Starting phenix.real_space_refine on Thu Feb 5 09:58:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vix_65097/02_2026/9vix_65097.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vix_65097/02_2026/9vix_65097.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vix_65097/02_2026/9vix_65097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vix_65097/02_2026/9vix_65097.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vix_65097/02_2026/9vix_65097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vix_65097/02_2026/9vix_65097.map" } resolution = 3.06 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= 0.009 sd= 0.078 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 10545 2.51 5 N 2610 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s 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: 16220 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3182 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, 3182 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: 3260 Chain: "B" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3182 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, 3182 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: 3260 Chain: "C" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3182 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, 3182 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: 3260 Chain: "D" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3182 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, 3182 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: 3260 Chain: "E" Number of atoms: 3189 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3182 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, 3182 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: 3260 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: 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 6.01, per 1000 atoms: 0.37 Number of scatterers: 16220 At special positions: 0 Unit cell: (89.88, 92.02, 166.92, 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 2950 8.00 N 2610 7.00 C 10545 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=2.04 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 602 " - " 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: 1.23 Conformation dependent library (CDL) restraints added in 1.3 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: 49 helices and 21 sheets defined 44.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.658A pdb=" N LYS A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 249 removed outlier: 3.672A pdb=" N CYS A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 260 through 281 Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.931A pdb=" N GLY A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 4.893A pdb=" N CYS A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 490 removed outlier: 3.874A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'B' and resid 24 through 35 removed outlier: 3.657A pdb=" N LYS B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 removed outlier: 3.551A pdb=" N CYS B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) 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 321 through 325 removed outlier: 3.774A pdb=" N GLY B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 4.922A pdb=" N CYS B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 490 removed outlier: 3.844A 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 35 removed outlier: 3.639A pdb=" N LYS C 35 " --> pdb=" O LYS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 249 removed outlier: 3.548A pdb=" N CYS C 241 " --> pdb=" O LEU C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 260 through 281 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 321 through 325 removed outlier: 3.841A pdb=" N GLY C 325 " --> pdb=" O PRO C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 344 removed outlier: 4.876A pdb=" N CYS C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 490 removed outlier: 3.836A pdb=" N ALA C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 501 Processing helix chain 'D' and resid 24 through 35 removed outlier: 3.668A 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 249 removed outlier: 3.737A pdb=" N CYS D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 260 through 281 Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 321 through 325 removed outlier: 3.958A pdb=" N GLY D 325 " --> pdb=" O PRO D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 344 removed outlier: 4.986A pdb=" N CYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ALA D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 490 removed outlier: 3.873A pdb=" N ALA D 490 " --> pdb=" O ILE D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'E' and resid 24 through 35 removed outlier: 3.693A pdb=" N LYS E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 249 Processing helix chain 'E' and resid 250 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 344 removed outlier: 4.849A pdb=" N CYS E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 490 removed outlier: 3.885A pdb=" N ALA E 490 " --> pdb=" O ILE E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.564A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.564A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N THR A 83 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 9.606A pdb=" N TYR A 54 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.384A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.839A 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: 4.384A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.518A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.518A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLN B 79 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N SER B 58 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N SER B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N SER B 56 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N THR B 83 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 9.620A pdb=" N TYR B 54 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.330A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.902A 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: 4.330A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 3.600A 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: 6.922A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN C 79 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N SER C 58 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER C 81 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N SER C 56 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N THR C 83 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N TYR C 54 " --> pdb=" O THR C 83 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU C 51 " --> pdb=" O ASP C 179 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN C 181 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.260A 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: 4.437A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.912A 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: 4.437A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 140 Processing sheet with id=AB5, first strand: chain 'D' and resid 137 through 140 removed outlier: 6.911A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.846A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N GLN D 79 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER D 58 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N SER D 81 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N SER D 56 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N THR D 83 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N TYR D 54 " --> pdb=" O THR D 83 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.531A pdb=" N VAL D 100 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.354A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.354A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 208 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.516A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.516A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 9.118A pdb=" N THR E 83 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N TYR E 54 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.407A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.407A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) 962 hydrogen bonds defined for protein. 2796 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: 2.89 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2570 1.31 - 1.44: 4656 1.44 - 1.57: 9259 1.57 - 1.70: 10 1.70 - 1.83: 170 Bond restraints: 16665 Sorted by residual: 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 7.46e+01 bond pdb=" C6 NCT A 601 " pdb=" N2 NCT A 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 B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C6 NCT E 601 " pdb=" N2 NCT E 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.35e+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 7.28e+01 ... (remaining 16660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 21846 1.54 - 3.09: 659 3.09 - 4.63: 135 4.63 - 6.17: 80 6.17 - 7.72: 15 Bond angle restraints: 22735 Sorted by residual: angle pdb=" CA GLU E 32 " pdb=" CB GLU E 32 " pdb=" CG GLU E 32 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CA GLU C 32 " pdb=" CB GLU C 32 " pdb=" CG GLU C 32 " ideal model delta sigma weight residual 114.10 120.35 -6.25 2.00e+00 2.50e-01 9.77e+00 angle pdb=" CA GLU B 32 " pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " ideal model delta sigma weight residual 114.10 119.89 -5.79 2.00e+00 2.50e-01 8.38e+00 angle pdb=" CG ARG B 441 " pdb=" CD ARG B 441 " pdb=" NE ARG B 441 " ideal model delta sigma weight residual 112.00 118.18 -6.18 2.20e+00 2.07e-01 7.88e+00 angle pdb=" CB GLU E 32 " pdb=" CG GLU E 32 " pdb=" CD GLU E 32 " ideal model delta sigma weight residual 112.60 116.93 -4.33 1.70e+00 3.46e-01 6.50e+00 ... (remaining 22730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.73: 8907 18.73 - 37.46: 859 37.46 - 56.19: 181 56.19 - 74.91: 83 74.91 - 93.64: 30 Dihedral angle restraints: 10060 sinusoidal: 4165 harmonic: 5895 Sorted by residual: dihedral pdb=" CB CYS C 150 " pdb=" SG CYS C 150 " pdb=" SG CYS C 164 " pdb=" CB CYS C 164 " ideal model delta sinusoidal sigma weight residual 93.00 41.76 51.24 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CB CYS E 150 " pdb=" SG CYS E 150 " pdb=" SG CYS E 164 " pdb=" CB CYS E 164 " ideal model delta sinusoidal sigma weight residual 93.00 42.10 50.90 1 1.00e+01 1.00e-02 3.54e+01 dihedral pdb=" CB CYS A 150 " pdb=" SG CYS A 150 " pdb=" SG CYS A 164 " pdb=" CB CYS A 164 " ideal model delta sinusoidal sigma weight residual 93.00 42.50 50.50 1 1.00e+01 1.00e-02 3.49e+01 ... (remaining 10057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2174 0.055 - 0.111: 384 0.111 - 0.166: 24 0.166 - 0.222: 11 0.222 - 0.277: 7 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CB ILE B 334 " pdb=" CA ILE B 334 " pdb=" CG1 ILE B 334 " pdb=" CG2 ILE B 334 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE A 334 " pdb=" CA ILE A 334 " pdb=" CG1 ILE A 334 " pdb=" CG2 ILE A 334 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CB ILE C 334 " pdb=" CA ILE C 334 " pdb=" CG1 ILE C 334 " pdb=" CG2 ILE C 334 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 2597 not shown) Planarity restraints: 2845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 157 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO D 158 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 158 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 158 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 191 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO D 192 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 192 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 192 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 334 " -0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ILE C 334 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE C 334 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU C 335 " -0.010 2.00e-02 2.50e+03 ... (remaining 2842 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2018 2.75 - 3.29: 15476 3.29 - 3.83: 27990 3.83 - 4.36: 31064 4.36 - 4.90: 56271 Nonbonded interactions: 132819 Sorted by model distance: nonbonded pdb=" OG1 THR A 286 " pdb=" OD1 ASP A 288 " model vdw 2.213 3.040 nonbonded pdb=" OG SER B 206 " pdb=" OD1 ASP B 219 " model vdw 2.240 3.040 nonbonded pdb=" O SER E 172 " pdb=" OG SER E 172 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP C 66 " pdb=" ND2 ASN C 69 " model vdw 2.304 3.120 nonbonded pdb=" OD2 ASP D 66 " pdb=" ND2 ASN D 69 " model vdw 2.321 3.120 ... (remaining 132814 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'B' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'C' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'D' and (resid 23 through 136 or resid 138 through 602)) selection = (chain 'E' and (resid 23 through 136 or resid 138 through 602)) } 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.230 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.009 0.173 16690 Z= 0.419 Angle : 0.709 7.717 22800 Z= 0.332 Chirality : 0.044 0.277 2600 Planarity : 0.004 0.051 2835 Dihedral : 17.111 93.644 6220 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.23 % Allowed : 17.56 % Favored : 82.22 % 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: 1.07 (0.19), residues: 1985 helix: 2.39 (0.18), residues: 805 sheet: -0.67 (0.24), residues: 420 loop : -0.23 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 441 TYR 0.019 0.001 TYR A 296 PHE 0.011 0.001 PHE D 157 TRP 0.009 0.001 TRP E 460 HIS 0.002 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00855 (16665) covalent geometry : angle 0.70093 (22735) SS BOND : bond 0.00751 ( 10) SS BOND : angle 1.34211 ( 20) hydrogen bonds : bond 0.13602 ( 871) hydrogen bonds : angle 6.41701 ( 2796) link_BETA1-4 : bond 0.00057 ( 5) link_BETA1-4 : angle 0.85546 ( 15) link_NAG-ASN : bond 0.00233 ( 10) link_NAG-ASN : angle 2.77875 ( 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 189 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6543 (ptm) cc_final: 0.5996 (mtm) REVERT: A 301 MET cc_start: 0.8379 (mmm) cc_final: 0.8112 (mmp) REVERT: B 119 ASP cc_start: 0.8277 (t0) cc_final: 0.7917 (t0) REVERT: B 276 MET cc_start: 0.7266 (ppp) cc_final: 0.6844 (mtm) REVERT: B 441 ARG cc_start: 0.7978 (ttm-80) cc_final: 0.7350 (ttm-80) REVERT: D 488 MET cc_start: 0.8686 (mmp) cc_final: 0.8469 (mmm) REVERT: E 341 TRP cc_start: 0.6845 (t60) cc_final: 0.6222 (m-10) outliers start: 4 outliers final: 2 residues processed: 186 average time/residue: 0.0993 time to fit residues: 29.3749 Evaluate side-chains 177 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain C residue 321 ASP 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: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.083732 restraints weight = 57502.724| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.04 r_work: 0.2881 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.0674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16690 Z= 0.187 Angle : 0.643 7.818 22800 Z= 0.314 Chirality : 0.045 0.387 2600 Planarity : 0.004 0.043 2835 Dihedral : 11.589 72.925 2549 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.48 % Allowed : 16.42 % Favored : 82.10 % 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: 0.90 (0.19), residues: 1985 helix: 2.16 (0.18), residues: 820 sheet: -1.02 (0.23), residues: 445 loop : -0.01 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 441 TYR 0.013 0.001 TYR B 115 PHE 0.013 0.001 PHE A 478 TRP 0.009 0.001 TRP B 156 HIS 0.003 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00438 (16665) covalent geometry : angle 0.62869 (22735) SS BOND : bond 0.00779 ( 10) SS BOND : angle 1.75516 ( 20) hydrogen bonds : bond 0.04608 ( 871) hydrogen bonds : angle 4.74178 ( 2796) link_BETA1-4 : bond 0.00331 ( 5) link_BETA1-4 : angle 1.72258 ( 15) link_NAG-ASN : bond 0.00219 ( 10) link_NAG-ASN : angle 3.40011 ( 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 220 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.6369 (mp10) REVERT: A 276 MET cc_start: 0.6842 (ptm) cc_final: 0.6273 (mtp) REVERT: B 49 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6636 (mp10) REVERT: B 69 ASN cc_start: 0.8962 (m-40) cc_final: 0.8621 (m110) REVERT: B 197 ASP cc_start: 0.8419 (t0) cc_final: 0.8207 (t0) REVERT: B 441 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7538 (ttm-80) REVERT: C 276 MET cc_start: 0.7347 (ptt) cc_final: 0.7056 (ptm) REVERT: D 488 MET cc_start: 0.8833 (mmp) cc_final: 0.8606 (mmm) REVERT: E 341 TRP cc_start: 0.6961 (t60) cc_final: 0.6464 (m-10) outliers start: 26 outliers final: 17 residues processed: 213 average time/residue: 0.1033 time to fit residues: 35.4134 Evaluate side-chains 196 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.083674 restraints weight = 64388.886| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 4.29 r_work: 0.2891 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16690 Z= 0.162 Angle : 0.619 9.048 22800 Z= 0.298 Chirality : 0.045 0.387 2600 Planarity : 0.004 0.041 2835 Dihedral : 9.202 60.734 2545 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.88 % Allowed : 17.39 % Favored : 80.74 % 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: 0.89 (0.19), residues: 1985 helix: 2.17 (0.18), residues: 820 sheet: -0.79 (0.23), residues: 420 loop : -0.26 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 441 TYR 0.013 0.001 TYR D 296 PHE 0.020 0.001 PHE C 478 TRP 0.008 0.001 TRP A 82 HIS 0.002 0.001 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00375 (16665) covalent geometry : angle 0.59873 (22735) SS BOND : bond 0.00770 ( 10) SS BOND : angle 1.51041 ( 20) hydrogen bonds : bond 0.04245 ( 871) hydrogen bonds : angle 4.46323 ( 2796) link_BETA1-4 : bond 0.00270 ( 5) link_BETA1-4 : angle 2.33707 ( 15) link_NAG-ASN : bond 0.00159 ( 10) link_NAG-ASN : angle 3.88715 ( 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 225 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6639 (ptm) cc_final: 0.6095 (mtp) REVERT: A 341 TRP cc_start: 0.7176 (t60) cc_final: 0.6397 (m-10) REVERT: B 69 ASN cc_start: 0.8950 (m-40) cc_final: 0.8677 (m110) REVERT: B 197 ASP cc_start: 0.8402 (t0) cc_final: 0.8158 (t0) REVERT: B 283 MET cc_start: 0.7882 (ttp) cc_final: 0.7675 (mtp) REVERT: B 341 TRP cc_start: 0.7164 (t60) cc_final: 0.6423 (m-10) REVERT: B 441 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7544 (ttm-80) REVERT: B 468 ASP cc_start: 0.8083 (t0) cc_final: 0.7854 (t0) REVERT: C 49 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.6637 (mp10) REVERT: C 276 MET cc_start: 0.7344 (ptt) cc_final: 0.7059 (ptm) REVERT: D 321 ASP cc_start: 0.8693 (p0) cc_final: 0.8485 (p0) REVERT: D 488 MET cc_start: 0.8829 (mmp) cc_final: 0.8580 (mmm) REVERT: E 341 TRP cc_start: 0.7188 (t60) cc_final: 0.6590 (m-10) outliers start: 33 outliers final: 26 residues processed: 220 average time/residue: 0.1016 time to fit residues: 36.6570 Evaluate side-chains 208 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 153 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 319 HIS E 139 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.084738 restraints weight = 47040.048| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.68 r_work: 0.2910 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16690 Z= 0.152 Angle : 0.603 9.215 22800 Z= 0.291 Chirality : 0.045 0.415 2600 Planarity : 0.004 0.039 2835 Dihedral : 7.509 50.830 2545 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.78 % Allowed : 16.59 % Favored : 80.62 % 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: 0.87 (0.19), residues: 1985 helix: 2.20 (0.18), residues: 825 sheet: -0.76 (0.23), residues: 420 loop : -0.39 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 441 TYR 0.012 0.001 TYR D 296 PHE 0.016 0.001 PHE A 478 TRP 0.008 0.001 TRP B 171 HIS 0.002 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00353 (16665) covalent geometry : angle 0.57986 (22735) SS BOND : bond 0.00773 ( 10) SS BOND : angle 1.50783 ( 20) hydrogen bonds : bond 0.04065 ( 871) hydrogen bonds : angle 4.33454 ( 2796) link_BETA1-4 : bond 0.00343 ( 5) link_BETA1-4 : angle 2.54623 ( 15) link_NAG-ASN : bond 0.00182 ( 10) link_NAG-ASN : angle 4.06823 ( 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 243 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8665 (t0) cc_final: 0.8358 (t0) REVERT: A 276 MET cc_start: 0.6626 (ptm) cc_final: 0.6080 (mtp) REVERT: A 341 TRP cc_start: 0.7247 (t60) cc_final: 0.6562 (m-10) REVERT: A 342 PHE cc_start: 0.8245 (t80) cc_final: 0.7098 (m-10) REVERT: B 33 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8217 (mp) REVERT: B 49 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: B 197 ASP cc_start: 0.8321 (t0) cc_final: 0.8088 (t0) REVERT: B 283 MET cc_start: 0.7801 (ttp) cc_final: 0.7575 (mtp) REVERT: B 341 TRP cc_start: 0.7255 (t60) cc_final: 0.6533 (m-10) REVERT: B 441 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7573 (ttm-80) REVERT: B 468 ASP cc_start: 0.8073 (t0) cc_final: 0.7800 (t0) REVERT: C 197 ASP cc_start: 0.8208 (t0) cc_final: 0.7999 (t0) REVERT: C 276 MET cc_start: 0.7188 (ptt) cc_final: 0.6928 (ptm) REVERT: C 296 TYR cc_start: 0.7996 (t80) cc_final: 0.7774 (t80) REVERT: D 321 ASP cc_start: 0.8608 (p0) cc_final: 0.8400 (p0) REVERT: D 488 MET cc_start: 0.8838 (mmp) cc_final: 0.8579 (mmm) REVERT: E 138 CYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8022 (m) REVERT: E 341 TRP cc_start: 0.7342 (t60) cc_final: 0.6638 (m-10) outliers start: 49 outliers final: 34 residues processed: 231 average time/residue: 0.1027 time to fit residues: 38.7671 Evaluate side-chains 214 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 484 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN B 69 ASN B 139 GLN C 139 GLN D 139 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.085218 restraints weight = 48247.167| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.83 r_work: 0.2929 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16690 Z= 0.136 Angle : 0.591 9.597 22800 Z= 0.283 Chirality : 0.045 0.438 2600 Planarity : 0.004 0.038 2835 Dihedral : 6.863 44.000 2545 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.44 % Allowed : 17.27 % Favored : 80.28 % 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: 0.96 (0.19), residues: 1985 helix: 2.30 (0.18), residues: 825 sheet: -0.69 (0.24), residues: 420 loop : -0.41 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 441 TYR 0.016 0.001 TYR C 151 PHE 0.022 0.001 PHE C 478 TRP 0.008 0.001 TRP E 171 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00311 (16665) covalent geometry : angle 0.56428 (22735) SS BOND : bond 0.00760 ( 10) SS BOND : angle 1.44346 ( 20) hydrogen bonds : bond 0.03915 ( 871) hydrogen bonds : angle 4.23742 ( 2796) link_BETA1-4 : bond 0.00272 ( 5) link_BETA1-4 : angle 2.66418 ( 15) link_NAG-ASN : bond 0.00128 ( 10) link_NAG-ASN : angle 4.37314 ( 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 237 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 194 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 MET cc_start: 0.6845 (ptm) cc_final: 0.6268 (mtp) REVERT: A 341 TRP cc_start: 0.7308 (t60) cc_final: 0.6636 (m-10) REVERT: A 342 PHE cc_start: 0.8242 (t80) cc_final: 0.7118 (m-10) REVERT: B 33 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 49 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: B 197 ASP cc_start: 0.8267 (t0) cc_final: 0.8042 (t0) REVERT: B 341 TRP cc_start: 0.7279 (t60) cc_final: 0.6649 (m-10) REVERT: B 441 ARG cc_start: 0.8058 (ttm-80) cc_final: 0.7612 (ttm-80) REVERT: B 451 ASP cc_start: 0.8514 (m-30) cc_final: 0.8303 (m-30) REVERT: B 468 ASP cc_start: 0.8117 (t0) cc_final: 0.7831 (t0) REVERT: C 49 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.6635 (mp10) REVERT: D 276 MET cc_start: 0.7314 (ppp) cc_final: 0.7104 (mtp) REVERT: D 321 ASP cc_start: 0.8522 (p0) cc_final: 0.8311 (p0) REVERT: D 342 PHE cc_start: 0.8356 (t80) cc_final: 0.7212 (m-10) REVERT: D 488 MET cc_start: 0.8813 (mmp) cc_final: 0.8548 (mmm) REVERT: E 341 TRP cc_start: 0.7375 (t60) cc_final: 0.6670 (m-10) outliers start: 43 outliers final: 35 residues processed: 225 average time/residue: 0.1015 time to fit residues: 37.7335 Evaluate side-chains 218 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 484 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 178 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 0.0570 chunk 35 optimal weight: 3.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.109921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.088892 restraints weight = 43888.623| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.54 r_work: 0.2994 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16690 Z= 0.113 Angle : 0.576 9.541 22800 Z= 0.276 Chirality : 0.045 0.446 2600 Planarity : 0.003 0.038 2835 Dihedral : 6.362 38.992 2545 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.93 % Allowed : 18.24 % Favored : 79.83 % 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: 1.14 (0.19), residues: 1985 helix: 2.54 (0.18), residues: 825 sheet: -0.60 (0.24), residues: 420 loop : -0.43 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 441 TYR 0.017 0.001 TYR C 151 PHE 0.017 0.001 PHE A 478 TRP 0.009 0.001 TRP D 171 HIS 0.002 0.000 HIS D 163 Details of bonding type rmsd covalent geometry : bond 0.00251 (16665) covalent geometry : angle 0.54685 (22735) SS BOND : bond 0.00768 ( 10) SS BOND : angle 1.45073 ( 20) hydrogen bonds : bond 0.03646 ( 871) hydrogen bonds : angle 4.08511 ( 2796) link_BETA1-4 : bond 0.00183 ( 5) link_BETA1-4 : angle 2.80143 ( 15) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 4.49499 ( 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 246 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 275 PHE cc_start: 0.8368 (t80) cc_final: 0.8104 (t80) REVERT: A 276 MET cc_start: 0.6808 (ptm) cc_final: 0.6234 (mtp) REVERT: A 341 TRP cc_start: 0.7334 (t60) cc_final: 0.6708 (m-10) REVERT: A 342 PHE cc_start: 0.8272 (t80) cc_final: 0.7160 (m-10) REVERT: A 451 ASP cc_start: 0.8399 (m-30) cc_final: 0.8112 (m-30) REVERT: B 49 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6614 (mp10) REVERT: B 283 MET cc_start: 0.8007 (tpp) cc_final: 0.7784 (tpp) REVERT: B 341 TRP cc_start: 0.7169 (t60) cc_final: 0.6593 (m-10) REVERT: B 342 PHE cc_start: 0.8339 (t80) cc_final: 0.7108 (m-10) REVERT: B 441 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7505 (ttm-80) REVERT: B 451 ASP cc_start: 0.8516 (m-30) cc_final: 0.8308 (m-30) REVERT: B 468 ASP cc_start: 0.8102 (t0) cc_final: 0.7795 (t0) REVERT: C 49 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6394 (mp10) REVERT: C 306 LEU cc_start: 0.8406 (mt) cc_final: 0.8205 (mm) REVERT: D 226 MET cc_start: 0.9191 (ptt) cc_final: 0.8956 (ptp) REVERT: D 276 MET cc_start: 0.7317 (ppp) cc_final: 0.7079 (mtp) REVERT: D 321 ASP cc_start: 0.8435 (p0) cc_final: 0.8214 (p0) REVERT: D 342 PHE cc_start: 0.8328 (t80) cc_final: 0.7198 (m-10) REVERT: D 488 MET cc_start: 0.8760 (mmp) cc_final: 0.8489 (mmm) REVERT: E 138 CYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8051 (m) REVERT: E 341 TRP cc_start: 0.7374 (t60) cc_final: 0.6756 (m-10) REVERT: E 459 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7616 (tm-30) outliers start: 34 outliers final: 22 residues processed: 231 average time/residue: 0.0998 time to fit residues: 38.2728 Evaluate side-chains 212 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 0.0070 chunk 115 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 99 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 178 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.089420 restraints weight = 47692.533| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.73 r_work: 0.2991 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16690 Z= 0.112 Angle : 0.575 9.858 22800 Z= 0.274 Chirality : 0.045 0.461 2600 Planarity : 0.003 0.037 2835 Dihedral : 6.010 35.856 2545 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.16 % Allowed : 17.95 % Favored : 79.89 % 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: 1.22 (0.19), residues: 1985 helix: 2.64 (0.18), residues: 825 sheet: -0.78 (0.23), residues: 445 loop : -0.26 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 441 TYR 0.020 0.001 TYR E 296 PHE 0.025 0.001 PHE C 478 TRP 0.008 0.001 TRP D 171 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00248 (16665) covalent geometry : angle 0.54408 (22735) SS BOND : bond 0.00752 ( 10) SS BOND : angle 1.39367 ( 20) hydrogen bonds : bond 0.03604 ( 871) hydrogen bonds : angle 3.99034 ( 2796) link_BETA1-4 : bond 0.00190 ( 5) link_BETA1-4 : angle 2.77461 ( 15) link_NAG-ASN : bond 0.00211 ( 10) link_NAG-ASN : angle 4.62615 ( 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 245 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 207 time to evaluate : 0.701 Fit side-chains REVERT: A 247 LEU cc_start: 0.8496 (tt) cc_final: 0.8285 (tt) REVERT: A 269 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8006 (tt) REVERT: A 275 PHE cc_start: 0.8317 (t80) cc_final: 0.8025 (t80) REVERT: A 276 MET cc_start: 0.6789 (ptm) cc_final: 0.6196 (mtp) REVERT: A 341 TRP cc_start: 0.7334 (t60) cc_final: 0.6768 (m-10) REVERT: A 342 PHE cc_start: 0.8241 (t80) cc_final: 0.7166 (m-10) REVERT: B 32 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8073 (tp30) REVERT: B 49 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6368 (mp10) REVERT: B 341 TRP cc_start: 0.7147 (t60) cc_final: 0.6706 (m-10) REVERT: B 342 PHE cc_start: 0.8350 (t80) cc_final: 0.7124 (m-10) REVERT: B 441 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7507 (ttm-80) REVERT: B 451 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: B 468 ASP cc_start: 0.8053 (t0) cc_final: 0.7740 (t0) REVERT: C 49 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6376 (mp10) REVERT: C 276 MET cc_start: 0.7474 (ptt) cc_final: 0.6867 (mtp) REVERT: C 306 LEU cc_start: 0.8358 (mt) cc_final: 0.8146 (mm) REVERT: D 226 MET cc_start: 0.9149 (ptt) cc_final: 0.8933 (ptp) REVERT: D 276 MET cc_start: 0.7349 (ppp) cc_final: 0.7082 (mtp) REVERT: D 321 ASP cc_start: 0.8481 (p0) cc_final: 0.8268 (p0) REVERT: D 342 PHE cc_start: 0.8385 (t80) cc_final: 0.7202 (m-10) REVERT: D 488 MET cc_start: 0.8720 (mmp) cc_final: 0.8450 (mmm) REVERT: E 138 CYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8050 (m) REVERT: E 341 TRP cc_start: 0.7508 (t60) cc_final: 0.6937 (m-10) REVERT: E 459 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7613 (tm-30) outliers start: 38 outliers final: 26 residues processed: 230 average time/residue: 0.1029 time to fit residues: 39.4499 Evaluate side-chains 228 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 451 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 130 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 195 optimal weight: 4.9990 chunk 183 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 GLN D 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087603 restraints weight = 57314.915| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.96 r_work: 0.2970 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16690 Z= 0.122 Angle : 0.587 12.075 22800 Z= 0.279 Chirality : 0.046 0.473 2600 Planarity : 0.003 0.037 2835 Dihedral : 5.773 33.880 2545 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.50 % Allowed : 17.90 % Favored : 79.60 % 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: 1.29 (0.19), residues: 1985 helix: 2.68 (0.18), residues: 825 sheet: -0.71 (0.24), residues: 425 loop : -0.24 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 441 TYR 0.017 0.001 TYR E 296 PHE 0.017 0.001 PHE A 478 TRP 0.007 0.001 TRP D 171 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00278 (16665) covalent geometry : angle 0.55639 (22735) SS BOND : bond 0.00741 ( 10) SS BOND : angle 1.41142 ( 20) hydrogen bonds : bond 0.03605 ( 871) hydrogen bonds : angle 3.96508 ( 2796) link_BETA1-4 : bond 0.00219 ( 5) link_BETA1-4 : angle 2.64789 ( 15) link_NAG-ASN : bond 0.00172 ( 10) link_NAG-ASN : angle 4.74842 ( 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 246 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 0.565 Fit side-chains REVERT: A 247 LEU cc_start: 0.8514 (tt) cc_final: 0.8289 (tt) REVERT: A 269 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8156 (tt) REVERT: A 275 PHE cc_start: 0.8427 (t80) cc_final: 0.8145 (t80) REVERT: A 276 MET cc_start: 0.6934 (ptm) cc_final: 0.6337 (mtp) REVERT: A 283 MET cc_start: 0.7702 (mmm) cc_final: 0.7450 (mmm) REVERT: A 341 TRP cc_start: 0.7369 (t60) cc_final: 0.6826 (m-10) REVERT: A 342 PHE cc_start: 0.8254 (t80) cc_final: 0.7197 (m-10) REVERT: A 451 ASP cc_start: 0.8412 (m-30) cc_final: 0.8125 (m-30) REVERT: B 32 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8102 (tp30) REVERT: B 49 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6454 (mp10) REVERT: B 341 TRP cc_start: 0.7155 (t60) cc_final: 0.6697 (m-10) REVERT: B 342 PHE cc_start: 0.8181 (t80) cc_final: 0.7087 (m-10) REVERT: B 441 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7562 (ttm-80) REVERT: B 451 ASP cc_start: 0.8518 (m-30) cc_final: 0.8300 (m-30) REVERT: B 468 ASP cc_start: 0.8112 (t0) cc_final: 0.7790 (t0) REVERT: C 49 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6453 (mp10) REVERT: C 276 MET cc_start: 0.7386 (ptt) cc_final: 0.7152 (ptm) REVERT: C 306 LEU cc_start: 0.8435 (mt) cc_final: 0.8211 (mm) REVERT: D 276 MET cc_start: 0.7438 (ppp) cc_final: 0.7162 (mtp) REVERT: D 321 ASP cc_start: 0.8519 (p0) cc_final: 0.8305 (p0) REVERT: D 342 PHE cc_start: 0.8373 (t80) cc_final: 0.7169 (m-10) REVERT: D 488 MET cc_start: 0.8810 (mmp) cc_final: 0.8562 (mmm) REVERT: E 138 CYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8102 (m) REVERT: E 341 TRP cc_start: 0.7505 (t60) cc_final: 0.6968 (m-10) REVERT: E 342 PHE cc_start: 0.8133 (t80) cc_final: 0.7153 (m-10) REVERT: E 459 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7697 (tm-30) outliers start: 44 outliers final: 34 residues processed: 229 average time/residue: 0.1071 time to fit residues: 40.4419 Evaluate side-chains 234 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 437 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.106773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085763 restraints weight = 49802.331| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.66 r_work: 0.2944 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16690 Z= 0.149 Angle : 0.603 10.500 22800 Z= 0.289 Chirality : 0.047 0.491 2600 Planarity : 0.003 0.037 2835 Dihedral : 5.528 30.969 2545 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.56 % Allowed : 17.84 % Favored : 79.60 % 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: 1.16 (0.19), residues: 1985 helix: 2.59 (0.18), residues: 825 sheet: -0.84 (0.24), residues: 445 loop : -0.24 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 441 TYR 0.021 0.001 TYR A 296 PHE 0.027 0.001 PHE D 478 TRP 0.009 0.001 TRP E 82 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00348 (16665) covalent geometry : angle 0.57179 (22735) SS BOND : bond 0.00733 ( 10) SS BOND : angle 1.45229 ( 20) hydrogen bonds : bond 0.03775 ( 871) hydrogen bonds : angle 4.02937 ( 2796) link_BETA1-4 : bond 0.00303 ( 5) link_BETA1-4 : angle 2.40779 ( 15) link_NAG-ASN : bond 0.00114 ( 10) link_NAG-ASN : angle 4.91232 ( 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 235 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 0.687 Fit side-chains REVERT: A 269 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8183 (tt) REVERT: A 275 PHE cc_start: 0.8469 (t80) cc_final: 0.8182 (t80) REVERT: A 276 MET cc_start: 0.6956 (ptm) cc_final: 0.6372 (mtp) REVERT: A 341 TRP cc_start: 0.7425 (t60) cc_final: 0.6885 (m-10) REVERT: A 342 PHE cc_start: 0.8306 (t80) cc_final: 0.7243 (m-10) REVERT: B 49 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6660 (mp10) REVERT: B 260 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7644 (mt-10) REVERT: B 321 ASP cc_start: 0.8727 (p0) cc_final: 0.8148 (p0) REVERT: B 341 TRP cc_start: 0.7247 (t60) cc_final: 0.6742 (m-10) REVERT: B 342 PHE cc_start: 0.8185 (t80) cc_final: 0.7090 (m-10) REVERT: B 441 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7573 (ttm-80) REVERT: B 451 ASP cc_start: 0.8498 (m-30) cc_final: 0.8277 (m-30) REVERT: B 468 ASP cc_start: 0.8086 (t0) cc_final: 0.7756 (t0) REVERT: C 49 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6429 (mp10) REVERT: C 276 MET cc_start: 0.7314 (ptt) cc_final: 0.7055 (ptm) REVERT: C 306 LEU cc_start: 0.8458 (mt) cc_final: 0.8230 (mm) REVERT: D 276 MET cc_start: 0.7396 (ppp) cc_final: 0.7161 (mtp) REVERT: D 342 PHE cc_start: 0.8379 (t80) cc_final: 0.7161 (m-10) REVERT: D 488 MET cc_start: 0.8868 (mmp) cc_final: 0.8621 (mmm) REVERT: E 138 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8082 (m) REVERT: E 341 TRP cc_start: 0.7534 (t60) cc_final: 0.6988 (m-10) REVERT: E 342 PHE cc_start: 0.8163 (t80) cc_final: 0.7009 (m-10) REVERT: E 459 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7753 (tm-30) outliers start: 45 outliers final: 38 residues processed: 221 average time/residue: 0.1030 time to fit residues: 38.0078 Evaluate side-chains 232 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 276 MET Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 0.0000 chunk 87 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 142 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.108324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086934 restraints weight = 54404.788| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.84 r_work: 0.2959 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16690 Z= 0.121 Angle : 0.588 11.383 22800 Z= 0.282 Chirality : 0.046 0.481 2600 Planarity : 0.003 0.037 2835 Dihedral : 5.523 31.589 2545 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.22 % Allowed : 18.24 % Favored : 79.55 % 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: 1.25 (0.19), residues: 1985 helix: 2.70 (0.18), residues: 825 sheet: -0.80 (0.24), residues: 445 loop : -0.26 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 441 TYR 0.020 0.001 TYR C 296 PHE 0.018 0.001 PHE A 478 TRP 0.007 0.001 TRP B 171 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00276 (16665) covalent geometry : angle 0.55612 (22735) SS BOND : bond 0.00765 ( 10) SS BOND : angle 1.42941 ( 20) hydrogen bonds : bond 0.03646 ( 871) hydrogen bonds : angle 3.98280 ( 2796) link_BETA1-4 : bond 0.00151 ( 5) link_BETA1-4 : angle 2.43604 ( 15) link_NAG-ASN : bond 0.00223 ( 10) link_NAG-ASN : angle 4.86952 ( 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 235 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.632 Fit side-chains REVERT: A 275 PHE cc_start: 0.8459 (t80) cc_final: 0.8150 (t80) REVERT: A 276 MET cc_start: 0.6952 (ptm) cc_final: 0.6369 (mtp) REVERT: A 341 TRP cc_start: 0.7609 (t60) cc_final: 0.6965 (m-10) REVERT: A 342 PHE cc_start: 0.8306 (t80) cc_final: 0.7252 (m-10) REVERT: A 451 ASP cc_start: 0.8398 (m-30) cc_final: 0.8114 (m-30) REVERT: B 49 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: B 119 ASP cc_start: 0.8747 (t0) cc_final: 0.8152 (t0) REVERT: B 321 ASP cc_start: 0.8722 (p0) cc_final: 0.8147 (p0) REVERT: B 341 TRP cc_start: 0.7293 (t60) cc_final: 0.6813 (m-10) REVERT: B 342 PHE cc_start: 0.8141 (t80) cc_final: 0.7090 (m-10) REVERT: B 441 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7582 (ttm-80) REVERT: B 451 ASP cc_start: 0.8484 (m-30) cc_final: 0.8264 (m-30) REVERT: B 468 ASP cc_start: 0.8081 (t0) cc_final: 0.7745 (t0) REVERT: C 49 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6445 (mp10) REVERT: C 276 MET cc_start: 0.7496 (ptt) cc_final: 0.7207 (ptm) REVERT: C 296 TYR cc_start: 0.7578 (t80) cc_final: 0.7141 (t80) REVERT: C 306 LEU cc_start: 0.8431 (mt) cc_final: 0.8204 (mm) REVERT: C 441 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7160 (ttm110) REVERT: D 276 MET cc_start: 0.7396 (ppp) cc_final: 0.7167 (mtp) REVERT: D 342 PHE cc_start: 0.8240 (t80) cc_final: 0.7183 (m-10) REVERT: D 488 MET cc_start: 0.8828 (mmp) cc_final: 0.8574 (mmm) REVERT: E 138 CYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8061 (m) REVERT: E 341 TRP cc_start: 0.7672 (t60) cc_final: 0.7059 (m-10) REVERT: E 342 PHE cc_start: 0.8167 (t80) cc_final: 0.7093 (m-10) REVERT: E 459 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7679 (tm-30) outliers start: 39 outliers final: 31 residues processed: 221 average time/residue: 0.1014 time to fit residues: 37.2680 Evaluate side-chains 225 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 467 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 437 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 459 GLU Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 169 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 110 optimal weight: 0.0570 chunk 4 optimal weight: 0.4980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 162 optimal weight: 0.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.109448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087830 restraints weight = 59488.452| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.02 r_work: 0.2955 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16690 Z= 0.114 Angle : 0.584 11.148 22800 Z= 0.279 Chirality : 0.045 0.477 2600 Planarity : 0.003 0.037 2835 Dihedral : 5.445 31.228 2545 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.05 % Allowed : 18.52 % Favored : 79.43 % 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: 1.29 (0.19), residues: 1985 helix: 2.74 (0.18), residues: 825 sheet: -0.76 (0.24), residues: 445 loop : -0.25 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 441 TYR 0.017 0.001 TYR C 296 PHE 0.025 0.001 PHE C 478 TRP 0.007 0.001 TRP B 171 HIS 0.002 0.000 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00255 (16665) covalent geometry : angle 0.55276 (22735) SS BOND : bond 0.00764 ( 10) SS BOND : angle 1.41543 ( 20) hydrogen bonds : bond 0.03566 ( 871) hydrogen bonds : angle 3.93598 ( 2796) link_BETA1-4 : bond 0.00136 ( 5) link_BETA1-4 : angle 2.48899 ( 15) link_NAG-ASN : bond 0.00233 ( 10) link_NAG-ASN : angle 4.82735 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3471.50 seconds wall clock time: 60 minutes 28.38 seconds (3628.38 seconds total)