Starting phenix.real_space_refine on Thu Sep 18 17:07:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bqi_44800/09_2025/9bqi_44800_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bqi_44800/09_2025/9bqi_44800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bqi_44800/09_2025/9bqi_44800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bqi_44800/09_2025/9bqi_44800.map" model { file = "/net/cci-nas-00/data/ceres_data/9bqi_44800/09_2025/9bqi_44800_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bqi_44800/09_2025/9bqi_44800_trim.cif" } resolution = 2.55 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: 6 Type Number sf(0) Gaussians S 69 5.16 5 Cl 3 4.86 5 C 6021 2.51 5 N 1509 2.21 5 O 1950 1.98 5 H 8589 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18141 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5851 Chain: "C" Number of atoms: 5788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5851 Chain: "B" Number of atoms: 5788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Conformer: "B" Number of residues, atoms: 374, 5787 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 359} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 bond proxies already assigned to first conformer: 5851 Chain: "D" 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: "E" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'LMT': 2, 'NAG': 1, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'LMT': 2, 'NAG': 1, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'LMT': 2, 'NAG': 1, 'P6E': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Time building chain proxies: 5.99, per 1000 atoms: 0.33 Number of scatterers: 18141 At special positions: 0 Unit cell: (92.016, 88.128, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 69 16.00 O 1950 8.00 N 1509 7.00 C 6021 6.00 H 8589 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.04 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 165 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.04 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.04 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 165 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.04 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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 I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG A 404 " - " ASN A 199 " " NAG B 404 " - " ASN B 199 " " NAG C 404 " - " ASN C 199 " " NAG D 1 " - " ASN A 75 " " NAG E 1 " - " ASN A 184 " " NAG F 1 " - " ASN A 208 " " NAG G 1 " - " ASN C 75 " " NAG H 1 " - " ASN C 184 " " NAG I 1 " - " ASN C 208 " " NAG J 1 " - " ASN B 75 " " NAG K 1 " - " ASN B 184 " " NAG L 1 " - " ASN B 208 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 594.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 21 sheets defined 29.5% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 3 through 13 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.514A pdb=" N VAL A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.560A pdb=" N ALA A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 183 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 215 removed outlier: 3.549A pdb=" N LYS A 215 " --> pdb=" O THR A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 248 removed outlier: 3.785A pdb=" N VAL A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.630A pdb=" N CYS A 270 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 346 removed outlier: 3.770A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.196A pdb=" N THR A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 Processing helix chain 'C' and resid 4 through 13 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.514A pdb=" N VAL C 90 " --> pdb=" O VAL C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.560A pdb=" N ALA C 182 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 183 " --> pdb=" O LYS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 215 removed outlier: 3.550A pdb=" N LYS C 215 " --> pdb=" O THR C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 248 removed outlier: 3.784A pdb=" N VAL C 248 " --> pdb=" O GLN C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.629A pdb=" N CYS C 270 " --> pdb=" O ALA C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 346 removed outlier: 3.770A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 360 removed outlier: 4.197A pdb=" N THR C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 Processing helix chain 'B' and resid 4 through 13 Processing helix chain 'B' and resid 25 through 46 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.514A pdb=" N VAL B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.560A pdb=" N ALA B 182 " --> pdb=" O LEU B 179 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU B 183 " --> pdb=" O LYS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 215 removed outlier: 3.550A pdb=" N LYS B 215 " --> pdb=" O THR B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 248 removed outlier: 3.784A pdb=" N VAL B 248 " --> pdb=" O GLN B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.627A pdb=" N CYS B 270 " --> pdb=" O ALA B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 346 removed outlier: 3.769A pdb=" N THR B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 360 removed outlier: 4.197A pdb=" N THR B 350 " --> pdb=" O LEU B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 4.274A pdb=" N ARG B 24 " --> pdb=" O VAL C 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 14 through 18 removed outlier: 6.646A pdb=" N ILE A 20 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL B 375 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 22 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 69 Processing sheet with id=AA6, first strand: chain 'A' and resid 72 through 76 removed outlier: 3.770A pdb=" N THR A 76 " --> pdb=" O GLY A 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP A 164 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR A 146 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR A 315 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL A 105 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS A 313 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 107 " --> pdb=" O LEU A 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU A 311 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N MET A 109 " --> pdb=" O ARG A 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG A 309 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN A 111 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU A 307 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 375 removed outlier: 4.278A pdb=" N ARG C 24 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 55 through 59 Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB3, first strand: chain 'C' and resid 61 through 69 Processing sheet with id=AB4, first strand: chain 'C' and resid 72 through 76 removed outlier: 3.769A pdb=" N THR C 76 " --> pdb=" O GLY C 80 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 144 through 151 removed outlier: 9.123A pdb=" N VAL C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.028A pdb=" N TRP C 164 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR C 146 " --> pdb=" O ALA C 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ARG C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TYR C 315 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL C 105 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS C 313 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 107 " --> pdb=" O LEU C 311 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU C 311 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 109 " --> pdb=" O ARG C 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG C 309 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN C 111 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLU C 307 " --> pdb=" O GLN C 111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 55 through 59 Processing sheet with id=AB8, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AB9, first strand: chain 'B' and resid 61 through 69 Processing sheet with id=AC1, first strand: chain 'B' and resid 72 through 76 removed outlier: 3.769A pdb=" N THR B 76 " --> pdb=" O GLY B 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.122A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 144 through 151 removed outlier: 9.122A pdb=" N VAL B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N TRP B 164 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR B 146 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ALA B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N TYR B 315 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL B 105 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS B 313 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LEU B 107 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU B 311 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET B 109 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ARG B 309 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN B 111 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU B 307 " --> pdb=" O GLN B 111 " (cutoff:3.500A) 454 hydrogen bonds defined for protein. 1263 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: 3.63 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8574 1.03 - 1.23: 141 1.23 - 1.43: 3906 1.43 - 1.62: 5475 1.62 - 1.82: 96 Bond restraints: 18192 Sorted by residual: bond pdb=" C LYS B 67 " pdb=" O LYS B 67 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C LYS C 67 " pdb=" O LYS C 67 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.18e-02 7.18e+03 1.15e+01 bond pdb=" C LYS A 67 " pdb=" O LYS A 67 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.18e-02 7.18e+03 1.08e+01 bond pdb=" N LYS A 363 " pdb=" CA LYS A 363 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.21e+00 bond pdb=" N LYS B 363 " pdb=" CA LYS B 363 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.74e+00 ... (remaining 18187 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 31990 1.88 - 3.77: 428 3.77 - 5.65: 51 5.65 - 7.53: 21 7.53 - 9.41: 15 Bond angle restraints: 32505 Sorted by residual: angle pdb=" N LEU B 365 " pdb=" CA LEU B 365 " pdb=" C LEU B 365 " ideal model delta sigma weight residual 112.90 108.41 4.49 1.31e+00 5.83e-01 1.18e+01 angle pdb=" N LEU C 365 " pdb=" CA LEU C 365 " pdb=" C LEU C 365 " ideal model delta sigma weight residual 112.90 108.42 4.48 1.31e+00 5.83e-01 1.17e+01 angle pdb=" N LEU A 365 " pdb=" CA LEU A 365 " pdb=" C LEU A 365 " ideal model delta sigma weight residual 112.90 108.44 4.46 1.31e+00 5.83e-01 1.16e+01 angle pdb=" CA LYS C 373 " pdb=" C LYS C 373 " pdb=" O LYS C 373 " ideal model delta sigma weight residual 120.32 116.63 3.69 1.10e+00 8.26e-01 1.12e+01 angle pdb=" CA THR B 210 " pdb=" C THR B 210 " pdb=" O THR B 210 " ideal model delta sigma weight residual 121.89 117.97 3.92 1.17e+00 7.31e-01 1.12e+01 ... (remaining 32500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.88: 8635 21.88 - 43.77: 426 43.77 - 65.65: 143 65.65 - 87.54: 30 87.54 - 109.42: 15 Dihedral angle restraints: 9249 sinusoidal: 5352 harmonic: 3897 Sorted by residual: dihedral pdb=" CB CYS C 261 " pdb=" SG CYS C 261 " pdb=" SG CYS C 270 " pdb=" CB CYS C 270 " ideal model delta sinusoidal sigma weight residual -86.00 -53.23 -32.77 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS A 261 " pdb=" SG CYS A 261 " pdb=" SG CYS A 270 " pdb=" CB CYS A 270 " ideal model delta sinusoidal sigma weight residual -86.00 -53.23 -32.77 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS B 261 " pdb=" SG CYS B 261 " pdb=" SG CYS B 270 " pdb=" CB CYS B 270 " ideal model delta sinusoidal sigma weight residual -86.00 -53.26 -32.74 1 1.00e+01 1.00e-02 1.52e+01 ... (remaining 9246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1232 0.054 - 0.109: 206 0.109 - 0.163: 110 0.163 - 0.218: 12 0.218 - 0.272: 6 Chirality restraints: 1566 Sorted by residual: chirality pdb=" C5 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C6 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 1563 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 365 " 0.015 2.00e-02 2.50e+03 2.79e-02 7.79e+00 pdb=" N TYR C 366 " -0.048 2.00e-02 2.50e+03 pdb=" CA TYR C 366 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR C 366 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 365 " 0.015 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" N TYR A 366 " -0.048 2.00e-02 2.50e+03 pdb=" CA TYR A 366 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR A 366 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 365 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" N TYR B 366 " -0.048 2.00e-02 2.50e+03 pdb=" CA TYR B 366 " 0.012 2.00e-02 2.50e+03 pdb=" H TYR B 366 " 0.021 2.00e-02 2.50e+03 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 607 2.17 - 2.78: 33941 2.78 - 3.38: 47326 3.38 - 3.99: 66430 3.99 - 4.60: 100791 Nonbonded interactions: 249095 Sorted by model distance: nonbonded pdb=" HH TYR C 299 " pdb=" OD1 ASP B 88 " model vdw 1.562 2.450 nonbonded pdb=" OD1 ASP A 88 " pdb=" HH TYR B 299 " model vdw 1.570 2.450 nonbonded pdb=" HH TYR A 299 " pdb=" OD1 ASP C 88 " model vdw 1.572 2.450 nonbonded pdb=" O GLY C 70 " pdb=" HH TYR C 89 " model vdw 1.701 2.450 nonbonded pdb=" O GLY B 70 " pdb=" HH TYR B 89 " model vdw 1.702 2.450 ... (remaining 249090 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 3 through 253 or resid 255 through 376)) selection = (chain 'B' and (resid 3 through 253 or resid 255 through 376)) selection = (chain 'C' and (resid 3 through 253 or resid 255 through 376)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 19.410 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: 0.120 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.390 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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 : 0.006 0.050 9636 Z= 0.301 Angle : 0.798 9.413 13125 Z= 0.371 Chirality : 0.055 0.272 1566 Planarity : 0.005 0.080 1578 Dihedral : 15.816 109.419 4128 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.35 (0.25), residues: 1116 helix: 0.18 (0.31), residues: 324 sheet: 0.40 (0.27), residues: 348 loop : -0.95 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 277 TYR 0.009 0.001 TYR B 213 PHE 0.013 0.001 PHE B 178 TRP 0.009 0.002 TRP B 259 HIS 0.002 0.000 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00581 ( 9603) covalent geometry : angle 0.78401 (13035) SS BOND : bond 0.00362 ( 9) SS BOND : angle 1.10444 ( 18) hydrogen bonds : bond 0.17871 ( 382) hydrogen bonds : angle 7.81106 ( 1263) link_BETA1-4 : bond 0.00509 ( 12) link_BETA1-4 : angle 1.90590 ( 36) link_NAG-ASN : bond 0.00351 ( 12) link_NAG-ASN : angle 2.31752 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 283 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8221 (t0) cc_final: 0.7875 (t0) REVERT: A 197 LYS cc_start: 0.8175 (ttmt) cc_final: 0.7969 (ttmt) REVERT: A 246 MET cc_start: 0.8485 (ttt) cc_final: 0.8240 (ttt) REVERT: C 159 CYS cc_start: 0.7720 (p) cc_final: 0.7386 (p) REVERT: C 234 LYS cc_start: 0.8114 (tttt) cc_final: 0.7873 (ttpp) REVERT: C 320 ASP cc_start: 0.7341 (m-30) cc_final: 0.7127 (m-30) REVERT: B 107 LEU cc_start: 0.8537 (mt) cc_final: 0.8328 (mp) REVERT: B 168 GLU cc_start: 0.7464 (tt0) cc_final: 0.7254 (tt0) REVERT: B 220 ASP cc_start: 0.7782 (t0) cc_final: 0.7490 (t70) outliers start: 0 outliers final: 1 residues processed: 283 average time/residue: 1.3095 time to fit residues: 393.3066 Evaluate side-chains 262 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 261 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.0000 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.0270 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 overall best weight: 0.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 262 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.110598 restraints weight = 34069.100| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.27 r_work: 0.3335 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9636 Z= 0.148 Angle : 0.565 4.751 13125 Z= 0.295 Chirality : 0.046 0.197 1566 Planarity : 0.004 0.029 1578 Dihedral : 12.446 73.150 2135 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.16 % Allowed : 9.39 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.14 (0.25), residues: 1116 helix: 0.28 (0.30), residues: 327 sheet: 0.62 (0.29), residues: 330 loop : -0.82 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 82 TYR 0.009 0.001 TYR A 299 PHE 0.011 0.001 PHE A 296 TRP 0.010 0.002 TRP C 259 HIS 0.002 0.001 HIS C 241 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 9603) covalent geometry : angle 0.55168 (13035) SS BOND : bond 0.00349 ( 9) SS BOND : angle 1.11770 ( 18) hydrogen bonds : bond 0.04948 ( 382) hydrogen bonds : angle 5.57308 ( 1263) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.85236 ( 36) link_NAG-ASN : bond 0.00480 ( 12) link_NAG-ASN : angle 1.48230 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 276 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8361 (t0) cc_final: 0.8058 (t0) REVERT: A 69 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8278 (mtmm) REVERT: A 112 THR cc_start: 0.8651 (p) cc_final: 0.8447 (m) REVERT: C 13 PHE cc_start: 0.8610 (m-80) cc_final: 0.8243 (m-80) REVERT: C 320 ASP cc_start: 0.7951 (m-30) cc_final: 0.7749 (m-30) REVERT: B 69 LYS cc_start: 0.8835 (mtpp) cc_final: 0.8307 (mtmm) REVERT: B 220 ASP cc_start: 0.8286 (t0) cc_final: 0.8007 (t70) outliers start: 11 outliers final: 5 residues processed: 278 average time/residue: 1.4447 time to fit residues: 426.0209 Evaluate side-chains 273 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 268 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 320 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 69 optimal weight: 0.1980 chunk 13 optimal weight: 0.0000 chunk 108 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 95 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 262 ASN B 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.109702 restraints weight = 34160.425| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.28 r_work: 0.3312 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9636 Z= 0.171 Angle : 0.579 5.103 13125 Z= 0.296 Chirality : 0.046 0.179 1566 Planarity : 0.004 0.076 1578 Dihedral : 10.285 58.852 2135 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.84 % Allowed : 11.50 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.16 (0.25), residues: 1116 helix: 0.25 (0.30), residues: 327 sheet: 0.66 (0.29), residues: 330 loop : -0.85 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 82 TYR 0.013 0.001 TYR B 89 PHE 0.010 0.001 PHE B 11 TRP 0.012 0.002 TRP C 259 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 9603) covalent geometry : angle 0.56123 (13035) SS BOND : bond 0.00416 ( 9) SS BOND : angle 1.27545 ( 18) hydrogen bonds : bond 0.04642 ( 382) hydrogen bonds : angle 5.17999 ( 1263) link_BETA1-4 : bond 0.00388 ( 12) link_BETA1-4 : angle 2.03070 ( 36) link_NAG-ASN : bond 0.00397 ( 12) link_NAG-ASN : angle 1.79507 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 278 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.8438 (t0) cc_final: 0.8186 (t0) REVERT: A 69 LYS cc_start: 0.8822 (mtpp) cc_final: 0.8231 (mtmm) REVERT: A 112 THR cc_start: 0.8661 (p) cc_final: 0.8442 (m) REVERT: A 222 LYS cc_start: 0.8188 (mtpp) cc_final: 0.7817 (mttp) REVERT: A 308 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7909 (mm110) REVERT: C 273 ARG cc_start: 0.8110 (mmt180) cc_final: 0.7857 (mmt180) REVERT: B 69 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8365 (mtmm) REVERT: B 168 GLU cc_start: 0.7883 (tt0) cc_final: 0.7643 (tt0) outliers start: 8 outliers final: 5 residues processed: 280 average time/residue: 1.4156 time to fit residues: 419.2036 Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 8 optimal weight: 0.0970 chunk 66 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN C 262 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108549 restraints weight = 34399.609| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.27 r_work: 0.3286 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 9636 Z= 0.213 Angle : 0.585 4.471 13125 Z= 0.303 Chirality : 0.047 0.281 1566 Planarity : 0.004 0.062 1578 Dihedral : 9.206 55.955 2135 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.84 % Allowed : 13.82 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.22 (0.25), residues: 1116 helix: 0.29 (0.30), residues: 324 sheet: 0.43 (0.28), residues: 360 loop : -0.88 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 295 TYR 0.015 0.002 TYR B 89 PHE 0.013 0.002 PHE B 11 TRP 0.011 0.003 TRP A 259 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 9603) covalent geometry : angle 0.56739 (13035) SS BOND : bond 0.00473 ( 9) SS BOND : angle 1.46332 ( 18) hydrogen bonds : bond 0.04644 ( 382) hydrogen bonds : angle 5.09179 ( 1263) link_BETA1-4 : bond 0.00507 ( 12) link_BETA1-4 : angle 2.07549 ( 36) link_NAG-ASN : bond 0.00285 ( 12) link_NAG-ASN : angle 1.73318 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 273 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8807 (mtpp) cc_final: 0.8217 (mtmm) REVERT: A 112 THR cc_start: 0.8622 (p) cc_final: 0.8417 (m) REVERT: A 363 LYS cc_start: 0.8445 (mtpt) cc_final: 0.8048 (mmpt) REVERT: C 273 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7868 (mmt180) REVERT: B 69 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8302 (mtmm) outliers start: 8 outliers final: 4 residues processed: 276 average time/residue: 1.4889 time to fit residues: 436.6085 Evaluate side-chains 273 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 355 ILE Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN C 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.107895 restraints weight = 34358.866| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.24 r_work: 0.3267 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 9636 Z= 0.308 Angle : 0.646 6.243 13125 Z= 0.332 Chirality : 0.048 0.222 1566 Planarity : 0.004 0.044 1578 Dihedral : 9.131 55.420 2135 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.05 % Allowed : 14.45 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.29 (0.25), residues: 1116 helix: 0.03 (0.30), residues: 324 sheet: 0.61 (0.28), residues: 354 loop : -0.93 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 295 TYR 0.017 0.002 TYR B 89 PHE 0.014 0.002 PHE B 11 TRP 0.015 0.003 TRP A 259 HIS 0.004 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00753 ( 9603) covalent geometry : angle 0.62341 (13035) SS BOND : bond 0.00574 ( 9) SS BOND : angle 1.78900 ( 18) hydrogen bonds : bond 0.05051 ( 382) hydrogen bonds : angle 5.20367 ( 1263) link_BETA1-4 : bond 0.00418 ( 12) link_BETA1-4 : angle 2.28262 ( 36) link_NAG-ASN : bond 0.00279 ( 12) link_NAG-ASN : angle 2.11128 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 271 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8125 (mmpt) REVERT: C 273 ARG cc_start: 0.8140 (mmt180) cc_final: 0.7911 (mmt180) REVERT: B 69 LYS cc_start: 0.8801 (mtpp) cc_final: 0.8291 (mtmm) outliers start: 10 outliers final: 3 residues processed: 275 average time/residue: 1.4163 time to fit residues: 413.6527 Evaluate side-chains 270 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 267 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain B residue 99 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 103 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 308 GLN C 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.108277 restraints weight = 34132.779| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.24 r_work: 0.3278 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9636 Z= 0.230 Angle : 0.598 5.390 13125 Z= 0.309 Chirality : 0.046 0.205 1566 Planarity : 0.004 0.042 1578 Dihedral : 8.736 55.736 2133 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.84 % Allowed : 15.30 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.33 (0.25), residues: 1116 helix: 0.00 (0.29), residues: 324 sheet: 0.45 (0.28), residues: 360 loop : -0.86 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.013 0.002 TYR A 213 PHE 0.012 0.002 PHE B 11 TRP 0.012 0.003 TRP A 259 HIS 0.004 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 9603) covalent geometry : angle 0.58015 (13035) SS BOND : bond 0.00511 ( 9) SS BOND : angle 1.59254 ( 18) hydrogen bonds : bond 0.04642 ( 382) hydrogen bonds : angle 5.08584 ( 1263) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 2.07983 ( 36) link_NAG-ASN : bond 0.00338 ( 12) link_NAG-ASN : angle 1.76382 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 270 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8790 (mtpp) cc_final: 0.8278 (mtmm) REVERT: A 363 LYS cc_start: 0.8457 (mtpt) cc_final: 0.8089 (mmpt) REVERT: C 273 ARG cc_start: 0.8125 (mmt180) cc_final: 0.7899 (mmt180) REVERT: B 69 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8281 (mtmm) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 1.3460 time to fit residues: 391.0792 Evaluate side-chains 273 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 104 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 110 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 0.2980 chunk 33 optimal weight: 0.0980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN C 110 ASN C 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.129131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.109515 restraints weight = 34685.185| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.27 r_work: 0.3296 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9636 Z= 0.129 Angle : 0.541 6.075 13125 Z= 0.280 Chirality : 0.044 0.217 1566 Planarity : 0.004 0.053 1578 Dihedral : 8.218 56.338 2133 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 14.98 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.21 (0.25), residues: 1116 helix: 0.16 (0.30), residues: 324 sheet: 0.48 (0.28), residues: 360 loop : -0.80 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 318 TYR 0.010 0.001 TYR A 89 PHE 0.010 0.001 PHE B 11 TRP 0.011 0.002 TRP C 259 HIS 0.002 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9603) covalent geometry : angle 0.52591 (13035) SS BOND : bond 0.00506 ( 9) SS BOND : angle 1.21529 ( 18) hydrogen bonds : bond 0.03977 ( 382) hydrogen bonds : angle 4.85202 ( 1263) link_BETA1-4 : bond 0.00414 ( 12) link_BETA1-4 : angle 1.80769 ( 36) link_NAG-ASN : bond 0.00315 ( 12) link_NAG-ASN : angle 1.54528 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 280 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 272 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8788 (mtpp) cc_final: 0.8291 (mtmm) REVERT: A 308 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7891 (mt0) REVERT: A 363 LYS cc_start: 0.8390 (mtpt) cc_final: 0.8001 (mmpt) REVERT: C 82 ARG cc_start: 0.7868 (mtp-110) cc_final: 0.7617 (mtt-85) REVERT: C 273 ARG cc_start: 0.8123 (mmt180) cc_final: 0.7885 (mmt180) REVERT: C 308 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8002 (mt0) REVERT: B 69 LYS cc_start: 0.8789 (mtpp) cc_final: 0.8290 (mtmm) outliers start: 8 outliers final: 5 residues processed: 275 average time/residue: 1.3260 time to fit residues: 387.9393 Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 270 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 99 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 101 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN C 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.107727 restraints weight = 34497.465| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.27 r_work: 0.3269 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 9636 Z= 0.272 Angle : 0.608 5.800 13125 Z= 0.316 Chirality : 0.046 0.184 1566 Planarity : 0.004 0.044 1578 Dihedral : 8.447 55.701 2133 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.74 % Allowed : 15.93 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.22 (0.25), residues: 1116 helix: 0.05 (0.30), residues: 324 sheet: 0.57 (0.28), residues: 360 loop : -0.80 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 318 TYR 0.017 0.002 TYR A 292 PHE 0.012 0.002 PHE B 11 TRP 0.013 0.003 TRP A 259 HIS 0.003 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00664 ( 9603) covalent geometry : angle 0.59031 (13035) SS BOND : bond 0.00529 ( 9) SS BOND : angle 1.59058 ( 18) hydrogen bonds : bond 0.04648 ( 382) hydrogen bonds : angle 5.05378 ( 1263) link_BETA1-4 : bond 0.00388 ( 12) link_BETA1-4 : angle 2.01170 ( 36) link_NAG-ASN : bond 0.00237 ( 12) link_NAG-ASN : angle 1.75456 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 271 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8791 (mtpp) cc_final: 0.8242 (mtmm) REVERT: A 308 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7931 (mt0) REVERT: A 363 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8045 (mmpt) REVERT: C 273 ARG cc_start: 0.8145 (mmt180) cc_final: 0.7906 (mmt180) REVERT: B 69 LYS cc_start: 0.8792 (mtpp) cc_final: 0.8291 (mtmm) outliers start: 7 outliers final: 4 residues processed: 276 average time/residue: 1.3660 time to fit residues: 399.7340 Evaluate side-chains 274 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 270 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain B residue 149 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 67 optimal weight: 0.0170 chunk 47 optimal weight: 0.6980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN ** C 110 ASN ** 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 = 0.3689 r_free = 0.3689 target = 0.128514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108832 restraints weight = 34324.606| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.26 r_work: 0.3287 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9636 Z= 0.154 Angle : 0.550 5.994 13125 Z= 0.285 Chirality : 0.044 0.208 1566 Planarity : 0.004 0.070 1578 Dihedral : 8.175 56.013 2133 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.53 % Allowed : 16.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.22 (0.25), residues: 1116 helix: 0.14 (0.30), residues: 324 sheet: 0.51 (0.28), residues: 360 loop : -0.82 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 273 TYR 0.012 0.001 TYR A 292 PHE 0.010 0.001 PHE B 11 TRP 0.011 0.002 TRP C 259 HIS 0.003 0.001 HIS B 286 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9603) covalent geometry : angle 0.53456 (13035) SS BOND : bond 0.00444 ( 9) SS BOND : angle 1.28119 ( 18) hydrogen bonds : bond 0.04095 ( 382) hydrogen bonds : angle 4.91333 ( 1263) link_BETA1-4 : bond 0.00398 ( 12) link_BETA1-4 : angle 1.79946 ( 36) link_NAG-ASN : bond 0.00267 ( 12) link_NAG-ASN : angle 1.64467 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 276 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 271 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8229 (mtmm) REVERT: A 363 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8013 (mmpt) REVERT: C 273 ARG cc_start: 0.8131 (mmt180) cc_final: 0.7904 (mmt180) REVERT: B 69 LYS cc_start: 0.8793 (mtpp) cc_final: 0.8300 (mtmm) outliers start: 5 outliers final: 4 residues processed: 274 average time/residue: 1.4082 time to fit residues: 408.4362 Evaluate side-chains 272 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 268 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain B residue 99 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9990 chunk 85 optimal weight: 0.0970 chunk 27 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 19 optimal weight: 0.0980 overall best weight: 0.2178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN C 97 ASN C 110 ASN C 238 ASN B 110 ASN B 308 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.109899 restraints weight = 34440.810| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.25 r_work: 0.3301 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9636 Z= 0.116 Angle : 0.521 6.165 13125 Z= 0.272 Chirality : 0.044 0.216 1566 Planarity : 0.004 0.068 1578 Dihedral : 7.870 57.369 2133 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.63 % Allowed : 15.93 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.16 (0.25), residues: 1116 helix: 0.29 (0.30), residues: 324 sheet: 0.49 (0.28), residues: 360 loop : -0.82 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 273 TYR 0.012 0.001 TYR A 366 PHE 0.008 0.001 PHE B 11 TRP 0.011 0.001 TRP C 259 HIS 0.002 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9603) covalent geometry : angle 0.50754 (13035) SS BOND : bond 0.00411 ( 9) SS BOND : angle 1.11404 ( 18) hydrogen bonds : bond 0.03746 ( 382) hydrogen bonds : angle 4.76388 ( 1263) link_BETA1-4 : bond 0.00403 ( 12) link_BETA1-4 : angle 1.64572 ( 36) link_NAG-ASN : bond 0.00337 ( 12) link_NAG-ASN : angle 1.54616 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue LYS 127 is missing expected H atoms. Skipping. Residue LYS 362 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 271 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8255 (mtmm) REVERT: A 363 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8003 (mmpt) REVERT: C 273 ARG cc_start: 0.8106 (mmt180) cc_final: 0.7883 (mmt180) REVERT: B 69 LYS cc_start: 0.8786 (mtpp) cc_final: 0.8292 (mtmm) outliers start: 6 outliers final: 5 residues processed: 274 average time/residue: 1.4581 time to fit residues: 423.1990 Evaluate side-chains 274 residues out of total 957 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 269 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain B residue 82 ARG Chi-restraints excluded: chain B residue 149 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 11 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN C 97 ASN C 262 ASN B 110 ASN B 308 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.128550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.108857 restraints weight = 34322.549| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.24 r_work: 0.3286 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3119 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3119 r_free = 0.3119 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9636 Z= 0.182 Angle : 0.555 6.124 13125 Z= 0.288 Chirality : 0.044 0.165 1566 Planarity : 0.004 0.064 1578 Dihedral : 8.002 56.535 2133 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.53 % Allowed : 16.14 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % 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 aren not related in a simple way. whole: -0.13 (0.25), residues: 1116 helix: 0.27 (0.30), residues: 324 sheet: 0.54 (0.28), residues: 360 loop : -0.80 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 273 TYR 0.013 0.001 TYR A 89 PHE 0.013 0.001 PHE C 198 TRP 0.010 0.002 TRP C 259 HIS 0.002 0.001 HIS C 286 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9603) covalent geometry : angle 0.53858 (13035) SS BOND : bond 0.00461 ( 9) SS BOND : angle 1.33771 ( 18) hydrogen bonds : bond 0.04141 ( 382) hydrogen bonds : angle 4.84887 ( 1263) link_BETA1-4 : bond 0.00364 ( 12) link_BETA1-4 : angle 1.73543 ( 36) link_NAG-ASN : bond 0.00323 ( 12) link_NAG-ASN : angle 1.78469 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9690.87 seconds wall clock time: 164 minutes 23.32 seconds (9863.32 seconds total)