Starting phenix.real_space_refine on Wed May 6 00:25:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzj_42841/05_2026/8uzj_42841_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzj_42841/05_2026/8uzj_42841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uzj_42841/05_2026/8uzj_42841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzj_42841/05_2026/8uzj_42841.map" model { file = "/net/cci-nas-00/data/ceres_data/8uzj_42841/05_2026/8uzj_42841_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzj_42841/05_2026/8uzj_42841_trim.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 5 5.49 5 S 115 5.16 5 Cl 5 4.86 5 C 11285 2.51 5 N 2620 2.21 5 O 3160 1.98 5 H 15835 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33030 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "B" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "C" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "D" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "E" Number of atoms: 6355 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6343 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6415 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" 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: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 177 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 10.57, per 1000 atoms: 0.32 Number of scatterers: 33030 At special positions: 0 Unit cell: (100.347, 101.426, 162.929, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 5 17.00 S 115 16.00 P 5 15.00 O 3160 8.00 N 2620 7.00 C 11285 6.00 H 15835 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 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 F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 604 " - " ASN B 67 " " NAG C 604 " - " ASN C 67 " " NAG D 604 " - " ASN D 67 " " NAG E 604 " - " ASN E 67 " " NAG F 1 " - " ASN A 110 " " NAG G 1 " - " ASN A 23 " " NAG H 1 " - " ASN B 110 " " NAG I 1 " - " ASN B 23 " " NAG J 1 " - " ASN C 110 " " NAG K 1 " - " ASN C 23 " " NAG L 1 " - " ASN D 110 " " NAG M 1 " - " ASN D 23 " " NAG N 1 " - " ASN E 110 " " NAG O 1 " - " ASN E 23 " Time building additional restraints: 3.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3770 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 43.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 removed outlier: 3.542A pdb=" N LYS A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 214 Processing helix chain 'A' and resid 214 through 227 removed outlier: 4.058A pdb=" N CYS A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 237 through 258 removed outlier: 3.709A pdb=" N GLU A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 296 Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 314 through 320 Processing helix chain 'A' and resid 409 through 466 Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'B' and resid 2 through 12 removed outlier: 3.543A pdb=" N LYS B 12 " --> pdb=" O LYS B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 214 Processing helix chain 'B' and resid 214 through 227 removed outlier: 4.058A pdb=" N CYS B 218 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 237 through 258 removed outlier: 3.708A pdb=" N GLU B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 296 Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 314 through 320 Processing helix chain 'B' and resid 409 through 466 Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'C' and resid 2 through 12 removed outlier: 3.541A pdb=" N LYS C 12 " --> pdb=" O LYS C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 214 Processing helix chain 'C' and resid 214 through 227 removed outlier: 4.058A pdb=" N CYS C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 231 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.709A pdb=" N GLU C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 296 Processing helix chain 'C' and resid 305 through 312 Processing helix chain 'C' and resid 314 through 320 Processing helix chain 'C' and resid 409 through 466 Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.542A pdb=" N LYS D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 214 through 227 removed outlier: 4.059A pdb=" N CYS D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 231 Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.709A pdb=" N GLU D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 296 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 314 through 320 Processing helix chain 'D' and resid 409 through 466 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 2 through 12 removed outlier: 3.542A pdb=" N LYS E 12 " --> pdb=" O LYS E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 214 Processing helix chain 'E' and resid 214 through 227 removed outlier: 4.059A pdb=" N CYS E 218 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 237 through 258 removed outlier: 3.709A pdb=" N GLU E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 296 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 409 through 466 Processing helix chain 'E' and resid 469 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS A 114 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN A 52 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE A 39 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N TRP A 54 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU A 37 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN A 56 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER A 35 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER A 58 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER A 33 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR A 60 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N TYR A 31 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 202 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU A 192 " --> pdb=" O TYR A 187 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR A 187 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS B 114 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN B 52 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE B 39 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N TRP B 54 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU B 37 " --> pdb=" O TRP B 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN B 56 " --> pdb=" O SER B 35 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER B 35 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER B 58 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER B 33 " --> pdb=" O SER B 58 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR B 60 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N TYR B 31 " --> pdb=" O THR B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N THR B 202 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU B 192 " --> pdb=" O TYR B 187 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 187 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS C 114 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN C 52 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE C 39 " --> pdb=" O ASN C 52 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N TRP C 54 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU C 37 " --> pdb=" O TRP C 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN C 56 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER C 35 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER C 58 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER C 33 " --> pdb=" O SER C 58 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR C 60 " --> pdb=" O TYR C 31 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N TYR C 31 " --> pdb=" O THR C 60 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR C 202 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU C 192 " --> pdb=" O TYR C 187 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N TYR C 187 " --> pdb=" O GLU C 192 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASN D 52 " --> pdb=" O ILE D 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE D 39 " --> pdb=" O ASN D 52 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N TRP D 54 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU D 37 " --> pdb=" O TRP D 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLN D 56 " --> pdb=" O SER D 35 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER D 35 " --> pdb=" O GLN D 56 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER D 58 " --> pdb=" O SER D 33 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER D 33 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR D 60 " --> pdb=" O TYR D 31 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N TYR D 31 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 202 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU D 192 " --> pdb=" O TYR D 187 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR D 187 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.063A pdb=" N HIS E 114 " --> pdb=" O ASN E 110 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASN E 52 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE E 39 " --> pdb=" O ASN E 52 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N TRP E 54 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU E 37 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLN E 56 " --> pdb=" O SER E 35 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N SER E 35 " --> pdb=" O GLN E 56 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER E 58 " --> pdb=" O SER E 33 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N SER E 33 " --> pdb=" O SER E 58 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR E 60 " --> pdb=" O TYR E 31 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N TYR E 31 " --> pdb=" O THR E 60 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR E 202 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.456A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLU E 192 " --> pdb=" O TYR E 187 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR E 187 " --> pdb=" O GLU E 192 " (cutoff:3.500A) 971 hydrogen bonds defined for protein. 2853 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: 7.60 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 15800 1.04 - 1.24: 2169 1.24 - 1.44: 5440 1.44 - 1.64: 9921 1.64 - 1.84: 175 Bond restraints: 33505 Sorted by residual: bond pdb=" NZ LYS D 191 " pdb=" HZ3 LYS D 191 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS E 124 " pdb=" HZ1 LYS E 124 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" NZ LYS D 86 " pdb=" HZ3 LYS D 86 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" NZ LYS C 191 " pdb=" HZ1 LYS C 191 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" NZ LYS D 323 " pdb=" HZ3 LYS D 323 " ideal model delta sigma weight residual 0.890 0.971 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 33500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 54841 2.33 - 4.66: 4939 4.66 - 7.00: 294 7.00 - 9.33: 46 9.33 - 11.66: 5 Bond angle restraints: 60125 Sorted by residual: angle pdb=" O11 POV C 602 " pdb=" P POV C 602 " pdb=" O12 POV C 602 " ideal model delta sigma weight residual 97.67 109.33 -11.66 3.00e+00 1.11e-01 1.51e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.30 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O11 POV D 602 " pdb=" P POV D 602 " pdb=" O12 POV D 602 " ideal model delta sigma weight residual 97.67 109.30 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O11 POV E 602 " pdb=" P POV E 602 " pdb=" O12 POV E 602 " ideal model delta sigma weight residual 97.67 109.28 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" O11 POV A 606 " pdb=" P POV A 606 " pdb=" O12 POV A 606 " ideal model delta sigma weight residual 97.67 109.27 -11.60 3.00e+00 1.11e-01 1.50e+01 ... (remaining 60120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.66: 16670 31.66 - 63.33: 480 63.33 - 94.99: 135 94.99 - 126.66: 45 126.66 - 158.32: 15 Dihedral angle restraints: 17345 sinusoidal: 10170 harmonic: 7175 Sorted by residual: dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual -180.00 -151.09 -28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 17342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2572 0.092 - 0.183: 213 0.183 - 0.274: 30 0.274 - 0.366: 5 0.366 - 0.457: 10 Chirality restraints: 2830 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.16e+01 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.71e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 7.70e+01 ... (remaining 2827 not shown) Planarity restraints: 4725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 602 " 0.311 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C7 NAG A 602 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A 602 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 602 " -0.451 2.00e-02 2.50e+03 pdb=" O7 NAG A 602 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 604 " 0.311 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C7 NAG B 604 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 604 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 604 " -0.451 2.00e-02 2.50e+03 pdb=" O7 NAG B 604 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.311 2.00e-02 2.50e+03 2.62e-01 8.60e+02 pdb=" C7 NAG C 604 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.451 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.035 2.00e-02 2.50e+03 ... (remaining 4722 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 422 2.09 - 2.72: 53092 2.72 - 3.34: 94881 3.34 - 3.97: 129821 3.97 - 4.60: 198161 Nonbonded interactions: 476377 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.461 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.461 2.100 ... (remaining 476372 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 1 through 113 or resid 115 through 478)) selection = (chain 'B' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'C' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'D' and (resid 1 through 113 or resid 115 through 478)) selection = (chain 'E' and (resid 1 through 113 or resid 115 through 478)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 36.010 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.007 0.063 17705 Z= 0.340 Angle : 1.049 11.662 24225 Z= 0.509 Chirality : 0.062 0.457 2830 Planarity : 0.014 0.262 2845 Dihedral : 19.242 158.319 7970 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 1955 helix: 0.51 (0.17), residues: 790 sheet: -0.37 (0.24), residues: 415 loop : -0.34 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 185 TYR 0.020 0.002 TYR B 14 PHE 0.026 0.003 PHE E 99 TRP 0.017 0.002 TRP D 307 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00728 (17665) covalent geometry : angle 1.03436 (24115) SS BOND : bond 0.01000 ( 10) SS BOND : angle 2.00867 ( 20) hydrogen bonds : bond 0.18895 ( 866) hydrogen bonds : angle 7.17439 ( 2853) link_BETA1-4 : bond 0.01467 ( 15) link_BETA1-4 : angle 2.48512 ( 45) link_NAG-ASN : bond 0.00864 ( 15) link_NAG-ASN : angle 3.35330 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 40 MET cc_start: 0.8356 (mtp) cc_final: 0.8076 (mtp) REVERT: B 447 LEU cc_start: 0.7740 (tp) cc_final: 0.7348 (mp) REVERT: C 40 MET cc_start: 0.8376 (mtp) cc_final: 0.7925 (mtp) REVERT: C 253 MET cc_start: 0.7559 (mtt) cc_final: 0.7331 (mtt) REVERT: D 252 PHE cc_start: 0.8150 (t80) cc_final: 0.7821 (t80) REVERT: D 418 ARG cc_start: 0.7496 (ttm170) cc_final: 0.7162 (ttm110) REVERT: E 40 MET cc_start: 0.8286 (mtp) cc_final: 0.7917 (mtp) REVERT: E 174 ASP cc_start: 0.7951 (t0) cc_final: 0.7712 (t70) REVERT: E 240 SER cc_start: 0.8318 (m) cc_final: 0.7763 (p) REVERT: E 322 MET cc_start: 0.7867 (mtp) cc_final: 0.7517 (mtp) REVERT: E 418 ARG cc_start: 0.7544 (ttm170) cc_final: 0.7321 (ttm170) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 1.3231 time to fit residues: 361.6117 Evaluate side-chains 191 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.121310 restraints weight = 55252.823| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.04 r_work: 0.3111 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2986 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2986 r_free = 0.2986 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17705 Z= 0.147 Angle : 0.659 5.576 24225 Z= 0.323 Chirality : 0.042 0.178 2830 Planarity : 0.005 0.047 2845 Dihedral : 15.666 148.823 4205 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.56 % Allowed : 4.99 % Favored : 94.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 1955 helix: 1.62 (0.17), residues: 795 sheet: -0.82 (0.21), residues: 435 loop : 0.15 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 78 TYR 0.013 0.001 TYR B 273 PHE 0.025 0.001 PHE B 99 TRP 0.008 0.001 TRP D 173 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00301 (17665) covalent geometry : angle 0.64472 (24115) SS BOND : bond 0.00842 ( 10) SS BOND : angle 1.32495 ( 20) hydrogen bonds : bond 0.04699 ( 866) hydrogen bonds : angle 5.26496 ( 2853) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.94200 ( 45) link_NAG-ASN : bond 0.00140 ( 15) link_NAG-ASN : angle 2.53616 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASN cc_start: 0.8482 (m110) cc_final: 0.8250 (m-40) REVERT: B 246 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7895 (tt) REVERT: B 249 LEU cc_start: 0.8202 (tp) cc_final: 0.7999 (tp) REVERT: B 253 MET cc_start: 0.7273 (mtt) cc_final: 0.7072 (mtt) REVERT: B 447 LEU cc_start: 0.7907 (tp) cc_final: 0.7564 (mp) REVERT: C 40 MET cc_start: 0.8696 (mtp) cc_final: 0.8241 (mtp) REVERT: C 188 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 191 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8083 (tmtt) REVERT: D 418 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7551 (ttm170) REVERT: E 40 MET cc_start: 0.8703 (mtp) cc_final: 0.8243 (mtp) REVERT: E 188 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7415 (tm-30) REVERT: E 322 MET cc_start: 0.7951 (mtp) cc_final: 0.7565 (mtp) REVERT: E 450 MET cc_start: 0.6811 (OUTLIER) cc_final: 0.6551 (mpt) outliers start: 10 outliers final: 1 residues processed: 232 average time/residue: 1.2169 time to fit residues: 320.0569 Evaluate side-chains 208 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 246 LEU Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain E residue 450 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 162 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119204 restraints weight = 57123.803| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.08 r_work: 0.3077 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17705 Z= 0.183 Angle : 0.621 7.108 24225 Z= 0.312 Chirality : 0.041 0.158 2830 Planarity : 0.005 0.052 2845 Dihedral : 13.209 131.594 4205 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.56 % Allowed : 6.55 % Favored : 92.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 1955 helix: 1.95 (0.17), residues: 800 sheet: -0.81 (0.21), residues: 440 loop : 0.32 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 78 TYR 0.015 0.002 TYR D 14 PHE 0.020 0.002 PHE B 99 TRP 0.010 0.001 TRP D 173 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00389 (17665) covalent geometry : angle 0.60735 (24115) SS BOND : bond 0.00787 ( 10) SS BOND : angle 1.43423 ( 20) hydrogen bonds : bond 0.04594 ( 866) hydrogen bonds : angle 5.09016 ( 2853) link_BETA1-4 : bond 0.00389 ( 15) link_BETA1-4 : angle 1.70250 ( 45) link_NAG-ASN : bond 0.00156 ( 15) link_NAG-ASN : angle 2.43908 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7369 (pm20) cc_final: 0.7110 (pm20) REVERT: B 253 MET cc_start: 0.7308 (mtt) cc_final: 0.7053 (mtt) REVERT: B 447 LEU cc_start: 0.7997 (tp) cc_final: 0.7621 (mp) REVERT: C 40 MET cc_start: 0.8832 (mtp) cc_final: 0.8440 (mtp) REVERT: C 188 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7914 (mm-30) REVERT: C 450 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.6343 (mpt) REVERT: D 418 ARG cc_start: 0.7793 (ttm170) cc_final: 0.7456 (ttm110) REVERT: E 40 MET cc_start: 0.8755 (mtp) cc_final: 0.8273 (mtp) REVERT: E 97 GLU cc_start: 0.7662 (pm20) cc_final: 0.7445 (pm20) REVERT: E 188 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7322 (tm-30) REVERT: E 322 MET cc_start: 0.7800 (mtp) cc_final: 0.7446 (mtp) outliers start: 10 outliers final: 2 residues processed: 216 average time/residue: 1.2408 time to fit residues: 303.4828 Evaluate side-chains 208 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 205 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 138 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 180 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.162251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.117082 restraints weight = 48385.992| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.61 r_work: 0.3109 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17705 Z= 0.194 Angle : 0.605 5.674 24225 Z= 0.307 Chirality : 0.040 0.154 2830 Planarity : 0.005 0.054 2845 Dihedral : 11.914 113.802 4205 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.73 % Allowed : 7.68 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.19 (0.18), residues: 1955 helix: 2.13 (0.17), residues: 800 sheet: -0.72 (0.21), residues: 430 loop : 0.40 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 78 TYR 0.014 0.002 TYR D 14 PHE 0.020 0.002 PHE B 99 TRP 0.010 0.001 TRP D 173 HIS 0.007 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00411 (17665) covalent geometry : angle 0.59131 (24115) SS BOND : bond 0.00746 ( 10) SS BOND : angle 1.42705 ( 20) hydrogen bonds : bond 0.04358 ( 866) hydrogen bonds : angle 5.01628 ( 2853) link_BETA1-4 : bond 0.00318 ( 15) link_BETA1-4 : angle 1.53269 ( 45) link_NAG-ASN : bond 0.00199 ( 15) link_NAG-ASN : angle 2.46797 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7305 (pm20) cc_final: 0.7054 (pm20) REVERT: B 253 MET cc_start: 0.7203 (mtt) cc_final: 0.6955 (mtt) REVERT: B 447 LEU cc_start: 0.8005 (tp) cc_final: 0.7593 (mp) REVERT: C 40 MET cc_start: 0.8755 (mtp) cc_final: 0.8297 (mtp) REVERT: C 450 MET cc_start: 0.6896 (OUTLIER) cc_final: 0.6342 (mpt) REVERT: D 418 ARG cc_start: 0.7800 (ttm170) cc_final: 0.7460 (ttm110) REVERT: E 40 MET cc_start: 0.8716 (mtp) cc_final: 0.8197 (mtp) REVERT: E 188 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7399 (tm-30) REVERT: E 260 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7677 (mmp) REVERT: E 322 MET cc_start: 0.7847 (mtp) cc_final: 0.7524 (mtp) outliers start: 13 outliers final: 7 residues processed: 208 average time/residue: 1.2649 time to fit residues: 298.5282 Evaluate side-chains 208 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 199 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 129 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.162224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.118291 restraints weight = 57902.172| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.03 r_work: 0.3072 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17705 Z= 0.203 Angle : 0.597 5.884 24225 Z= 0.306 Chirality : 0.040 0.156 2830 Planarity : 0.005 0.053 2845 Dihedral : 11.446 104.536 4205 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.67 % Allowed : 7.79 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.24 (0.18), residues: 1955 helix: 2.23 (0.17), residues: 800 sheet: -0.75 (0.21), residues: 430 loop : 0.38 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 78 TYR 0.013 0.002 TYR E 14 PHE 0.020 0.002 PHE B 99 TRP 0.010 0.002 TRP D 173 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00432 (17665) covalent geometry : angle 0.58461 (24115) SS BOND : bond 0.00739 ( 10) SS BOND : angle 1.44862 ( 20) hydrogen bonds : bond 0.04373 ( 866) hydrogen bonds : angle 4.99379 ( 2853) link_BETA1-4 : bond 0.00291 ( 15) link_BETA1-4 : angle 1.31629 ( 45) link_NAG-ASN : bond 0.00223 ( 15) link_NAG-ASN : angle 2.47371 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 253 MET cc_start: 0.7156 (mtt) cc_final: 0.6924 (mtt) REVERT: B 447 LEU cc_start: 0.8001 (tp) cc_final: 0.7578 (mp) REVERT: C 40 MET cc_start: 0.8797 (mtp) cc_final: 0.8311 (mtp) REVERT: C 191 LYS cc_start: 0.8282 (mtpt) cc_final: 0.8023 (tptp) REVERT: C 450 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6286 (mpt) REVERT: D 418 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7442 (ttm110) REVERT: E 40 MET cc_start: 0.8787 (mtp) cc_final: 0.8265 (mtp) REVERT: E 188 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7346 (tm-30) REVERT: E 322 MET cc_start: 0.7845 (mtp) cc_final: 0.7500 (mtp) outliers start: 12 outliers final: 7 residues processed: 206 average time/residue: 1.2193 time to fit residues: 284.1392 Evaluate side-chains 204 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.162285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.118334 restraints weight = 52151.604| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.92 r_work: 0.3128 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17705 Z= 0.193 Angle : 0.586 5.589 24225 Z= 0.301 Chirality : 0.040 0.151 2830 Planarity : 0.005 0.049 2845 Dihedral : 11.006 95.596 4205 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.78 % Allowed : 7.96 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.27 (0.18), residues: 1955 helix: 2.28 (0.17), residues: 800 sheet: -0.76 (0.21), residues: 430 loop : 0.38 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 78 TYR 0.013 0.002 TYR E 14 PHE 0.018 0.002 PHE B 99 TRP 0.010 0.001 TRP D 173 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00409 (17665) covalent geometry : angle 0.57356 (24115) SS BOND : bond 0.00747 ( 10) SS BOND : angle 1.46762 ( 20) hydrogen bonds : bond 0.04258 ( 866) hydrogen bonds : angle 4.94711 ( 2853) link_BETA1-4 : bond 0.00282 ( 15) link_BETA1-4 : angle 1.29247 ( 45) link_NAG-ASN : bond 0.00213 ( 15) link_NAG-ASN : angle 2.42716 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7288 (pm20) cc_final: 0.7030 (pm20) REVERT: B 253 MET cc_start: 0.7205 (mtt) cc_final: 0.6971 (mtt) REVERT: B 447 LEU cc_start: 0.8009 (tp) cc_final: 0.7566 (mp) REVERT: C 40 MET cc_start: 0.8699 (mtp) cc_final: 0.8301 (mtp) REVERT: C 450 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6325 (mpt) REVERT: D 418 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7462 (ttm110) REVERT: E 40 MET cc_start: 0.8740 (mtp) cc_final: 0.8186 (mtp) REVERT: E 97 GLU cc_start: 0.7628 (pm20) cc_final: 0.7387 (pm20) REVERT: E 188 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7354 (tm-30) REVERT: E 210 TYR cc_start: 0.8171 (m-80) cc_final: 0.7862 (m-80) outliers start: 14 outliers final: 9 residues processed: 204 average time/residue: 1.2763 time to fit residues: 294.5402 Evaluate side-chains 203 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 148 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.117413 restraints weight = 52482.444| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.65 r_work: 0.3146 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17705 Z= 0.134 Angle : 0.542 4.980 24225 Z= 0.275 Chirality : 0.039 0.146 2830 Planarity : 0.005 0.040 2845 Dihedral : 10.463 84.592 4205 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.56 % Allowed : 8.52 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.37 (0.19), residues: 1955 helix: 2.39 (0.17), residues: 800 sheet: -0.83 (0.22), residues: 430 loop : 0.49 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.010 0.001 TYR B 273 PHE 0.014 0.001 PHE B 455 TRP 0.008 0.001 TRP C 307 HIS 0.003 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00281 (17665) covalent geometry : angle 0.52942 (24115) SS BOND : bond 0.00751 ( 10) SS BOND : angle 1.27219 ( 20) hydrogen bonds : bond 0.03921 ( 866) hydrogen bonds : angle 4.79025 ( 2853) link_BETA1-4 : bond 0.00301 ( 15) link_BETA1-4 : angle 1.28376 ( 45) link_NAG-ASN : bond 0.00110 ( 15) link_NAG-ASN : angle 2.31319 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 1.015 Fit side-chains REVERT: A 97 GLU cc_start: 0.7244 (pm20) cc_final: 0.6988 (pm20) REVERT: B 253 MET cc_start: 0.7117 (mtt) cc_final: 0.6916 (mtt) REVERT: B 447 LEU cc_start: 0.8008 (tp) cc_final: 0.7563 (mp) REVERT: C 40 MET cc_start: 0.8601 (mtp) cc_final: 0.8194 (mtp) REVERT: C 450 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.6301 (mpt) REVERT: E 40 MET cc_start: 0.8751 (mtp) cc_final: 0.8239 (mtp) REVERT: E 188 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7355 (tm-30) REVERT: E 210 TYR cc_start: 0.8165 (m-80) cc_final: 0.7857 (m-80) outliers start: 10 outliers final: 5 residues processed: 197 average time/residue: 1.2315 time to fit residues: 274.4905 Evaluate side-chains 194 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 188 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.162467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.117269 restraints weight = 48767.888| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.63 r_work: 0.3088 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2967 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2967 r_free = 0.2967 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2967 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17705 Z= 0.196 Angle : 0.582 5.883 24225 Z= 0.299 Chirality : 0.040 0.162 2830 Planarity : 0.005 0.057 2845 Dihedral : 10.524 81.173 4205 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.78 % Allowed : 8.35 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.37 (0.19), residues: 1955 helix: 2.39 (0.17), residues: 800 sheet: -0.77 (0.22), residues: 430 loop : 0.45 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 418 TYR 0.014 0.002 TYR E 14 PHE 0.018 0.002 PHE B 99 TRP 0.010 0.001 TRP D 173 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00420 (17665) covalent geometry : angle 0.57018 (24115) SS BOND : bond 0.00746 ( 10) SS BOND : angle 1.47935 ( 20) hydrogen bonds : bond 0.04198 ( 866) hydrogen bonds : angle 4.88359 ( 2853) link_BETA1-4 : bond 0.00298 ( 15) link_BETA1-4 : angle 1.24275 ( 45) link_NAG-ASN : bond 0.00217 ( 15) link_NAG-ASN : angle 2.41355 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 0.938 Fit side-chains REVERT: B 253 MET cc_start: 0.7171 (mtt) cc_final: 0.6955 (mtt) REVERT: B 447 LEU cc_start: 0.8037 (tp) cc_final: 0.7596 (mp) REVERT: C 40 MET cc_start: 0.8754 (mtp) cc_final: 0.8353 (mtp) REVERT: C 161 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: C 450 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6360 (mpt) REVERT: E 40 MET cc_start: 0.8810 (mtp) cc_final: 0.8364 (mtp) REVERT: E 188 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7352 (tm-30) REVERT: E 210 TYR cc_start: 0.8212 (m-80) cc_final: 0.7911 (m-80) outliers start: 14 outliers final: 5 residues processed: 195 average time/residue: 1.2568 time to fit residues: 276.2987 Evaluate side-chains 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.119995 restraints weight = 56357.570| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.08 r_work: 0.3119 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17705 Z= 0.140 Angle : 0.542 7.191 24225 Z= 0.276 Chirality : 0.039 0.147 2830 Planarity : 0.005 0.038 2845 Dihedral : 10.104 81.882 4205 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.39 % Allowed : 8.68 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.42 (0.19), residues: 1955 helix: 2.48 (0.17), residues: 800 sheet: -0.76 (0.21), residues: 440 loop : 0.45 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.009 0.001 TYR E 14 PHE 0.013 0.001 PHE B 99 TRP 0.007 0.001 TRP A 307 HIS 0.003 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00293 (17665) covalent geometry : angle 0.52988 (24115) SS BOND : bond 0.00756 ( 10) SS BOND : angle 1.32458 ( 20) hydrogen bonds : bond 0.03894 ( 866) hydrogen bonds : angle 4.75678 ( 2853) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.26667 ( 45) link_NAG-ASN : bond 0.00118 ( 15) link_NAG-ASN : angle 2.31130 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: B 447 LEU cc_start: 0.8029 (tp) cc_final: 0.7571 (mp) REVERT: C 161 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: C 450 MET cc_start: 0.6818 (OUTLIER) cc_final: 0.6313 (mpt) REVERT: E 40 MET cc_start: 0.8774 (mtp) cc_final: 0.8379 (mtp) REVERT: E 188 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7317 (tm-30) REVERT: E 210 TYR cc_start: 0.8193 (m-80) cc_final: 0.7922 (m-80) outliers start: 7 outliers final: 3 residues processed: 192 average time/residue: 1.1879 time to fit residues: 259.0210 Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 183 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain E residue 458 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 123 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.163853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119374 restraints weight = 48592.252| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.59 r_work: 0.3150 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17705 Z= 0.143 Angle : 0.543 7.196 24225 Z= 0.276 Chirality : 0.039 0.148 2830 Planarity : 0.005 0.072 2845 Dihedral : 9.698 81.589 4205 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.28 % Allowed : 8.91 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.44 (0.19), residues: 1955 helix: 2.56 (0.17), residues: 800 sheet: -0.86 (0.21), residues: 450 loop : 0.47 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 418 TYR 0.010 0.001 TYR E 14 PHE 0.012 0.001 PHE B 99 TRP 0.007 0.001 TRP C 307 HIS 0.004 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00303 (17665) covalent geometry : angle 0.53152 (24115) SS BOND : bond 0.00762 ( 10) SS BOND : angle 1.32053 ( 20) hydrogen bonds : bond 0.03852 ( 866) hydrogen bonds : angle 4.71174 ( 2853) link_BETA1-4 : bond 0.00312 ( 15) link_BETA1-4 : angle 1.22170 ( 45) link_NAG-ASN : bond 0.00104 ( 15) link_NAG-ASN : angle 2.24870 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3910 Ramachandran restraints generated. 1955 Oldfield, 0 Emsley, 1955 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 0.939 Fit side-chains REVERT: A 26 GLN cc_start: 0.8265 (mt0) cc_final: 0.8034 (mm110) REVERT: A 97 GLU cc_start: 0.7279 (pm20) cc_final: 0.7069 (pm20) REVERT: B 447 LEU cc_start: 0.8005 (tp) cc_final: 0.7535 (mp) REVERT: C 161 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: C 240 SER cc_start: 0.8295 (m) cc_final: 0.7891 (p) REVERT: C 450 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6283 (mpt) REVERT: E 40 MET cc_start: 0.8764 (mtp) cc_final: 0.8323 (mtp) REVERT: E 188 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7286 (tm-30) REVERT: E 210 TYR cc_start: 0.8169 (m-80) cc_final: 0.7901 (m-80) outliers start: 5 outliers final: 1 residues processed: 190 average time/residue: 1.2347 time to fit residues: 264.2641 Evaluate side-chains 188 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 185 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 450 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 151 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.164672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114706 restraints weight = 47191.703| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.53 r_work: 0.3168 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3041 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3041 r_free = 0.3041 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3041 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17705 Z= 0.122 Angle : 0.522 7.368 24225 Z= 0.264 Chirality : 0.038 0.145 2830 Planarity : 0.004 0.036 2845 Dihedral : 9.328 80.467 4205 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.11 % Allowed : 9.02 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.48 (0.19), residues: 1955 helix: 2.63 (0.17), residues: 800 sheet: -0.85 (0.22), residues: 445 loop : 0.45 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 78 TYR 0.009 0.001 TYR E 14 PHE 0.009 0.001 PHE B 99 TRP 0.007 0.001 TRP B 307 HIS 0.003 0.001 HIS E 104 Details of bonding type rmsd covalent geometry : bond 0.00257 (17665) covalent geometry : angle 0.51038 (24115) SS BOND : bond 0.00764 ( 10) SS BOND : angle 1.25357 ( 20) hydrogen bonds : bond 0.03670 ( 866) hydrogen bonds : angle 4.61620 ( 2853) link_BETA1-4 : bond 0.00294 ( 15) link_BETA1-4 : angle 1.23085 ( 45) link_NAG-ASN : bond 0.00084 ( 15) link_NAG-ASN : angle 2.20775 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13983.38 seconds wall clock time: 236 minutes 43.64 seconds (14203.64 seconds total)