Starting phenix.real_space_refine on Mon Jul 6 09:14:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uzj_42841/07_2026/8uzj_42841_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uzj_42841/07_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_42841/07_2026/8uzj_42841.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uzj_42841/07_2026/8uzj_42841.map" model { file = "/net/cci-nas-00/data/ceres_data/8uzj_42841/07_2026/8uzj_42841_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uzj_42841/07_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-dev-6108/lib/python3.11/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, 176 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain breaks: 1 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, 176 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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, 176 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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, 176 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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, 176 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'9Z9': 1, 'EPJ': 1, 'IVM': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 1 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: 9.48, per 1000 atoms: 0.29 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: 2.78 Conformation dependent library (CDL) restraints added in 1.3 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: 0.50 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: 7.27 Time building geometry restraints manager: 3.80 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: 1.060 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: 0.220 Extract box with map and model: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.800 Find NCS groups from input model: 0.690 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:6.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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/Z covalent geometry : bond 0.00728 / 0.34 (17665) covalent geometry : angle 1.03436 / 0.51 (24115) SS BOND : bond 0.01000 / 0.54 ( 10) SS BOND : angle 2.00867 / 1.23 ( 20) hydrogen bonds : bond 0.18895 / 11.99 ( 866) hydrogen bonds : angle 7.17439 / 4.99 ( 2853) link_BETA1-4 : bond 0.01467 / 0.84 ( 15) link_BETA1-4 : angle 2.48512 / 1.67 ( 45) link_NAG-ASN : bond 0.00864 / 0.50 ( 15) link_NAG-ASN : angle 3.35330 / 2.21 ( 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 : 0.733 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: 1.0410 time to fit residues: 288.4412 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 : 0.776 ------------------------------------------------------------------------------- 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... 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 = 0.3931 r_free = 0.3931 target = 0.163787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121316 restraints weight = 55250.596| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.01 r_work: 0.3111 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2986 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17705 Z= 0.146 Angle : 0.657 5.888 24225 Z= 0.322 Chirality : 0.042 0.180 2830 Planarity : 0.005 0.047 2845 Dihedral : 15.702 149.183 4205 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.50 % Allowed : 5.04 % 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 (0.22), residues: 435 loop : 0.14 (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 0.027 0.002 PHE B 99 TRP 0.009 0.001 TRP A 66 HIS 0.004 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (17665) covalent geometry : angle 0.64251 / 0.32 (24115) SS BOND : bond 0.00844 / 0.46 ( 10) SS BOND : angle 1.37664 / 0.79 ( 20) hydrogen bonds : bond 0.04680 / 3.02 ( 866) hydrogen bonds : angle 5.25955 / 3.66 ( 2853) link_BETA1-4 : bond 0.00225 / 0.15 ( 15) link_BETA1-4 : angle 1.94857 / 1.35 ( 45) link_NAG-ASN : bond 0.00215 / 0.13 ( 15) link_NAG-ASN : angle 2.53730 / 1.64 ( 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 236 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 227 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 ASN cc_start: 0.8472 (m110) cc_final: 0.8246 (m-40) REVERT: B 249 LEU cc_start: 0.8189 (tp) cc_final: 0.7979 (tp) REVERT: B 253 MET cc_start: 0.7266 (mtt) cc_final: 0.7037 (mtt) REVERT: B 447 LEU cc_start: 0.7906 (tp) cc_final: 0.7561 (mp) REVERT: C 40 MET cc_start: 0.8697 (mtp) cc_final: 0.8248 (mtp) REVERT: C 188 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 191 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8076 (tmtt) REVERT: D 418 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7541 (ttm170) REVERT: E 40 MET cc_start: 0.8703 (mtp) cc_final: 0.8246 (mtp) REVERT: E 188 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7407 (tm-30) REVERT: E 322 MET cc_start: 0.7943 (mtp) cc_final: 0.7556 (mtp) REVERT: E 450 MET cc_start: 0.6808 (OUTLIER) cc_final: 0.6548 (mpt) outliers start: 9 outliers final: 1 residues processed: 231 average time/residue: 0.9796 time to fit residues: 261.0146 Evaluate side-chains 210 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 208 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3923 r_free = 0.3923 target = 0.163024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.119588 restraints weight = 56901.607| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.06 r_work: 0.3097 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17705 Z= 0.165 Angle : 0.607 5.849 24225 Z= 0.304 Chirality : 0.041 0.190 2830 Planarity : 0.005 0.049 2845 Dihedral : 12.673 126.604 4205 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.62 % Allowed : 6.67 % Favored : 92.72 % 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: 1.03 (0.18), residues: 1955 helix: 1.99 (0.17), residues: 800 sheet: -0.81 (0.21), residues: 440 loop : 0.35 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 78 TYR 0.015 0.002 TYR D 14 PHE 0.016 0.002 PHE B 99 TRP 0.009 0.001 TRP D 173 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (17665) covalent geometry : angle 0.59414 / 0.30 (24115) SS BOND : bond 0.00778 / 0.43 ( 10) SS BOND : angle 1.35594 / 0.78 ( 20) hydrogen bonds : bond 0.04437 / 2.86 ( 866) hydrogen bonds : angle 5.00425 / 3.49 ( 2853) link_BETA1-4 : bond 0.00438 / 0.28 ( 15) link_BETA1-4 : angle 1.66045 / 1.12 ( 45) link_NAG-ASN : bond 0.00119 / 0.06 ( 15) link_NAG-ASN : angle 2.39124 / 1.58 ( 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 230 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 219 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7349 (pm20) cc_final: 0.7138 (pm20) REVERT: A 210 TYR cc_start: 0.8158 (m-80) cc_final: 0.7942 (m-80) REVERT: B 253 MET cc_start: 0.7234 (mtt) cc_final: 0.6958 (mtt) REVERT: B 447 LEU cc_start: 0.7987 (tp) cc_final: 0.7604 (mp) REVERT: C 40 MET cc_start: 0.8851 (mtp) cc_final: 0.8478 (mtp) REVERT: C 188 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7931 (mm-30) REVERT: C 191 LYS cc_start: 0.8327 (mtpt) cc_final: 0.8082 (tptp) REVERT: C 450 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6376 (mpt) REVERT: D 170 ASN cc_start: 0.7779 (t0) cc_final: 0.7577 (t0) REVERT: D 418 ARG cc_start: 0.7779 (ttm170) cc_final: 0.7440 (ttm110) REVERT: E 40 MET cc_start: 0.8745 (mtp) cc_final: 0.8095 (mtp) REVERT: E 188 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7314 (tm-30) REVERT: E 322 MET cc_start: 0.7804 (mtp) cc_final: 0.7482 (mtp) outliers start: 11 outliers final: 2 residues processed: 223 average time/residue: 0.9813 time to fit residues: 252.0658 Evaluate side-chains 210 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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: 4.9990 chunk 185 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3911 r_free = 0.3911 target = 0.161928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117305 restraints weight = 48226.115| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.63 r_work: 0.3075 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1781 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= 0.208 Angle : 0.612 5.636 24225 Z= 0.311 Chirality : 0.041 0.155 2830 Planarity : 0.005 0.057 2845 Dihedral : 11.789 111.438 4205 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.78 % Allowed : 7.34 % Favored : 91.88 % 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: 1.20 (0.18), residues: 1955 helix: 2.14 (0.17), residues: 800 sheet: -0.71 (0.22), residues: 430 loop : 0.39 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 4 TYR 0.015 0.002 TYR D 14 PHE 0.022 0.002 PHE B 99 TRP 0.011 0.002 TRP D 173 HIS 0.008 0.002 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.21 (17665) covalent geometry : angle 0.59860 / 0.31 (24115) SS BOND : bond 0.00739 / 0.41 ( 10) SS BOND : angle 1.46160 / 0.85 ( 20) hydrogen bonds : bond 0.04387 / 2.84 ( 866) hydrogen bonds : angle 5.01235 / 3.49 ( 2853) link_BETA1-4 : bond 0.00247 / 0.16 ( 15) link_BETA1-4 : angle 1.45740 / 0.99 ( 45) link_NAG-ASN : bond 0.00239 / 0.12 ( 15) link_NAG-ASN : angle 2.49732 / 1.64 ( 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 215 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7359 (pm20) cc_final: 0.7091 (pm20) REVERT: B 253 MET cc_start: 0.7239 (mtt) cc_final: 0.7009 (mtt) REVERT: B 447 LEU cc_start: 0.8028 (tp) cc_final: 0.7611 (mp) REVERT: C 40 MET cc_start: 0.8820 (mtp) cc_final: 0.8374 (mtp) REVERT: C 450 MET cc_start: 0.6952 (OUTLIER) cc_final: 0.6405 (mpt) REVERT: D 418 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7490 (ttm110) REVERT: E 40 MET cc_start: 0.8771 (mtp) cc_final: 0.8266 (mtp) REVERT: E 97 GLU cc_start: 0.7741 (pm20) cc_final: 0.7496 (pm20) REVERT: E 188 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7404 (tm-30) REVERT: E 210 TYR cc_start: 0.8349 (m-80) cc_final: 0.8024 (m-80) REVERT: E 322 MET cc_start: 0.7844 (mtp) cc_final: 0.7520 (mtp) outliers start: 14 outliers final: 7 residues processed: 205 average time/residue: 0.9829 time to fit residues: 231.4673 Evaluate side-chains 207 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 458 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 129 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3912 r_free = 0.3912 target = 0.161922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.117737 restraints weight = 57656.748| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.03 r_work: 0.3066 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17705 Z= 0.223 Angle : 0.611 5.898 24225 Z= 0.314 Chirality : 0.041 0.159 2830 Planarity : 0.005 0.059 2845 Dihedral : 11.436 103.939 4205 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.01 % Allowed : 7.62 % Favored : 91.37 % 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: 1.20 (0.18), residues: 1955 helix: 2.19 (0.17), residues: 800 sheet: -0.76 (0.21), residues: 430 loop : 0.37 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 78 TYR 0.015 0.002 TYR B 31 PHE 0.022 0.002 PHE B 99 TRP 0.011 0.002 TRP D 173 HIS 0.007 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (17665) covalent geometry : angle 0.59833 / 0.31 (24115) SS BOND : bond 0.00734 / 0.40 ( 10) SS BOND : angle 1.49892 / 0.88 ( 20) hydrogen bonds : bond 0.04469 / 2.89 ( 866) hydrogen bonds : angle 5.02808 / 3.50 ( 2853) link_BETA1-4 : bond 0.00307 / 0.20 ( 15) link_BETA1-4 : angle 1.30967 / 0.87 ( 45) link_NAG-ASN : bond 0.00277 / 0.15 ( 15) link_NAG-ASN : angle 2.49664 / 1.64 ( 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: 18 poor density : 196 time to evaluate : 0.840 Fit side-chains REVERT: B 253 MET cc_start: 0.7219 (mtt) cc_final: 0.6998 (mtt) REVERT: B 447 LEU cc_start: 0.8033 (tp) cc_final: 0.7615 (mp) REVERT: C 40 MET cc_start: 0.8815 (mtp) cc_final: 0.8335 (mtp) REVERT: C 191 LYS cc_start: 0.8289 (mtpt) cc_final: 0.8055 (tptp) REVERT: C 431 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6864 (pp20) REVERT: C 450 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.6338 (mpt) REVERT: D 418 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7482 (ttm110) REVERT: E 40 MET cc_start: 0.8804 (mtp) cc_final: 0.8284 (mtp) REVERT: E 188 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7346 (tm-30) outliers start: 18 outliers final: 9 residues processed: 202 average time/residue: 1.0021 time to fit residues: 231.6316 Evaluate side-chains 206 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain B residue 234 ASP Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 431 GLU Chi-restraints excluded: chain C residue 450 MET Chi-restraints excluded: chain C residue 458 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 13 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3933 r_free = 0.3933 target = 0.163817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.120189 restraints weight = 52087.984| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.94 r_work: 0.3157 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 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 = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17705 Z= 0.135 Angle : 0.544 5.479 24225 Z= 0.276 Chirality : 0.039 0.147 2830 Planarity : 0.005 0.039 2845 Dihedral : 10.712 92.040 4205 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.67 % Allowed : 8.12 % Favored : 91.20 % 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: 1.33 (0.19), residues: 1955 helix: 2.33 (0.17), residues: 800 sheet: -0.82 (0.21), residues: 430 loop : 0.48 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.012 0.001 TYR B 273 PHE 0.014 0.001 PHE C 455 TRP 0.007 0.001 TRP C 307 HIS 0.003 0.001 HIS C 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (17665) covalent geometry : angle 0.53164 / 0.27 (24115) SS BOND : bond 0.00748 / 0.41 ( 10) SS BOND : angle 1.29623 / 0.76 ( 20) hydrogen bonds : bond 0.03939 / 2.55 ( 866) hydrogen bonds : angle 4.81763 / 3.35 ( 2853) link_BETA1-4 : bond 0.00272 / 0.17 ( 15) link_BETA1-4 : angle 1.31414 / 0.89 ( 45) link_NAG-ASN : bond 0.00120 / 0.06 ( 15) link_NAG-ASN : angle 2.31603 / 1.50 ( 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 214 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.735 Fit side-chains REVERT: B 253 MET cc_start: 0.7196 (mtt) cc_final: 0.6950 (mtt) REVERT: B 447 LEU cc_start: 0.7991 (tp) cc_final: 0.7541 (mp) REVERT: C 40 MET cc_start: 0.8697 (mtp) cc_final: 0.8177 (mtp) REVERT: C 450 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6297 (mpt) REVERT: E 40 MET cc_start: 0.8695 (mtp) cc_final: 0.8180 (mtp) REVERT: E 188 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7353 (tm-30) REVERT: E 210 TYR cc_start: 0.8218 (m-80) cc_final: 0.7886 (m-80) REVERT: E 322 MET cc_start: 0.7852 (mtp) cc_final: 0.7508 (mtp) outliers start: 12 outliers final: 6 residues processed: 209 average time/residue: 0.9727 time to fit residues: 233.3908 Evaluate side-chains 204 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 C residue 472 GLU Chi-restraints excluded: chain D residue 458 ILE 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: 0.0770 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 124 optimal weight: 0.5980 chunk 184 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3947 r_free = 0.3947 target = 0.165080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121785 restraints weight = 52376.847| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.93 r_work: 0.3181 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 17705 Z= 0.116 Angle : 0.523 5.778 24225 Z= 0.264 Chirality : 0.038 0.147 2830 Planarity : 0.004 0.070 2845 Dihedral : 10.100 77.734 4205 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.39 % Allowed : 8.63 % Favored : 90.98 % 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: 1.51 (0.19), residues: 1955 helix: 2.46 (0.17), residues: 800 sheet: -0.62 (0.21), residues: 470 loop : 0.60 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 418 TYR 0.009 0.001 TYR B 273 PHE 0.013 0.001 PHE C 455 TRP 0.007 0.001 TRP C 307 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (17665) covalent geometry : angle 0.51158 / 0.26 (24115) SS BOND : bond 0.00770 / 0.42 ( 10) SS BOND : angle 1.18723 / 0.70 ( 20) hydrogen bonds : bond 0.03706 / 2.41 ( 866) hydrogen bonds : angle 4.65843 / 3.24 ( 2853) link_BETA1-4 : bond 0.00320 / 0.20 ( 15) link_BETA1-4 : angle 1.25834 / 0.85 ( 45) link_NAG-ASN : bond 0.00041 / 0.02 ( 15) link_NAG-ASN : angle 2.20188 / 1.44 ( 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 203 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 196 time to evaluate : 0.876 Fit side-chains REVERT: A 26 GLN cc_start: 0.8307 (mt0) cc_final: 0.8066 (mm110) REVERT: B 249 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7254 (mp) REVERT: B 253 MET cc_start: 0.7109 (mtt) cc_final: 0.6887 (mtt) REVERT: B 447 LEU cc_start: 0.7984 (tp) cc_final: 0.7539 (mp) REVERT: C 249 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7536 (mp) REVERT: C 450 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6318 (mpt) REVERT: E 40 MET cc_start: 0.8729 (mtp) cc_final: 0.8214 (mtp) REVERT: E 188 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7236 (tm-30) REVERT: E 210 TYR cc_start: 0.8268 (m-80) cc_final: 0.7949 (m-80) REVERT: E 322 MET cc_start: 0.7867 (mtp) cc_final: 0.7491 (mtp) outliers start: 7 outliers final: 2 residues processed: 201 average time/residue: 0.9837 time to fit residues: 226.2556 Evaluate side-chains 194 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 450 MET 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: 0.0980 chunk 142 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 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: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.163263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118512 restraints weight = 48601.549| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.63 r_work: 0.3134 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17705 Z= 0.178 Angle : 0.563 5.867 24225 Z= 0.287 Chirality : 0.039 0.151 2830 Planarity : 0.005 0.043 2845 Dihedral : 10.215 81.198 4205 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.50 % Allowed : 8.74 % Favored : 90.76 % 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: 1.46 (0.19), residues: 1955 helix: 2.47 (0.17), residues: 800 sheet: -0.71 (0.22), residues: 440 loop : 0.50 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 19 TYR 0.012 0.002 TYR E 14 PHE 0.016 0.002 PHE B 99 TRP 0.008 0.001 TRP D 173 HIS 0.006 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (17665) covalent geometry : angle 0.55110 / 0.28 (24115) SS BOND : bond 0.00747 / 0.41 ( 10) SS BOND : angle 1.45490 / 0.85 ( 20) hydrogen bonds : bond 0.04019 / 2.60 ( 866) hydrogen bonds : angle 4.77975 / 3.33 ( 2853) link_BETA1-4 : bond 0.00283 / 0.18 ( 15) link_BETA1-4 : angle 1.20061 / 0.80 ( 45) link_NAG-ASN : bond 0.00167 / 0.09 ( 15) link_NAG-ASN : angle 2.31569 / 1.52 ( 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 196 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8297 (mt0) cc_final: 0.8055 (mm110) REVERT: B 249 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7116 (mp) REVERT: B 447 LEU cc_start: 0.7977 (tp) cc_final: 0.7517 (mp) REVERT: C 450 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6278 (mpt) REVERT: E 40 MET cc_start: 0.8750 (mtp) cc_final: 0.8163 (mtp) REVERT: E 97 GLU cc_start: 0.7617 (pm20) cc_final: 0.7379 (pm20) REVERT: E 188 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7281 (tm-30) REVERT: E 210 TYR cc_start: 0.8215 (m-80) cc_final: 0.7889 (m-80) outliers start: 9 outliers final: 1 residues processed: 193 average time/residue: 1.0529 time to fit residues: 232.7198 Evaluate side-chains 189 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 186 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 450 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 79 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.164845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122341 restraints weight = 56124.067| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.01 r_work: 0.3146 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17705 Z= 0.122 Angle : 0.526 5.631 24225 Z= 0.265 Chirality : 0.038 0.146 2830 Planarity : 0.004 0.064 2845 Dihedral : 9.668 81.314 4205 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.17 % Allowed : 8.91 % 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: 1.46 (0.19), residues: 1955 helix: 2.57 (0.17), residues: 800 sheet: -0.85 (0.22), residues: 445 loop : 0.48 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 418 TYR 0.008 0.001 TYR E 14 PHE 0.022 0.001 PHE E 319 TRP 0.007 0.001 TRP B 307 HIS 0.002 0.001 HIS E 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (17665) covalent geometry : angle 0.51397 / 0.26 (24115) SS BOND : bond 0.00765 / 0.42 ( 10) SS BOND : angle 1.22860 / 0.70 ( 20) hydrogen bonds : bond 0.03719 / 2.41 ( 866) hydrogen bonds : angle 4.64759 / 3.24 ( 2853) link_BETA1-4 : bond 0.00286 / 0.18 ( 15) link_BETA1-4 : angle 1.24951 / 0.84 ( 45) link_NAG-ASN : bond 0.00095 / 0.05 ( 15) link_NAG-ASN : angle 2.21059 / 1.44 ( 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 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 192 time to evaluate : 0.920 Fit side-chains REVERT: A 26 GLN cc_start: 0.8320 (mt0) cc_final: 0.8055 (mm110) REVERT: B 447 LEU cc_start: 0.7993 (tp) cc_final: 0.7522 (mp) REVERT: C 450 MET cc_start: 0.6840 (OUTLIER) cc_final: 0.6336 (mpt) REVERT: E 40 MET cc_start: 0.8757 (mtp) cc_final: 0.8225 (mtp) REVERT: E 97 GLU cc_start: 0.7333 (pm20) cc_final: 0.7111 (pm20) REVERT: E 188 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7267 (tm-30) REVERT: E 210 TYR cc_start: 0.8228 (m-80) cc_final: 0.7932 (m-80) REVERT: E 322 MET cc_start: 0.7819 (mtp) cc_final: 0.7442 (mtp) outliers start: 3 outliers final: 1 residues processed: 193 average time/residue: 1.0768 time to fit residues: 238.6718 Evaluate side-chains 189 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 ASP 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 123 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 162 optimal weight: 0.0010 chunk 18 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.121326 restraints weight = 48549.574| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.59 r_work: 0.3175 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17705 Z= 0.116 Angle : 0.514 5.402 24225 Z= 0.259 Chirality : 0.038 0.146 2830 Planarity : 0.004 0.037 2845 Dihedral : 9.273 80.232 4205 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.39 % Allowed : 8.74 % 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: 1.53 (0.19), residues: 1955 helix: 2.67 (0.17), residues: 800 sheet: -0.87 (0.22), residues: 445 loop : 0.51 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 78 TYR 0.008 0.001 TYR E 14 PHE 0.013 0.001 PHE C 455 TRP 0.007 0.001 TRP A 148 HIS 0.002 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (17665) covalent geometry : angle 0.50255 / 0.26 (24115) SS BOND : bond 0.00777 / 0.42 ( 10) SS BOND : angle 1.21920 / 0.71 ( 20) hydrogen bonds : bond 0.03610 / 2.34 ( 866) hydrogen bonds : angle 4.56973 / 3.18 ( 2853) link_BETA1-4 : bond 0.00335 / 0.21 ( 15) link_BETA1-4 : angle 1.20129 / 0.81 ( 45) link_NAG-ASN : bond 0.00050 / 0.03 ( 15) link_NAG-ASN : angle 2.12454 / 1.39 ( 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 195 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8300 (mt0) cc_final: 0.8043 (mm110) REVERT: B 447 LEU cc_start: 0.7945 (tp) cc_final: 0.7466 (mp) REVERT: C 240 SER cc_start: 0.8235 (m) cc_final: 0.7883 (p) REVERT: C 450 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6332 (mpt) REVERT: E 40 MET cc_start: 0.8714 (mtp) cc_final: 0.8173 (mtp) REVERT: E 188 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7224 (tm-30) REVERT: E 210 TYR cc_start: 0.8244 (m-80) cc_final: 0.7959 (m-80) REVERT: E 322 MET cc_start: 0.7848 (mtp) cc_final: 0.7495 (mtp) REVERT: E 447 LEU cc_start: 0.7911 (tp) cc_final: 0.7691 (mp) outliers start: 7 outliers final: 1 residues processed: 192 average time/residue: 1.0427 time to fit residues: 226.9912 Evaluate side-chains 187 residues out of total 1775 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 445 ASP 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: 1.9990 chunk 38 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 193 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.163864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113084 restraints weight = 46736.867| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.55 r_work: 0.3144 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17705 Z= 0.159 Angle : 0.545 5.744 24225 Z= 0.277 Chirality : 0.039 0.150 2830 Planarity : 0.005 0.058 2845 Dihedral : 9.425 81.176 4205 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.11 % Allowed : 9.30 % Favored : 90.59 % 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: 1.52 (0.19), residues: 1955 helix: 2.64 (0.17), residues: 800 sheet: -0.82 (0.22), residues: 450 loop : 0.49 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 418 TYR 0.011 0.001 TYR E 14 PHE 0.015 0.001 PHE E 319 TRP 0.008 0.001 TRP D 173 HIS 0.005 0.001 HIS E 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (17665) covalent geometry : angle 0.53365 / 0.27 (24115) SS BOND : bond 0.00748 / 0.41 ( 10) SS BOND : angle 1.42224 / 0.84 ( 20) hydrogen bonds : bond 0.03850 / 2.49 ( 866) hydrogen bonds : angle 4.68343 / 3.27 ( 2853) link_BETA1-4 : bond 0.00305 / 0.19 ( 15) link_BETA1-4 : angle 1.17865 / 0.79 ( 45) link_NAG-ASN : bond 0.00150 / 0.08 ( 15) link_NAG-ASN : angle 2.24016 / 1.47 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11878.67 seconds wall clock time: 201 minutes 5.91 seconds (12065.91 seconds total)