 - 8.61: 15 8.61 - 10.77: 9 Bond angle restraints: 22715 Sorted by residual: angle pdb=" CA GLU A 452 " pdb=" CB GLU A 452 " pdb=" CG GLU A 452 " ideal model delta sigma weight residual 114.10 121.82 -7.72 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CA GLU B 454 " pdb=" CB GLU B 454 " pdb=" CG GLU B 454 " ideal model delta sigma weight residual 114.10 121.76 -7.66 2.00e+00 2.50e-01 1.47e+01 angle pdb=" CA PRO B 348 " pdb=" N PRO B 348 " pdb=" CD PRO B 348 " ideal model delta sigma weight residual 112.00 106.76 5.24 1.40e+00 5.10e-01 1.40e+01 angle pdb=" CA GLU A 454 " pdb=" CB GLU A 454 " pdb=" CG GLU A 454 " ideal model delta sigma weight residual 114.10 121.37 -7.27 2.00e+00 2.50e-01 1.32e+01 angle pdb=" CB MET B 276 " pdb=" CG MET B 276 " pdb=" SD MET B 276 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 ... (remaining 22710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.64: 9173 22.64 - 45.27: 722 45.27 - 67.91: 108 67.91 - 90.55: 31 90.55 - 113.18: 16 Dihedral angle restraints: 10050 sinusoidal: 4155 harmonic: 5895 Sorted by residual: dihedral pdb=" CA CYS D 212 " pdb=" C CYS D 212 " pdb=" N CYS D 213 " pdb=" CA CYS D 213 " ideal model delta harmonic sigma weight residual -180.00 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA CYS A 212 " pdb=" C CYS A 212 " pdb=" N CYS A 213 " pdb=" CA CYS A 213 " ideal model delta harmonic sigma weight residual -180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA CYS B 212 " pdb=" C CYS B 212 " pdb=" N CYS B 213 " pdb=" CA CYS B 213 " ideal model delta harmonic sigma weight residual -180.00 -155.59 -24.41 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 10047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2308 0.065 - 0.130: 263 0.130 - 0.195: 29 0.195 - 0.260: 2 0.260 - 0.325: 2 Chirality restraints: 2604 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 133 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN D 133 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2601 not shown) Planarity restraints: 2842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 347 " 0.099 5.00e-02 4.00e+02 1.48e-01 3.51e+01 pdb=" N PRO B 348 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO B 348 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO B 348 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 191 " 0.051 5.00e-02 4.00e+02 7.74e-02 9.60e+00 pdb=" N PRO E 192 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO E 192 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 192 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 327 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO D 328 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " 0.040 5.00e-02 4.00e+02 ... (remaining 2839 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2422 2.76 - 3.29: 14797 3.29 - 3.83: 26923 3.83 - 4.36: 30641 4.36 - 4.90: 53980 Nonbonded interactions: 128763 Sorted by model distance: nonbonded pdb=" OG SER E 206 " pdb=" OD1 ASP E 219 " model vdw 2.221 3.040 nonbonded pdb=" OG1 THR D 230 " pdb=" OD2 ASP D 500 " model vdw 2.244 3.040 nonbonded pdb=" O SER C 263 " pdb=" OG1 THR C 267 " model vdw 2.261 3.040 nonbonded pdb=" OG SER B 206 " pdb=" OD1 ASP B 219 " model vdw 2.263 3.040 nonbonded pdb=" OG SER E 117 " pdb=" OD1 ASP E 119 " model vdw 2.278 3.040 ... (remaining 128758 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 23 through 136 or resid 138 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 346 or \ (resid 347 and (name N or name CA or name C or name O or name CB )) or resid 34 \ 8 through 502)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 502)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 17.270 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 0.008 0.173 16675 Z= 0.399 Angle : 0.745 12.552 22780 Z= 0.342 Chirality : 0.044 0.325 2604 Planarity : 0.006 0.148 2832 Dihedral : 16.939 113.182 6210 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.17 % Allowed : 14.58 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.19), residues: 1985 helix: 2.19 (0.18), residues: 822 sheet: 0.94 (0.25), residues: 434 loop : -0.26 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 347 TYR 0.024 0.001 TYR E 296 PHE 0.020 0.001 PHE B 342 TRP 0.017 0.001 TRP C 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00814 (16650) covalent geometry : angle 0.72855 (22715) SS BOND : bond 0.01201 ( 10) SS BOND : angle 1.91140 ( 20) hydrogen bonds : bond 0.08081 ( 867) hydrogen bonds : angle 4.69510 ( 2808) link_BETA1-4 : bond 0.00213 ( 5) link_BETA1-4 : angle 0.77950 ( 15) link_NAG-ASN : bond 0.00286 ( 10) link_NAG-ASN : angle 4.04811 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.610 Fit side-chains revert: symmetry clash REVERT: B 482 CYS cc_start: 0.8509 (t) cc_final: 0.8298 (t) REVERT: D 471 CYS cc_start: 0.8740 (m) cc_final: 0.8494 (m) outliers start: 3 outliers final: 3 residues processed: 202 average time/residue: 0.4423 time to fit residues: 100.5115 Evaluate side-chains 188 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN C 137 HIS A D 137 HIS B Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.081340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.063327 restraints weight = 74498.502| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.13 r_work: 0.2617 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16675 Z= 0.146 Angle : 0.640 12.037 22780 Z= 0.304 Chirality : 0.044 0.522 2604 Planarity : 0.005 0.119 2832 Dihedral : 10.022 71.933 2537 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.33 % Allowed : 13.95 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 1985 helix: 2.28 (0.17), residues: 830 sheet: 0.98 (0.25), residues: 434 loop : -0.19 (0.22), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 347 TYR 0.008 0.001 TYR B 296 PHE 0.017 0.001 PHE B 342 TRP 0.013 0.001 TRP C 176 HIS 0.003 0.001 HIS C 127 Details of bonding type rmsd covalent geometry : bond 0.00331 (16650) covalent geometry : angle 0.61403 (22715) SS BOND : bond 0.00809 ( 10) SS BOND : angle 2.27198 ( 20) hydrogen bonds : bond 0.05348 ( 867) hydrogen bonds : angle 4.25252 ( 2808) link_BETA1-4 : bond 0.00427 ( 5) link_BETA1-4 : angle 1.87023 ( 15) link_NAG-ASN : bond 0.00380 ( 10) link_NAG-ASN : angle 4.52708 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9131 (pt0) cc_final: 0.8581 (pp20) REVERT: A 237 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8175 (tt) REVERT: A 275 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 451 ASP cc_start: 0.8683 (m-30) cc_final: 0.8414 (m-30) REVERT: B 276 MET cc_start: 0.8719 (ttt) cc_final: 0.7747 (tmm) REVERT: B 296 TYR cc_start: 0.8214 (t80) cc_final: 0.7659 (t80) REVERT: B 317 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7664 (t80) REVERT: C 119 ASP cc_start: 0.8375 (t70) cc_final: 0.8058 (t70) REVERT: C 197 ASP cc_start: 0.8717 (t70) cc_final: 0.8307 (t0) REVERT: C 275 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7636 (t80) REVERT: C 277 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8702 (mm) REVERT: D 471 CYS cc_start: 0.8817 (m) cc_final: 0.8559 (m) REVERT: E 120 GLU cc_start: 0.9143 (mp0) cc_final: 0.8934 (mp0) REVERT: E 276 MET cc_start: 0.8974 (ttt) cc_final: 0.8287 (tmm) outliers start: 41 outliers final: 16 residues processed: 213 average time/residue: 0.4287 time to fit residues: 103.6787 Evaluate side-chains 212 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 273 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 473 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 151 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.0970 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 = 0.3147 r_free = 0.3147 target = 0.081138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.063303 restraints weight = 74457.227| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.09 r_work: 0.2614 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.0755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16675 Z= 0.146 Angle : 0.630 12.502 22780 Z= 0.299 Chirality : 0.044 0.516 2604 Planarity : 0.004 0.093 2832 Dihedral : 7.650 63.058 2531 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.99 % Allowed : 14.63 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.19), residues: 1985 helix: 2.39 (0.17), residues: 829 sheet: 1.01 (0.25), residues: 434 loop : -0.17 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 347 TYR 0.021 0.001 TYR E 296 PHE 0.015 0.001 PHE B 342 TRP 0.011 0.001 TRP C 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00334 (16650) covalent geometry : angle 0.60308 (22715) SS BOND : bond 0.00814 ( 10) SS BOND : angle 2.22707 ( 20) hydrogen bonds : bond 0.05354 ( 867) hydrogen bonds : angle 4.18376 ( 2808) link_BETA1-4 : bond 0.00311 ( 5) link_BETA1-4 : angle 1.87617 ( 15) link_NAG-ASN : bond 0.00308 ( 10) link_NAG-ASN : angle 4.60935 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9168 (pt0) cc_final: 0.8626 (pp20) REVERT: A 275 PHE cc_start: 0.8833 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 275 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8243 (t80) REVERT: B 276 MET cc_start: 0.8676 (ttt) cc_final: 0.7732 (tmm) REVERT: B 296 TYR cc_start: 0.8181 (t80) cc_final: 0.7352 (t80) REVERT: B 317 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.7624 (t80) REVERT: C 119 ASP cc_start: 0.8470 (t70) cc_final: 0.8159 (t70) REVERT: C 197 ASP cc_start: 0.8685 (t70) cc_final: 0.8258 (t0) REVERT: C 275 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7699 (t80) REVERT: D 471 CYS cc_start: 0.8840 (m) cc_final: 0.8565 (m) REVERT: E 243 LEU cc_start: 0.8737 (mt) cc_final: 0.8508 (mm) REVERT: E 276 MET cc_start: 0.8997 (ttt) cc_final: 0.8296 (tmm) outliers start: 35 outliers final: 18 residues processed: 212 average time/residue: 0.4548 time to fit residues: 110.1070 Evaluate side-chains 216 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 172 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 48 optimal weight: 0.0170 chunk 136 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 overall best weight: 0.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS B Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.082192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.064688 restraints weight = 59813.038| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.72 r_work: 0.2661 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16675 Z= 0.118 Angle : 0.608 12.168 22780 Z= 0.289 Chirality : 0.043 0.515 2604 Planarity : 0.004 0.087 2832 Dihedral : 6.465 56.639 2531 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.87 % Allowed : 15.09 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.19), residues: 1985 helix: 2.44 (0.17), residues: 829 sheet: 1.04 (0.25), residues: 434 loop : -0.16 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 208 TYR 0.023 0.001 TYR E 296 PHE 0.011 0.001 PHE D 157 TRP 0.009 0.001 TRP C 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00259 (16650) covalent geometry : angle 0.58007 (22715) SS BOND : bond 0.00812 ( 10) SS BOND : angle 2.20813 ( 20) hydrogen bonds : bond 0.05006 ( 867) hydrogen bonds : angle 4.08897 ( 2808) link_BETA1-4 : bond 0.00408 ( 5) link_BETA1-4 : angle 2.08446 ( 15) link_NAG-ASN : bond 0.00348 ( 10) link_NAG-ASN : angle 4.55788 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9148 (pt0) cc_final: 0.8593 (pp20) REVERT: A 235 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 237 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 275 PHE cc_start: 0.8810 (OUTLIER) cc_final: 0.8099 (t80) REVERT: B 120 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8900 (mm-30) REVERT: B 197 ASP cc_start: 0.8858 (t0) cc_final: 0.8634 (t0) REVERT: B 275 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.8294 (t80) REVERT: B 276 MET cc_start: 0.8675 (ttt) cc_final: 0.7773 (tmm) REVERT: B 296 TYR cc_start: 0.8097 (t80) cc_final: 0.7180 (t80) REVERT: B 317 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.7591 (t80) REVERT: C 119 ASP cc_start: 0.8455 (t70) cc_final: 0.8174 (t70) REVERT: C 197 ASP cc_start: 0.8597 (t70) cc_final: 0.8236 (t0) REVERT: C 275 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7660 (t80) REVERT: D 471 CYS cc_start: 0.8859 (m) cc_final: 0.8576 (m) REVERT: E 276 MET cc_start: 0.8948 (ttt) cc_final: 0.8286 (tmm) outliers start: 33 outliers final: 17 residues processed: 221 average time/residue: 0.4263 time to fit residues: 107.5201 Evaluate side-chains 225 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 277 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 124 optimal weight: 0.0070 chunk 187 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 chunk 194 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** 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 = 0.3208 r_free = 0.3208 target = 0.085703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.068100 restraints weight = 73871.385| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.16 r_work: 0.2691 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 16675 Z= 0.110 Angle : 0.598 11.779 22780 Z= 0.282 Chirality : 0.043 0.498 2604 Planarity : 0.004 0.078 2832 Dihedral : 5.774 46.892 2531 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.47 % Allowed : 15.94 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.89 (0.19), residues: 1985 helix: 2.52 (0.17), residues: 835 sheet: 1.05 (0.25), residues: 442 loop : -0.14 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 208 TYR 0.025 0.001 TYR E 296 PHE 0.013 0.001 PHE D 157 TRP 0.009 0.001 TRP C 176 HIS 0.003 0.000 HIS C 163 Details of bonding type rmsd covalent geometry : bond 0.00238 (16650) covalent geometry : angle 0.56910 (22715) SS BOND : bond 0.00825 ( 10) SS BOND : angle 2.20819 ( 20) hydrogen bonds : bond 0.04487 ( 867) hydrogen bonds : angle 3.91417 ( 2808) link_BETA1-4 : bond 0.00455 ( 5) link_BETA1-4 : angle 2.36683 ( 15) link_NAG-ASN : bond 0.00412 ( 10) link_NAG-ASN : angle 4.48202 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9125 (pt0) cc_final: 0.8589 (pp20) REVERT: A 237 LEU cc_start: 0.8917 (tp) cc_final: 0.8659 (mp) REVERT: A 260 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: A 275 PHE cc_start: 0.8688 (OUTLIER) cc_final: 0.8088 (t80) REVERT: B 120 GLU cc_start: 0.9187 (mt-10) cc_final: 0.8897 (mm-30) REVERT: B 197 ASP cc_start: 0.8828 (t0) cc_final: 0.8612 (t0) REVERT: B 276 MET cc_start: 0.8636 (ttt) cc_final: 0.7626 (tmm) REVERT: B 296 TYR cc_start: 0.7946 (t80) cc_final: 0.6997 (t80) REVERT: B 317 TYR cc_start: 0.8740 (OUTLIER) cc_final: 0.7533 (t80) REVERT: C 119 ASP cc_start: 0.8396 (t70) cc_final: 0.8181 (t70) REVERT: C 197 ASP cc_start: 0.8570 (t70) cc_final: 0.8220 (t0) REVERT: C 275 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7462 (t80) REVERT: D 471 CYS cc_start: 0.8885 (m) cc_final: 0.8626 (m) REVERT: E 276 MET cc_start: 0.8894 (ttt) cc_final: 0.8200 (tmm) outliers start: 26 outliers final: 13 residues processed: 238 average time/residue: 0.3992 time to fit residues: 109.1448 Evaluate side-chains 223 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 206 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 260 GLU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 58 optimal weight: 0.0170 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 161 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 overall best weight: 3.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.080079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.062648 restraints weight = 61719.074| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.79 r_work: 0.2582 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16675 Z= 0.229 Angle : 0.676 13.205 22780 Z= 0.328 Chirality : 0.046 0.589 2604 Planarity : 0.004 0.075 2832 Dihedral : 5.659 33.698 2531 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.16 % Allowed : 16.17 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.19), residues: 1985 helix: 2.39 (0.17), residues: 829 sheet: 1.04 (0.25), residues: 439 loop : -0.06 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 347 TYR 0.019 0.001 TYR E 296 PHE 0.015 0.001 PHE D 157 TRP 0.015 0.001 TRP C 176 HIS 0.005 0.001 HIS D 318 Details of bonding type rmsd covalent geometry : bond 0.00538 (16650) covalent geometry : angle 0.64625 (22715) SS BOND : bond 0.00808 ( 10) SS BOND : angle 2.22449 ( 20) hydrogen bonds : bond 0.05922 ( 867) hydrogen bonds : angle 4.29535 ( 2808) link_BETA1-4 : bond 0.00346 ( 5) link_BETA1-4 : angle 2.24875 ( 15) link_NAG-ASN : bond 0.00555 ( 10) link_NAG-ASN : angle 5.04083 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.593 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9193 (pt0) cc_final: 0.8646 (pp20) REVERT: A 237 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8795 (mp) REVERT: A 275 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 347 ARG cc_start: 0.7162 (tmm160) cc_final: 0.6852 (tmm-80) REVERT: B 120 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8957 (mm-30) REVERT: B 296 TYR cc_start: 0.8204 (t80) cc_final: 0.6986 (t80) REVERT: B 317 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8188 (t80) REVERT: B 347 ARG cc_start: 0.8828 (mmm160) cc_final: 0.8552 (mmm-85) REVERT: C 119 ASP cc_start: 0.8478 (t70) cc_final: 0.8152 (t70) REVERT: C 197 ASP cc_start: 0.8660 (t70) cc_final: 0.8261 (t0) REVERT: C 275 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7655 (t80) REVERT: C 473 MET cc_start: 0.8685 (tpp) cc_final: 0.8441 (mmt) REVERT: E 276 MET cc_start: 0.8966 (ttt) cc_final: 0.8278 (tmm) outliers start: 38 outliers final: 17 residues processed: 207 average time/residue: 0.4584 time to fit residues: 107.4760 Evaluate side-chains 206 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 301 MET Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 23 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 185 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 2.0184 ------------------------------------------------------------------------------- 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 = 0.3122 r_free = 0.3122 target = 0.081166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.063745 restraints weight = 63745.372| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.85 r_work: 0.2622 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16675 Z= 0.157 Angle : 0.647 13.254 22780 Z= 0.309 Chirality : 0.045 0.563 2604 Planarity : 0.004 0.070 2832 Dihedral : 5.549 32.129 2531 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.99 % Allowed : 16.56 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.19), residues: 1985 helix: 2.44 (0.17), residues: 829 sheet: 1.02 (0.25), residues: 434 loop : -0.08 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 347 TYR 0.020 0.001 TYR E 296 PHE 0.014 0.001 PHE B 342 TRP 0.013 0.001 TRP C 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00363 (16650) covalent geometry : angle 0.61575 (22715) SS BOND : bond 0.00801 ( 10) SS BOND : angle 2.24661 ( 20) hydrogen bonds : bond 0.05590 ( 867) hydrogen bonds : angle 4.21123 ( 2808) link_BETA1-4 : bond 0.00321 ( 5) link_BETA1-4 : angle 2.00061 ( 15) link_NAG-ASN : bond 0.00318 ( 10) link_NAG-ASN : angle 5.04035 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9196 (pt0) cc_final: 0.8652 (pp20) REVERT: A 235 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8692 (mp) REVERT: A 237 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8812 (mp) REVERT: A 275 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8188 (t80) REVERT: A 347 ARG cc_start: 0.7218 (tmm160) cc_final: 0.6905 (tmm-80) REVERT: B 120 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8945 (mm-30) REVERT: B 275 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.8288 (t80) REVERT: B 296 TYR cc_start: 0.8193 (t80) cc_final: 0.6997 (t80) REVERT: B 317 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8043 (t80) REVERT: C 119 ASP cc_start: 0.8436 (t70) cc_final: 0.8102 (t70) REVERT: C 197 ASP cc_start: 0.8636 (t70) cc_final: 0.8249 (t0) REVERT: C 275 PHE cc_start: 0.8599 (OUTLIER) cc_final: 0.7584 (t80) REVERT: C 473 MET cc_start: 0.8592 (tpp) cc_final: 0.8370 (mmt) REVERT: D 120 GLU cc_start: 0.8854 (pt0) cc_final: 0.8551 (pm20) REVERT: D 471 CYS cc_start: 0.8837 (m) cc_final: 0.8554 (m) REVERT: E 276 MET cc_start: 0.8980 (ttt) cc_final: 0.8264 (tmm) REVERT: E 281 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8253 (mt-10) outliers start: 35 outliers final: 21 residues processed: 208 average time/residue: 0.4527 time to fit residues: 107.2577 Evaluate side-chains 214 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 129 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 chunk 81 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.081816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.064188 restraints weight = 69727.377| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 4.04 r_work: 0.2628 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16675 Z= 0.135 Angle : 0.628 13.134 22780 Z= 0.303 Chirality : 0.045 0.552 2604 Planarity : 0.004 0.069 2832 Dihedral : 5.458 32.082 2531 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.76 % Allowed : 17.13 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.19), residues: 1985 helix: 2.46 (0.17), residues: 829 sheet: 1.04 (0.25), residues: 434 loop : -0.07 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 347 TYR 0.022 0.001 TYR E 296 PHE 0.010 0.001 PHE D 157 TRP 0.011 0.001 TRP C 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00307 (16650) covalent geometry : angle 0.59662 (22715) SS BOND : bond 0.00803 ( 10) SS BOND : angle 2.22893 ( 20) hydrogen bonds : bond 0.05336 ( 867) hydrogen bonds : angle 4.15942 ( 2808) link_BETA1-4 : bond 0.00367 ( 5) link_BETA1-4 : angle 1.95572 ( 15) link_NAG-ASN : bond 0.00306 ( 10) link_NAG-ASN : angle 4.98873 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9177 (pt0) cc_final: 0.8614 (pp20) REVERT: A 237 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8821 (mp) REVERT: A 275 PHE cc_start: 0.8821 (OUTLIER) cc_final: 0.8164 (t80) REVERT: A 347 ARG cc_start: 0.7267 (tmm160) cc_final: 0.6928 (tmm-80) REVERT: B 120 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8921 (mm-30) REVERT: B 197 ASP cc_start: 0.8834 (t0) cc_final: 0.8579 (t0) REVERT: B 275 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8266 (t80) REVERT: B 296 TYR cc_start: 0.8202 (t80) cc_final: 0.7104 (t80) REVERT: B 317 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7938 (t80) REVERT: C 119 ASP cc_start: 0.8442 (t70) cc_final: 0.8087 (t70) REVERT: C 197 ASP cc_start: 0.8626 (t70) cc_final: 0.8262 (t0) REVERT: C 275 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7548 (t80) REVERT: C 473 MET cc_start: 0.8548 (tpp) cc_final: 0.8321 (mmt) REVERT: D 120 GLU cc_start: 0.8834 (pt0) cc_final: 0.8533 (pm20) REVERT: D 471 CYS cc_start: 0.8814 (m) cc_final: 0.8540 (m) REVERT: E 276 MET cc_start: 0.8914 (ttt) cc_final: 0.8204 (tmm) outliers start: 31 outliers final: 22 residues processed: 207 average time/residue: 0.4159 time to fit residues: 98.0339 Evaluate side-chains 216 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 121 ARG Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 4 optimal weight: 0.0040 chunk 14 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 110 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- 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 = 0.3145 r_free = 0.3145 target = 0.082573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.064840 restraints weight = 70049.731| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 4.06 r_work: 0.2617 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16675 Z= 0.126 Angle : 0.635 12.990 22780 Z= 0.303 Chirality : 0.044 0.542 2604 Planarity : 0.004 0.068 2832 Dihedral : 5.381 31.997 2531 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.76 % Allowed : 17.13 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.19), residues: 1985 helix: 2.47 (0.17), residues: 829 sheet: 1.08 (0.25), residues: 434 loop : -0.06 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 347 TYR 0.023 0.001 TYR E 296 PHE 0.010 0.001 PHE D 157 TRP 0.010 0.001 TRP C 176 HIS 0.003 0.000 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00285 (16650) covalent geometry : angle 0.60430 (22715) SS BOND : bond 0.00803 ( 10) SS BOND : angle 2.22156 ( 20) hydrogen bonds : bond 0.05130 ( 867) hydrogen bonds : angle 4.10385 ( 2808) link_BETA1-4 : bond 0.00341 ( 5) link_BETA1-4 : angle 1.95929 ( 15) link_NAG-ASN : bond 0.00333 ( 10) link_NAG-ASN : angle 4.92915 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9180 (pt0) cc_final: 0.8602 (pp20) REVERT: A 237 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8847 (mp) REVERT: A 275 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.8133 (t80) REVERT: A 347 ARG cc_start: 0.7269 (tmm160) cc_final: 0.6926 (tmm-80) REVERT: B 120 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8934 (mm-30) REVERT: B 197 ASP cc_start: 0.8828 (t0) cc_final: 0.8586 (t0) REVERT: B 296 TYR cc_start: 0.8233 (t80) cc_final: 0.7202 (t80) REVERT: B 317 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7842 (t80) REVERT: C 119 ASP cc_start: 0.8513 (t70) cc_final: 0.8177 (t70) REVERT: C 197 ASP cc_start: 0.8644 (t70) cc_final: 0.8307 (t0) REVERT: C 275 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7552 (t80) REVERT: D 120 GLU cc_start: 0.8841 (pt0) cc_final: 0.8553 (pm20) REVERT: D 471 CYS cc_start: 0.8892 (m) cc_final: 0.8633 (m) REVERT: E 276 MET cc_start: 0.8943 (ttt) cc_final: 0.8249 (tmm) REVERT: E 281 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8186 (mt-10) outliers start: 31 outliers final: 22 residues processed: 211 average time/residue: 0.3975 time to fit residues: 95.9881 Evaluate side-chains 223 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 481 ILE Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 317 TYR Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 155 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 180 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.084112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066284 restraints weight = 71966.345| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 4.16 r_work: 0.2657 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16675 Z= 0.119 Angle : 0.627 12.638 22780 Z= 0.298 Chirality : 0.044 0.521 2604 Planarity : 0.004 0.068 2832 Dihedral : 5.201 31.720 2531 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.42 % Allowed : 17.53 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.19), residues: 1985 helix: 2.53 (0.17), residues: 829 sheet: 1.03 (0.25), residues: 452 loop : -0.04 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 347 TYR 0.024 0.001 TYR E 296 PHE 0.011 0.001 PHE B 342 TRP 0.009 0.001 TRP C 176 HIS 0.003 0.000 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00269 (16650) covalent geometry : angle 0.59784 (22715) SS BOND : bond 0.00813 ( 10) SS BOND : angle 2.22930 ( 20) hydrogen bonds : bond 0.04728 ( 867) hydrogen bonds : angle 4.02447 ( 2808) link_BETA1-4 : bond 0.00356 ( 5) link_BETA1-4 : angle 1.94212 ( 15) link_NAG-ASN : bond 0.00358 ( 10) link_NAG-ASN : angle 4.78466 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3970 Ramachandran restraints generated. 1985 Oldfield, 0 Emsley, 1985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.9141 (pt0) cc_final: 0.8578 (pp20) REVERT: A 347 ARG cc_start: 0.7231 (tmm160) cc_final: 0.6892 (tmm-80) REVERT: B 120 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8927 (mm-30) REVERT: B 197 ASP cc_start: 0.8795 (t0) cc_final: 0.8523 (t0) REVERT: B 296 TYR cc_start: 0.8094 (t80) cc_final: 0.7323 (t80) REVERT: B 317 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 119 ASP cc_start: 0.8441 (t70) cc_final: 0.8119 (t70) REVERT: C 197 ASP cc_start: 0.8572 (t70) cc_final: 0.8250 (t0) REVERT: C 275 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.7606 (t80) REVERT: D 120 GLU cc_start: 0.8825 (pt0) cc_final: 0.8538 (pm20) REVERT: D 276 MET cc_start: 0.8133 (mtp) cc_final: 0.7667 (mtp) REVERT: D 471 CYS cc_start: 0.8843 (m) cc_final: 0.8634 (m) REVERT: E 276 MET cc_start: 0.8903 (ttt) cc_final: 0.8182 (tmm) outliers start: 25 outliers final: 21 residues processed: 222 average time/residue: 0.3673 time to fit residues: 93.2050 Evaluate side-chains 219 residues out of total 1790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 226 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 317 TYR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 481 ILE Chi-restraints excluded: chain B residue 482 CYS Chi-restraints excluded: chain B residue 487 LEU Chi-restraints excluded: chain C residue 274 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 TYR Chi-restraints excluded: chain C residue 302 ILE Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain E residue 317 TYR Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 165 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3156 r_free = 0.3156 target = 0.083178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.065709 restraints weight = 61523.076| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 3.82 r_work: 0.2652 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16675 Z= 0.145 Angle : 0.639 12.819 22780 Z= 0.305 Chirality : 0.045 0.529 2604 Planarity : 0.004 0.067 2832 Dihedral : 5.198 30.480 2531 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.36 % Allowed : 17.92 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.90 (0.19), residues: 1985 helix: 2.46 (0.17), residues: 835 sheet: 1.04 (0.25), residues: 442 loop : -0.02 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 347 TYR 0.023 0.001 TYR E 296 PHE 0.011 0.001 PHE D 157 TRP 0.010 0.001 TRP C 176 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd covalent geometry : bond 0.00339 (16650) covalent geometry : angle 0.60940 (22715) SS BOND : bond 0.00804 ( 10) SS BOND : angle 2.22001 ( 20) hydrogen bonds : bond 0.04874 ( 867) hydrogen bonds : angle 4.08536 ( 2808) link_BETA1-4 : bond 0.00273 ( 5) link_BETA1-4 : angle 1.89708 ( 15) link_NAG-ASN : bond 0.00277 ( 10) link_NAG-ASN : angle 4.86280 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4683.32 seconds wall clock time: 80 minutes 31.11 seconds (4831.11 seconds total)