Starting phenix.real_space_refine on Thu Feb 5 09:58:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9viq_65096/02_2026/9viq_65096.cif Found real_map, /net/cci-nas-00/data/ceres_data/9viq_65096/02_2026/9viq_65096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9viq_65096/02_2026/9viq_65096.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9viq_65096/02_2026/9viq_65096.map" model { file = "/net/cci-nas-00/data/ceres_data/9viq_65096/02_2026/9viq_65096.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9viq_65096/02_2026/9viq_65096.cif" } resolution = 3.24 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= 0.066 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 10 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: 6.19, per 1000 atoms: 0.38 Number of scatterers: 16220 At special positions: 0 Unit cell: (92.02, 92.02, 167.99, 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: 1.30 Conformation dependent library (CDL) restraints added in 1.2 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: 48 helices and 20 sheets defined 44.1% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 23 through 34 removed outlier: 3.719A pdb=" N VAL A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 237 through 249 Processing helix chain 'A' and resid 250 through 253 Processing helix chain 'A' and resid 260 through 280 removed outlier: 3.607A pdb=" N ALA A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 319 Processing helix chain 'A' and resid 328 through 344 removed outlier: 4.765A pdb=" N CYS A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ALA A 340 " --> pdb=" O LEU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 490 removed outlier: 4.002A 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 34 removed outlier: 3.656A pdb=" N VAL B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 237 through 249 Processing helix chain 'B' and resid 250 through 253 Processing helix chain 'B' and resid 260 through 280 Processing helix chain 'B' and resid 291 through 319 Processing helix chain 'B' and resid 321 through 325 removed outlier: 3.941A pdb=" N GLY B 325 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 4.899A pdb=" N CYS B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 490 removed outlier: 4.022A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 501 Processing helix chain 'C' and resid 24 through 34 removed outlier: 3.727A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 237 through 249 Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 260 through 280 Processing helix chain 'C' and resid 291 through 319 Processing helix chain 'C' and resid 328 through 344 removed outlier: 4.733A pdb=" N CYS C 339 " --> pdb=" O LEU C 335 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 490 removed outlier: 4.148A 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: 3.522A pdb=" N VAL D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.565A 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 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 260 through 280 Processing helix chain 'D' and resid 291 through 319 Processing helix chain 'D' and resid 328 through 344 removed outlier: 4.562A pdb=" N CYS D 339 " --> pdb=" O LEU D 335 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA D 340 " --> pdb=" O LEU D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 490 removed outlier: 4.125A 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 34 removed outlier: 3.723A pdb=" N VAL E 34 " --> pdb=" O TYR E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 237 through 249 removed outlier: 3.512A pdb=" N LEU E 249 " --> pdb=" O SER E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 253 Processing helix chain 'E' and resid 260 through 280 Processing helix chain 'E' and resid 291 through 319 Processing helix chain 'E' and resid 328 through 344 removed outlier: 5.011A pdb=" N CYS E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA E 340 " --> pdb=" O LEU E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 490 removed outlier: 4.119A 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 143 through 149 removed outlier: 6.861A pdb=" N ASN A 75 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ILE A 62 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP A 77 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N LEU A 60 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N GLN A 79 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N SER A 58 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N SER A 81 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N SER A 56 " --> pdb=" O SER A 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.529A pdb=" N VAL A 100 " --> pdb=" O VAL A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 114 removed outlier: 4.335A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.976A 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: 4.335A pdb=" N SER A 170 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 208 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 143 through 149 removed outlier: 3.508A pdb=" N ILE B 76 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN B 75 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE B 62 " --> pdb=" O ASN B 75 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N TRP B 77 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LEU B 60 " --> pdb=" O TRP B 77 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N GLN B 79 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER B 58 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER B 81 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 56 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU B 51 " --> pdb=" O ASP B 179 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN B 181 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 53 " --> pdb=" O GLN B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 102 removed outlier: 3.532A pdb=" N VAL B 100 " --> pdb=" O VAL B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 112 through 114 removed outlier: 4.406A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.931A 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: 4.406A pdb=" N SER B 170 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ARG B 208 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 143 through 149 removed outlier: 6.784A pdb=" N ASN C 75 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ILE C 62 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N TRP C 77 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU C 60 " --> pdb=" O TRP C 77 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N GLN C 79 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N SER C 58 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER C 81 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N SER C 56 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.507A pdb=" N VAL C 100 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 112 through 114 removed outlier: 4.370A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.857A 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: 4.370A pdb=" N SER C 170 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU C 215 " --> pdb=" O TYR C 210 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR C 210 " --> pdb=" O GLU C 215 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG C 208 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 145 through 149 removed outlier: 6.731A pdb=" N ASN D 75 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N ILE D 62 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N TRP D 77 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU D 60 " --> pdb=" O TRP D 77 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN D 79 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N SER D 58 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N SER D 81 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER D 56 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 100 through 102 removed outlier: 3.563A pdb=" N VAL D 100 " --> pdb=" O VAL D 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.336A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR D 225 " --> pdb=" O VAL D 199 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 112 through 114 removed outlier: 4.336A pdb=" N SER D 170 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG D 208 " --> pdb=" O TYR D 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 143 through 149 removed outlier: 6.941A pdb=" N ASN E 75 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE E 62 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 8.774A pdb=" N TRP E 77 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU E 60 " --> pdb=" O TRP E 77 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N GLN E 79 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N SER E 58 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER E 81 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N SER E 56 " --> pdb=" O SER E 81 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU E 51 " --> pdb=" O ASP E 179 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN E 181 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 53 " --> pdb=" O GLN E 181 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 102 removed outlier: 3.571A pdb=" N VAL E 100 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E 131 " --> pdb=" O GLN E 139 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.355A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR E 225 " --> pdb=" O VAL E 199 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 112 through 114 removed outlier: 4.355A pdb=" N SER E 170 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 208 " --> pdb=" O TYR E 217 " (cutoff:3.500A) 897 hydrogen bonds defined for protein. 2619 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: 2.20 Time building geometry restraints manager: 1.75 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: 4651 1.44 - 1.57: 9264 1.57 - 1.70: 10 1.70 - 1.83: 170 Bond restraints: 16665 Sorted by residual: 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 7.52e+01 bond pdb=" C6 NCT E 601 " pdb=" N2 NCT E 601 " ideal model delta sigma weight residual 1.452 1.625 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C6 NCT C 601 " pdb=" N2 NCT C 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C6 NCT D 601 " pdb=" N2 NCT D 601 " ideal model delta sigma weight residual 1.452 1.624 -0.172 2.00e-02 2.50e+03 7.37e+01 bond pdb=" C6 NCT B 601 " pdb=" N2 NCT B 601 " ideal model delta sigma weight residual 1.452 1.623 -0.171 2.00e-02 2.50e+03 7.33e+01 ... (remaining 16660 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 22127 2.01 - 4.02: 471 4.02 - 6.04: 103 6.04 - 8.05: 28 8.05 - 10.06: 6 Bond angle restraints: 22735 Sorted by residual: angle pdb=" CA MET B 283 " pdb=" CB MET B 283 " pdb=" CG MET B 283 " ideal model delta sigma weight residual 114.10 120.96 -6.86 2.00e+00 2.50e-01 1.18e+01 angle pdb=" CB MET B 283 " pdb=" CG MET B 283 " pdb=" SD MET B 283 " ideal model delta sigma weight residual 112.70 122.32 -9.62 3.00e+00 1.11e-01 1.03e+01 angle pdb=" N VAL E 199 " pdb=" CA VAL E 199 " pdb=" C VAL E 199 " ideal model delta sigma weight residual 113.39 108.87 4.52 1.47e+00 4.63e-01 9.44e+00 angle pdb=" CA GLU D 438 " pdb=" CB GLU D 438 " pdb=" CG GLU D 438 " ideal model delta sigma weight residual 114.10 120.19 -6.09 2.00e+00 2.50e-01 9.28e+00 angle pdb=" N VAL C 199 " pdb=" CA VAL C 199 " pdb=" C VAL C 199 " ideal model delta sigma weight residual 113.39 108.99 4.40 1.47e+00 4.63e-01 8.97e+00 ... (remaining 22730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8586 17.95 - 35.90: 1103 35.90 - 53.86: 274 53.86 - 71.81: 56 71.81 - 89.76: 41 Dihedral angle restraints: 10060 sinusoidal: 4165 harmonic: 5895 Sorted by residual: 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 17.26 75.74 1 1.00e+01 1.00e-02 7.23e+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 17.92 75.08 1 1.00e+01 1.00e-02 7.13e+01 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 19.21 73.79 1 1.00e+01 1.00e-02 6.92e+01 ... (remaining 10057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2315 0.065 - 0.130: 251 0.130 - 0.195: 26 0.195 - 0.260: 6 0.260 - 0.325: 2 Chirality restraints: 2600 Sorted by residual: chirality pdb=" CB ILE D 201 " pdb=" CA ILE D 201 " pdb=" CG1 ILE D 201 " pdb=" CG2 ILE D 201 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CG LEU D 437 " pdb=" CB LEU D 437 " pdb=" CD1 LEU D 437 " pdb=" CD2 LEU D 437 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 133 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2597 not shown) Planarity restraints: 2845 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 493 " -0.016 2.00e-02 2.50e+03 2.21e-02 8.56e+00 pdb=" CG PHE E 493 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE E 493 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE E 493 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE E 493 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE E 493 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE E 493 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 191 " -0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO A 192 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 157 " -0.031 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO E 158 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 158 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 158 " -0.023 5.00e-02 4.00e+02 ... (remaining 2842 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4905 2.82 - 3.34: 14915 3.34 - 3.86: 27644 3.86 - 4.38: 29937 4.38 - 4.90: 53770 Nonbonded interactions: 131171 Sorted by model distance: nonbonded pdb=" O SER C 263 " pdb=" OG1 THR C 267 " model vdw 2.304 3.040 nonbonded pdb=" O SER A 263 " pdb=" OG1 THR A 267 " model vdw 2.309 3.040 nonbonded pdb=" O SER E 263 " pdb=" OG1 THR E 267 " model vdw 2.316 3.040 nonbonded pdb=" OD1 ASN B 445 " pdb=" NH1 ARG B 448 " model vdw 2.326 3.120 nonbonded pdb=" OD2 ASP B 119 " pdb=" NH1 ARG B 121 " model vdw 2.334 3.120 ... (remaining 131166 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=0.33 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: 0.830 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: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.180 Find NCS groups from input model: 0.430 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.173 16690 Z= 0.412 Angle : 0.737 10.061 22800 Z= 0.338 Chirality : 0.043 0.325 2600 Planarity : 0.004 0.048 2835 Dihedral : 17.745 89.758 6220 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.06 % Allowed : 25.51 % Favored : 74.43 % 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: 1.39 (0.19), residues: 1985 helix: 2.39 (0.17), residues: 790 sheet: -0.12 (0.25), residues: 395 loop : 0.06 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 441 TYR 0.017 0.001 TYR D 296 PHE 0.050 0.001 PHE E 493 TRP 0.014 0.001 TRP E 176 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00837 (16665) covalent geometry : angle 0.73006 (22735) SS BOND : bond 0.00693 ( 10) SS BOND : angle 1.35217 ( 20) hydrogen bonds : bond 0.12266 ( 847) hydrogen bonds : angle 5.88833 ( 2619) link_BETA1-4 : bond 0.00091 ( 5) link_BETA1-4 : angle 0.77158 ( 15) link_NAG-ASN : bond 0.00213 ( 10) link_NAG-ASN : angle 2.81185 ( 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 226 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.459 Fit side-chains REVERT: B 327 MET cc_start: 0.5632 (mtt) cc_final: 0.5368 (mtp) REVERT: B 332 ARG cc_start: 0.6592 (ttm110) cc_final: 0.6187 (ttm110) REVERT: C 435 LYS cc_start: 0.9112 (mttp) cc_final: 0.8826 (mtmt) REVERT: D 80 MET cc_start: 0.9136 (mtt) cc_final: 0.8661 (mtt) REVERT: D 327 MET cc_start: 0.6984 (mmm) cc_final: 0.6742 (mtt) REVERT: E 332 ARG cc_start: 0.6850 (ttm-80) cc_final: 0.6627 (ttm-80) REVERT: E 480 ILE cc_start: 0.8211 (mm) cc_final: 0.7989 (tt) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1270 time to fit residues: 42.2001 Evaluate side-chains 209 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 492 ASN B 79 GLN B 139 GLN B 492 ASN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 295 GLN E 69 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.108784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.082073 restraints weight = 57028.945| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 4.39 r_work: 0.2991 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3019 r_free = 0.3019 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16690 Z= 0.226 Angle : 0.683 9.456 22800 Z= 0.324 Chirality : 0.045 0.371 2600 Planarity : 0.004 0.045 2835 Dihedral : 9.857 61.648 2545 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.95 % Allowed : 22.05 % Favored : 75.00 % 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: 1.32 (0.18), residues: 1985 helix: 2.05 (0.17), residues: 830 sheet: -0.33 (0.23), residues: 435 loop : 0.42 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 441 TYR 0.014 0.001 TYR D 115 PHE 0.012 0.001 PHE D 493 TRP 0.012 0.001 TRP E 171 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00522 (16665) covalent geometry : angle 0.66681 (22735) SS BOND : bond 0.00748 ( 10) SS BOND : angle 1.60190 ( 20) hydrogen bonds : bond 0.04165 ( 847) hydrogen bonds : angle 4.70508 ( 2619) link_BETA1-4 : bond 0.01133 ( 5) link_BETA1-4 : angle 2.67880 ( 15) link_NAG-ASN : bond 0.00749 ( 10) link_NAG-ASN : angle 3.51350 ( 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 259 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 207 time to evaluate : 0.676 Fit side-chains REVERT: B 327 MET cc_start: 0.6283 (mtt) cc_final: 0.5909 (mtp) REVERT: B 332 ARG cc_start: 0.6719 (ttm110) cc_final: 0.6329 (ttm110) REVERT: C 208 ARG cc_start: 0.7558 (mtp85) cc_final: 0.7355 (ptp-110) REVERT: C 321 ASP cc_start: 0.8732 (t0) cc_final: 0.8294 (t0) REVERT: C 327 MET cc_start: 0.6833 (mtp) cc_final: 0.6273 (mtt) REVERT: C 332 ARG cc_start: 0.7369 (ttm110) cc_final: 0.7035 (ttm110) REVERT: C 435 LYS cc_start: 0.9171 (mttp) cc_final: 0.8916 (mtmt) REVERT: D 63 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8665 (mmm) REVERT: D 80 MET cc_start: 0.9276 (mtt) cc_final: 0.8917 (mtt) REVERT: D 208 ARG cc_start: 0.7284 (ptm160) cc_final: 0.6971 (ptm160) REVERT: D 327 MET cc_start: 0.7102 (mmm) cc_final: 0.6810 (mtt) REVERT: D 438 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8649 (tm-30) REVERT: E 332 ARG cc_start: 0.6774 (ttm-80) cc_final: 0.6422 (ttm110) outliers start: 52 outliers final: 38 residues processed: 238 average time/residue: 0.1231 time to fit residues: 43.7141 Evaluate side-chains 238 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 471 CYS Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 488 MET Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 477 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 60 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 162 optimal weight: 0.1980 chunk 35 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.083936 restraints weight = 73546.987| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.95 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16690 Z= 0.133 Angle : 0.629 10.444 22800 Z= 0.289 Chirality : 0.044 0.399 2600 Planarity : 0.004 0.044 2835 Dihedral : 8.134 50.026 2545 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.88 % Allowed : 22.56 % Favored : 75.57 % 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: 1.57 (0.19), residues: 1985 helix: 2.57 (0.17), residues: 795 sheet: -0.11 (0.23), residues: 445 loop : 0.17 (0.23), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 441 TYR 0.010 0.001 TYR B 115 PHE 0.019 0.001 PHE E 493 TRP 0.011 0.001 TRP B 156 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00301 (16665) covalent geometry : angle 0.60521 (22735) SS BOND : bond 0.00747 ( 10) SS BOND : angle 1.57854 ( 20) hydrogen bonds : bond 0.03779 ( 847) hydrogen bonds : angle 4.43566 ( 2619) link_BETA1-4 : bond 0.00329 ( 5) link_BETA1-4 : angle 2.58401 ( 15) link_NAG-ASN : bond 0.00219 ( 10) link_NAG-ASN : angle 4.23948 ( 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 254 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 221 time to evaluate : 0.615 Fit side-chains REVERT: A 480 ILE cc_start: 0.8342 (mm) cc_final: 0.8118 (tt) REVERT: B 208 ARG cc_start: 0.6231 (ptm160) cc_final: 0.5932 (ptm160) REVERT: B 275 PHE cc_start: 0.7582 (t80) cc_final: 0.7362 (t80) REVERT: B 327 MET cc_start: 0.6219 (mtt) cc_final: 0.5778 (mtp) REVERT: B 332 ARG cc_start: 0.6816 (ttm110) cc_final: 0.6408 (ttm110) REVERT: C 208 ARG cc_start: 0.7034 (mtp85) cc_final: 0.6775 (ptp-110) REVERT: C 321 ASP cc_start: 0.8677 (t0) cc_final: 0.8258 (t0) REVERT: C 438 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8525 (tm-30) REVERT: C 439 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8165 (mm-30) REVERT: D 208 ARG cc_start: 0.6795 (ptm160) cc_final: 0.6534 (ptm160) REVERT: D 327 MET cc_start: 0.7143 (mmm) cc_final: 0.6890 (mtt) REVERT: D 438 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8642 (tm-30) REVERT: D 454 GLU cc_start: 0.7479 (mp0) cc_final: 0.7152 (mp0) outliers start: 33 outliers final: 24 residues processed: 242 average time/residue: 0.1297 time to fit residues: 46.5054 Evaluate side-chains 231 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 467 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 123 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 134 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 157 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 GLN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.083413 restraints weight = 54309.147| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 4.34 r_work: 0.3047 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16690 Z= 0.142 Angle : 0.616 9.691 22800 Z= 0.285 Chirality : 0.044 0.430 2600 Planarity : 0.004 0.041 2835 Dihedral : 7.169 42.427 2545 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.95 % Allowed : 21.25 % Favored : 75.80 % 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: 1.58 (0.18), residues: 1985 helix: 2.61 (0.17), residues: 795 sheet: -0.06 (0.23), residues: 435 loop : 0.11 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 121 TYR 0.015 0.001 TYR D 296 PHE 0.022 0.001 PHE C 493 TRP 0.014 0.001 TRP E 460 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00326 (16665) covalent geometry : angle 0.58984 (22735) SS BOND : bond 0.00749 ( 10) SS BOND : angle 1.54374 ( 20) hydrogen bonds : bond 0.03535 ( 847) hydrogen bonds : angle 4.27582 ( 2619) link_BETA1-4 : bond 0.00616 ( 5) link_BETA1-4 : angle 2.88749 ( 15) link_NAG-ASN : bond 0.00309 ( 10) link_NAG-ASN : angle 4.34184 ( 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 266 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 214 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 332 ARG cc_start: 0.7235 (tpp80) cc_final: 0.6569 (ttm-80) REVERT: A 437 LEU cc_start: 0.8386 (tt) cc_final: 0.8066 (tp) REVERT: A 438 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 480 ILE cc_start: 0.8306 (mm) cc_final: 0.8066 (tt) REVERT: B 275 PHE cc_start: 0.7574 (t80) cc_final: 0.7373 (t80) REVERT: B 296 TYR cc_start: 0.7881 (t80) cc_final: 0.7566 (t80) REVERT: B 332 ARG cc_start: 0.6689 (ttm110) cc_final: 0.6431 (ttm110) REVERT: C 208 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7101 (ptp-110) REVERT: C 321 ASP cc_start: 0.8730 (t0) cc_final: 0.8291 (t0) REVERT: C 327 MET cc_start: 0.6805 (mtt) cc_final: 0.5943 (mtp) REVERT: C 332 ARG cc_start: 0.7262 (ttm110) cc_final: 0.6695 (ttm110) REVERT: C 435 LYS cc_start: 0.9174 (mttp) cc_final: 0.8841 (mtmt) REVERT: C 438 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8578 (tm-30) REVERT: D 63 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8749 (mmm) REVERT: D 438 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8575 (tm-30) REVERT: E 66 ASP cc_start: 0.8623 (t0) cc_final: 0.8002 (t70) REVERT: E 327 MET cc_start: 0.7230 (mtp) cc_final: 0.7026 (mtp) REVERT: E 438 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8591 (tm-30) outliers start: 52 outliers final: 46 residues processed: 251 average time/residue: 0.1272 time to fit residues: 48.0179 Evaluate side-chains 257 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 210 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 471 CYS Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 451 ASP 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: 2.9990 chunk 184 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 141 optimal weight: 0.4980 chunk 136 optimal weight: 0.0670 chunk 128 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.110061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.083547 restraints weight = 55989.519| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.35 r_work: 0.3025 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1576 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= 0.145 Angle : 0.618 10.337 22800 Z= 0.284 Chirality : 0.045 0.458 2600 Planarity : 0.004 0.049 2835 Dihedral : 6.569 37.521 2545 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.07 % Allowed : 20.97 % Favored : 75.97 % 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: 1.55 (0.18), residues: 1985 helix: 2.58 (0.17), residues: 800 sheet: 0.29 (0.24), residues: 420 loop : -0.17 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 441 TYR 0.014 0.001 TYR D 296 PHE 0.016 0.001 PHE C 493 TRP 0.007 0.001 TRP E 176 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00334 (16665) covalent geometry : angle 0.58854 (22735) SS BOND : bond 0.00753 ( 10) SS BOND : angle 1.54424 ( 20) hydrogen bonds : bond 0.03451 ( 847) hydrogen bonds : angle 4.20733 ( 2619) link_BETA1-4 : bond 0.00494 ( 5) link_BETA1-4 : angle 2.78939 ( 15) link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 4.75721 ( 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 272 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: A 437 LEU cc_start: 0.8484 (tt) cc_final: 0.8107 (tp) REVERT: A 438 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8680 (tm-30) REVERT: A 480 ILE cc_start: 0.8336 (mm) cc_final: 0.8030 (tt) REVERT: B 119 ASP cc_start: 0.8527 (t0) cc_final: 0.8327 (t0) REVERT: B 327 MET cc_start: 0.7176 (mtp) cc_final: 0.6235 (mtm) REVERT: B 332 ARG cc_start: 0.6600 (ttm110) cc_final: 0.6060 (ttm110) REVERT: B 435 LYS cc_start: 0.9222 (mtmt) cc_final: 0.9019 (mttp) REVERT: C 208 ARG cc_start: 0.7432 (mtp85) cc_final: 0.7130 (ptp-110) REVERT: C 321 ASP cc_start: 0.8737 (t0) cc_final: 0.8367 (t0) REVERT: C 332 ARG cc_start: 0.7229 (ttm110) cc_final: 0.6919 (ttm110) REVERT: C 435 LYS cc_start: 0.9165 (mttp) cc_final: 0.8828 (mtmt) REVERT: C 438 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8548 (tm-30) REVERT: D 63 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8777 (mmm) REVERT: D 156 TRP cc_start: 0.8727 (m100) cc_final: 0.8413 (m100) REVERT: D 435 LYS cc_start: 0.9173 (mtmt) cc_final: 0.8817 (mtmt) REVERT: D 438 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8509 (tm-30) REVERT: E 66 ASP cc_start: 0.8651 (t0) cc_final: 0.8020 (t70) REVERT: E 327 MET cc_start: 0.7197 (mtp) cc_final: 0.6879 (mtp) REVERT: E 438 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8610 (tm-30) REVERT: E 473 MET cc_start: 0.7337 (ttp) cc_final: 0.7127 (ttm) outliers start: 54 outliers final: 45 residues processed: 255 average time/residue: 0.1200 time to fit residues: 45.3561 Evaluate side-chains 257 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 86 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.110027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.083391 restraints weight = 51516.707| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 4.21 r_work: 0.2978 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16690 Z= 0.158 Angle : 0.617 10.592 22800 Z= 0.286 Chirality : 0.045 0.471 2600 Planarity : 0.004 0.040 2835 Dihedral : 6.310 34.621 2545 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.18 % Allowed : 20.51 % Favored : 76.31 % 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: 1.58 (0.18), residues: 1985 helix: 2.57 (0.17), residues: 795 sheet: 0.29 (0.24), residues: 420 loop : -0.08 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 441 TYR 0.019 0.001 TYR A 296 PHE 0.018 0.001 PHE D 493 TRP 0.007 0.001 TRP C 176 HIS 0.003 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00366 (16665) covalent geometry : angle 0.58671 (22735) SS BOND : bond 0.00746 ( 10) SS BOND : angle 1.51214 ( 20) hydrogen bonds : bond 0.03405 ( 847) hydrogen bonds : angle 4.19161 ( 2619) link_BETA1-4 : bond 0.00540 ( 5) link_BETA1-4 : angle 2.76485 ( 15) link_NAG-ASN : bond 0.00315 ( 10) link_NAG-ASN : angle 4.83495 ( 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 277 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8505 (t0) cc_final: 0.8168 (t0) REVERT: A 332 ARG cc_start: 0.7172 (tpp80) cc_final: 0.6536 (ttm-80) REVERT: A 437 LEU cc_start: 0.8459 (tt) cc_final: 0.8056 (tp) REVERT: A 438 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8661 (tm-30) REVERT: A 480 ILE cc_start: 0.8353 (mm) cc_final: 0.8049 (tt) REVERT: B 327 MET cc_start: 0.7215 (mtp) cc_final: 0.6425 (mtm) REVERT: B 332 ARG cc_start: 0.6558 (ttm110) cc_final: 0.5964 (ttm110) REVERT: B 435 LYS cc_start: 0.9246 (mtmt) cc_final: 0.8959 (mttp) REVERT: C 208 ARG cc_start: 0.7478 (mtp85) cc_final: 0.7190 (ptp-110) REVERT: C 321 ASP cc_start: 0.8735 (t0) cc_final: 0.8376 (t0) REVERT: C 327 MET cc_start: 0.6959 (mtt) cc_final: 0.6627 (mtp) REVERT: C 332 ARG cc_start: 0.7223 (ttm110) cc_final: 0.6889 (ttm110) REVERT: C 435 LYS cc_start: 0.9180 (mttp) cc_final: 0.8837 (mtmt) REVERT: C 438 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8508 (tm-30) REVERT: D 63 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8800 (mmm) REVERT: D 156 TRP cc_start: 0.8753 (m100) cc_final: 0.8421 (m100) REVERT: D 435 LYS cc_start: 0.9244 (mtmt) cc_final: 0.8875 (mtmt) REVERT: D 438 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8504 (tm-30) REVERT: E 66 ASP cc_start: 0.8669 (t0) cc_final: 0.8266 (t70) REVERT: E 327 MET cc_start: 0.7414 (mtp) cc_final: 0.7134 (mtp) REVERT: E 438 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8604 (tm-30) outliers start: 56 outliers final: 49 residues processed: 256 average time/residue: 0.1200 time to fit residues: 45.8113 Evaluate side-chains 261 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 211 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 138 CYS Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 470 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 31 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.111002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.084072 restraints weight = 56023.551| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 4.41 r_work: 0.2986 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16690 Z= 0.125 Angle : 0.615 10.637 22800 Z= 0.281 Chirality : 0.045 0.481 2600 Planarity : 0.003 0.039 2835 Dihedral : 6.176 34.308 2545 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.01 % Allowed : 21.02 % Favored : 75.97 % 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: 1.58 (0.18), residues: 1985 helix: 2.60 (0.17), residues: 800 sheet: 0.35 (0.24), residues: 420 loop : -0.19 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 441 TYR 0.017 0.001 TYR A 296 PHE 0.026 0.001 PHE E 493 TRP 0.007 0.001 TRP C 176 HIS 0.002 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00288 (16665) covalent geometry : angle 0.58369 (22735) SS BOND : bond 0.00745 ( 10) SS BOND : angle 1.52424 ( 20) hydrogen bonds : bond 0.03297 ( 847) hydrogen bonds : angle 4.14396 ( 2619) link_BETA1-4 : bond 0.00356 ( 5) link_BETA1-4 : angle 2.60234 ( 15) link_NAG-ASN : bond 0.00196 ( 10) link_NAG-ASN : angle 4.97912 ( 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 286 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 233 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8379 (t0) cc_final: 0.8093 (t0) REVERT: A 208 ARG cc_start: 0.7290 (ptm160) cc_final: 0.7081 (ptm160) REVERT: A 332 ARG cc_start: 0.7172 (tpp80) cc_final: 0.6513 (ttm-80) REVERT: A 437 LEU cc_start: 0.8428 (tt) cc_final: 0.8034 (tp) REVERT: A 438 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8637 (tm-30) REVERT: A 480 ILE cc_start: 0.8330 (mm) cc_final: 0.8028 (tt) REVERT: B 327 MET cc_start: 0.7168 (mtp) cc_final: 0.6739 (mtt) REVERT: B 332 ARG cc_start: 0.6577 (ttm110) cc_final: 0.6207 (ttm110) REVERT: B 435 LYS cc_start: 0.9278 (mtmt) cc_final: 0.8990 (mttp) REVERT: C 208 ARG cc_start: 0.7459 (mtp85) cc_final: 0.7188 (ptp-110) REVERT: C 321 ASP cc_start: 0.8759 (t0) cc_final: 0.8399 (t0) REVERT: C 327 MET cc_start: 0.6974 (mtt) cc_final: 0.6564 (mtp) REVERT: C 435 LYS cc_start: 0.9167 (mttp) cc_final: 0.8797 (mtmt) REVERT: C 437 LEU cc_start: 0.8479 (tp) cc_final: 0.8223 (tt) REVERT: C 438 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8505 (tm-30) REVERT: D 66 ASP cc_start: 0.8383 (t0) cc_final: 0.7930 (t70) REVERT: D 156 TRP cc_start: 0.8732 (m100) cc_final: 0.8398 (m100) REVERT: D 435 LYS cc_start: 0.9239 (mtmt) cc_final: 0.8837 (mtmt) REVERT: D 438 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8466 (tm-30) REVERT: E 66 ASP cc_start: 0.8646 (t0) cc_final: 0.8246 (t70) REVERT: E 327 MET cc_start: 0.7449 (mtp) cc_final: 0.7215 (mtp) REVERT: E 438 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8594 (tm-30) outliers start: 53 outliers final: 48 residues processed: 267 average time/residue: 0.1205 time to fit residues: 48.1471 Evaluate side-chains 265 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 336 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 130 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 492 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.079028 restraints weight = 66643.920| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 4.69 r_work: 0.2922 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 16690 Z= 0.251 Angle : 0.703 11.371 22800 Z= 0.327 Chirality : 0.048 0.518 2600 Planarity : 0.004 0.042 2835 Dihedral : 5.965 33.122 2545 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.41 % Allowed : 20.85 % Favored : 75.74 % 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: 1.38 (0.18), residues: 1985 helix: 2.28 (0.17), residues: 800 sheet: 0.19 (0.25), residues: 395 loop : -0.06 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 441 TYR 0.017 0.002 TYR A 296 PHE 0.025 0.001 PHE E 342 TRP 0.013 0.001 TRP B 156 HIS 0.004 0.001 HIS A 85 Details of bonding type rmsd covalent geometry : bond 0.00585 (16665) covalent geometry : angle 0.67300 (22735) SS BOND : bond 0.00755 ( 10) SS BOND : angle 1.39209 ( 20) hydrogen bonds : bond 0.03590 ( 847) hydrogen bonds : angle 4.28682 ( 2619) link_BETA1-4 : bond 0.00873 ( 5) link_BETA1-4 : angle 2.91785 ( 15) link_NAG-ASN : bond 0.00832 ( 10) link_NAG-ASN : angle 5.15900 ( 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 275 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 215 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 66 ASP cc_start: 0.8626 (t0) cc_final: 0.8231 (t0) REVERT: A 332 ARG cc_start: 0.7326 (tpp80) cc_final: 0.6711 (ttm-80) REVERT: A 438 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8696 (tm-30) REVERT: B 301 MET cc_start: 0.7703 (tpp) cc_final: 0.7491 (mmt) REVERT: B 327 MET cc_start: 0.7302 (mtp) cc_final: 0.7021 (mtm) REVERT: B 332 ARG cc_start: 0.6626 (ttm110) cc_final: 0.6333 (ttm110) REVERT: B 435 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8889 (mttp) REVERT: B 438 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8676 (tm-30) REVERT: C 208 ARG cc_start: 0.7575 (mtp85) cc_final: 0.7262 (ptp-110) REVERT: C 321 ASP cc_start: 0.8772 (t0) cc_final: 0.8361 (t0) REVERT: C 332 ARG cc_start: 0.7300 (ttm110) cc_final: 0.6775 (ttm110) REVERT: C 438 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8538 (tm-30) REVERT: D 66 ASP cc_start: 0.8579 (t0) cc_final: 0.8052 (t70) REVERT: D 208 ARG cc_start: 0.7335 (ptm160) cc_final: 0.7082 (ptm160) REVERT: D 435 LYS cc_start: 0.9297 (mtmt) cc_final: 0.8896 (mtmt) REVERT: D 438 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8478 (tm-30) REVERT: E 66 ASP cc_start: 0.8762 (t0) cc_final: 0.8339 (t70) REVERT: E 435 LYS cc_start: 0.9265 (mtmt) cc_final: 0.8972 (mttp) REVERT: E 438 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8523 (tm-30) outliers start: 60 outliers final: 52 residues processed: 257 average time/residue: 0.1198 time to fit residues: 45.8157 Evaluate side-chains 257 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 205 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 139 optimal weight: 2.9990 chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 0.0020 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 492 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.082379 restraints weight = 57373.282| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 4.41 r_work: 0.2990 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16690 Z= 0.126 Angle : 0.636 11.244 22800 Z= 0.290 Chirality : 0.045 0.503 2600 Planarity : 0.004 0.039 2835 Dihedral : 6.040 32.203 2545 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.73 % Allowed : 21.99 % Favored : 75.28 % 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: 1.45 (0.18), residues: 1985 helix: 2.42 (0.17), residues: 800 sheet: 0.26 (0.25), residues: 415 loop : -0.16 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 441 TYR 0.019 0.001 TYR A 296 PHE 0.024 0.001 PHE E 493 TRP 0.012 0.001 TRP B 156 HIS 0.002 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00289 (16665) covalent geometry : angle 0.60328 (22735) SS BOND : bond 0.00734 ( 10) SS BOND : angle 1.53483 ( 20) hydrogen bonds : bond 0.03334 ( 847) hydrogen bonds : angle 4.18081 ( 2619) link_BETA1-4 : bond 0.00280 ( 5) link_BETA1-4 : angle 2.20260 ( 15) link_NAG-ASN : bond 0.00239 ( 10) link_NAG-ASN : angle 5.25055 ( 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 266 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.7139 (tpp80) cc_final: 0.6504 (ttm-80) REVERT: A 438 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 480 ILE cc_start: 0.8283 (mm) cc_final: 0.7995 (tt) REVERT: B 332 ARG cc_start: 0.6609 (ttm110) cc_final: 0.6370 (ttm110) REVERT: B 435 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8994 (mttp) REVERT: C 208 ARG cc_start: 0.7469 (mtp85) cc_final: 0.7125 (ptp-110) REVERT: C 321 ASP cc_start: 0.8727 (t0) cc_final: 0.8286 (t0) REVERT: C 332 ARG cc_start: 0.7208 (ttm110) cc_final: 0.6674 (ttm110) REVERT: C 435 LYS cc_start: 0.9186 (mttp) cc_final: 0.8845 (mtmt) REVERT: C 438 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8378 (tm-30) REVERT: D 208 ARG cc_start: 0.7246 (ptm160) cc_final: 0.6872 (ptm160) REVERT: D 435 LYS cc_start: 0.9257 (mtmt) cc_final: 0.8833 (mtmt) REVERT: D 438 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8429 (tm-30) REVERT: E 66 ASP cc_start: 0.8630 (t0) cc_final: 0.8213 (t70) REVERT: E 435 LYS cc_start: 0.9254 (mtmt) cc_final: 0.8805 (mttp) REVERT: E 438 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8474 (tm-30) outliers start: 48 outliers final: 44 residues processed: 252 average time/residue: 0.1216 time to fit residues: 45.1789 Evaluate side-chains 254 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 467 VAL Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 95 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 99 optimal weight: 0.1980 chunk 146 optimal weight: 0.0020 chunk 62 optimal weight: 0.8980 chunk 196 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 0.2980 chunk 158 optimal weight: 3.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.083847 restraints weight = 62882.651| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 4.64 r_work: 0.3017 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2265 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= 0.112 Angle : 0.634 10.600 22800 Z= 0.288 Chirality : 0.045 0.492 2600 Planarity : 0.004 0.038 2835 Dihedral : 5.874 32.166 2545 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.33 % Allowed : 22.27 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.19), residues: 1985 helix: 2.53 (0.17), residues: 800 sheet: 0.39 (0.25), residues: 415 loop : -0.19 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 441 TYR 0.019 0.001 TYR E 296 PHE 0.025 0.001 PHE E 493 TRP 0.016 0.001 TRP B 156 HIS 0.002 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00256 (16665) covalent geometry : angle 0.60289 (22735) SS BOND : bond 0.00757 ( 10) SS BOND : angle 1.52246 ( 20) hydrogen bonds : bond 0.03186 ( 847) hydrogen bonds : angle 4.08632 ( 2619) link_BETA1-4 : bond 0.00249 ( 5) link_BETA1-4 : angle 2.41056 ( 15) link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 5.02882 ( 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 265 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 332 ARG cc_start: 0.7043 (tpp80) cc_final: 0.6405 (ttm-80) REVERT: A 480 ILE cc_start: 0.8249 (mm) cc_final: 0.7965 (tt) REVERT: B 66 ASP cc_start: 0.7975 (t0) cc_final: 0.7492 (t70) REVERT: B 208 ARG cc_start: 0.7393 (ptm160) cc_final: 0.7175 (ptm160) REVERT: B 321 ASP cc_start: 0.8827 (OUTLIER) cc_final: 0.8624 (t0) REVERT: B 327 MET cc_start: 0.7194 (mtt) cc_final: 0.6940 (mtp) REVERT: B 332 ARG cc_start: 0.6645 (ttm110) cc_final: 0.6273 (ttm110) REVERT: B 435 LYS cc_start: 0.9259 (mtmt) cc_final: 0.8850 (mttp) REVERT: B 438 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8580 (tm-30) REVERT: C 66 ASP cc_start: 0.8705 (t0) cc_final: 0.8026 (t70) REVERT: C 321 ASP cc_start: 0.8724 (t0) cc_final: 0.8252 (t0) REVERT: C 327 MET cc_start: 0.7193 (mtt) cc_final: 0.6290 (mtp) REVERT: C 332 ARG cc_start: 0.7173 (ttm110) cc_final: 0.6645 (ttm110) REVERT: C 435 LYS cc_start: 0.9207 (mttp) cc_final: 0.8879 (mtmt) REVERT: C 438 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8182 (tm-30) REVERT: D 66 ASP cc_start: 0.8339 (t0) cc_final: 0.7858 (t70) REVERT: D 435 LYS cc_start: 0.9221 (mtmt) cc_final: 0.8790 (mtmt) REVERT: D 438 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8360 (tm-30) REVERT: E 435 LYS cc_start: 0.9236 (mtmt) cc_final: 0.8776 (mttp) REVERT: E 438 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8467 (tm-30) REVERT: E 457 CYS cc_start: 0.8485 (t) cc_final: 0.8207 (m) REVERT: E 480 ILE cc_start: 0.8238 (mm) cc_final: 0.7919 (tt) outliers start: 41 outliers final: 38 residues processed: 249 average time/residue: 0.1279 time to fit residues: 46.9395 Evaluate side-chains 255 residues out of total 1785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 216 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 138 CYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 138 CYS Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 453 SER Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 63 MET Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 470 LEU Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 288 ASP Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 470 LEU Chi-restraints excluded: chain D residue 494 VAL Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 138 CYS Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 451 ASP Chi-restraints excluded: chain E residue 494 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 169 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 151 optimal weight: 0.3980 chunk 110 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.0370 chunk 113 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 162 optimal weight: 10.0000 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.111249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.083701 restraints weight = 69462.158| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 4.89 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16690 Z= 0.125 Angle : 0.642 12.845 22800 Z= 0.291 Chirality : 0.045 0.496 2600 Planarity : 0.004 0.038 2835 Dihedral : 5.773 31.191 2545 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.33 % Allowed : 22.39 % Favored : 75.28 % 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: 1.55 (0.19), residues: 1985 helix: 2.54 (0.17), residues: 800 sheet: 0.31 (0.25), residues: 420 loop : -0.15 (0.22), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 441 TYR 0.017 0.001 TYR A 296 PHE 0.030 0.001 PHE C 493 TRP 0.014 0.001 TRP B 156 HIS 0.002 0.001 HIS E 318 Details of bonding type rmsd covalent geometry : bond 0.00290 (16665) covalent geometry : angle 0.61028 (22735) SS BOND : bond 0.00750 ( 10) SS BOND : angle 1.51628 ( 20) hydrogen bonds : bond 0.03170 ( 847) hydrogen bonds : angle 4.06101 ( 2619) link_BETA1-4 : bond 0.00346 ( 5) link_BETA1-4 : angle 2.45802 ( 15) link_NAG-ASN : bond 0.00179 ( 10) link_NAG-ASN : angle 5.09898 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3348.28 seconds wall clock time: 58 minutes 11.25 seconds (3491.25 seconds total)